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In brief, for each voxel in the MR image that needs to be segmented, the neighbourhood of the voxel is compared with similar neighbourhoods in previously labelled MR image datasets that serve as a library of templates. A weight, proportional to the neighbourhood similarity between the image and the templates, is computed and used as a label voting mechanism to achieve segmentation.

Here, the gold standard labels are used to define the template library, and experiments are completed in a leave-one-out fashion i. For each patient, the patch-based method was used to obtain the same labels as those identified manually for the gold standard. We first processed the method on the T1w images of the 10 patients, but the substantia nigra, red nuclei, and STN were only visualized on the T2w sequences. For these six labels, the patch-based method was applied to the T2w images using the T2w data from the gold standard template library.

Finally, the eight labels obtained from the T1w patch-based procedure and those obtained from the T2w patch-based procedure were combined to complete the patch-based segmentation for each patient. Figure 4 presents a view of the different labels obtained with the patch-based method. The kappa was measured as follows:. K takes on a value between 0 and 1. Before the kappa metric is used to evaluate the automated methods, it was first used to estimate intra- and inter-rater variability of manual structure segmentation to establish a baseline for comparison.

The center of gravity was estimated for each segmented structure obtained with the 3 methods, the ANIMAL and SyN registrations and the patch-based method. The Euclidean co-ordinates of the center of gravity were used to estimate a distance between the automatic segmentations and their respective gold standard. A p -value of less than 0. We also computed the center-of-gravity values between the repeated manual segmentations of the two experts, to estimate inter-rater variability.

The resulting kappa values were not Gaussian distributed; therefore, a nonparametric Friedman test for paired data was used to compare the kappa values obtained with ANIMAL and SyN and with the patch-based method. When a significant difference was detected by the Friedman test, a nonparametric post-hoc multicomparison test was used to determine which pair of methods was significantly different.

The results of intra- and inter-rater variability of manual segmentation are presented in Table 2. The results of the center-of-gravity values between the deep brain structures obtained with 2 registration methods and the patch-based method are presented in Table 3.

Mean distances and standard deviation SD in mm between the center of gravity positions between manually segmented deep brain structures, and the automatically segmented labels from the 3 different methods: ANIMAL, SyN and the patch-based. The mean distances measured between the repeated segmentations of the two experts were 0. The kappa index values obtained with the three methods are presented in Table 4 and Figure 5.

Box plots of the kappa index distribution for ANIMAL registration top row , SyN registration second row , and patch-based method of segmentation bottom row. Boxes represent the lower quartile, median red line , and upper quartile of the kappa index distribution. Whiskers show the most extreme values within 1. The median kappa values computed between the labels obtained with the patch-based method and the manual labels were greater than 0.

The template-based segmentation approach is one method that has been developed to assist neurosurgeons in the target planning step of deep brain stimulation procedures. For example, Bardinet et al. This process allowed us to obtain T1w and T2w templates with a high degree of anatomical detail for deep brain structures and the cerebral cortex.

In contrast to the atlases of Bardinet et al. One of the limits of our study was that the segmentation used during methods comparison was performed by only one expert. However, the segmentation quality was verified by a second expert, Xavier Morandi and two experts Claire Heagelen and D. The intra-rater segmentation reliability was quite high with values above 0. The inter-rater segmentation variability was slighty higher than the intra-rater for putamen and SN while significantly higher for STN.

In the literature, many segmentation methods [ 18 , 29 , 34 , 36 ] are first tested on lateral ventricles, hippocampus or amygdala, structures for which the boundaries and limits are better defined. In our opinion, these facts explain why in our study the STN had higher inter-rater variability compare to other reports of automatic segmentation techniques.

Considering these manual segmentation difficulties, our results should be taken with the caveat that the inter-rater variability is relatively high. Nevertheless, the mean distances between centers of gravity were not different in the two sets of manual segmentations, and these distances were lower in labels obtained with the patch-based method than with the two registration methods. Overall, the mean distance of 1. Furthermore, the mean Dice Kappa values for inter-rater segmentation are at approximately the same level as the mean Dice Kappa values comparing the manual labels and those generated by the three automatic techniques.

In the future, we will investigate the effect of consensus segmentations from multiple experts. We applied two nonlinear registration-based segmentation tools to MR images, as nonlinear registration has been shown to perform better than linear registration for the automated identification of subcortical targets [ 30 — 32 ].

The accuracy of the automated segmentation depends on the accuracy of registration. In Klein et al. SyN was one of the methods that reached top rank for all label sets [ 33 ]. In our case, the two nonlinear registrations were quite similar for all the structures, even for the smallest ones, except for the left thalamus and red nucleus, for which ANIMAL performed better than SyN.

The advantage of this type of segmentation approach is that the manual segmentation is performed on a high-contrast image i. However, the difficulty is then in registering the template with an individual MR image because of inter-subject variability. Instead, nonlinear transformations are needed to address this issue. By using nonlinear transformations, we obtained a more accurate segmentation result; however, the nonlinear registration of the template to the patient MR image is time consuming, taking in our case from thirty minutes to one hour per patient for ANIMAL and from one to three hours per patient for SyN.

Another way to obtain better segmentation accuracy than by registering images to a single labelled template is to fuse several labelled images [ 34 ]. Fusing the labelled images in the training library can be done by nonlinear registration [ 34 — 35 ] or patch comparison [ 18 ]. The advantage of label fusion approaches is that they can handle inter-subject variability correctly by aggregating labels from several images.

The patch-based label fusion approach evaluated here is also less time consuming than nonlinear registration, since it required only one minute of processing. The difficulty with the patch-based label fusion approach is that it requires manual segmentation of structures on the MR images of several subjects to form the library.

While the overall segmentation quality was similar for the patch-based and registration-based methods, there was more variability in the segmentation quality of the patch-based approach see Fig. As shown in Coupe et al. During our leave-one-out experiment, only nine templates were used to segment the subject under study. This number of training templates is small compared with what is suggested in Coupe et al. By increasing the number of training templates, the segmentation quality is expected to increase and the robustness of the segmentation to improve.

The kappa metric is often used to compare the agreement between structures in the literature [ 18 , 32 , 34 — 36 ]. The kappa metric depends on the surface-to-volume ratio of the structure, with decreasing kappa values in small structures for which the ratio increases. We found lower kappa values for the hippocampus than what is reported in Coupe et al.

As mentioned, this lower segmentation quality may be due to the smaller number of training subjects used in our segmentation procedure. Patenaude et al. They found that the best structures in terms of kappa values were the thalamus and putamen with a median kappa as high as 0. We also found lower median kappa values for the smallest structures, the STN and substantia nigra, but not for the red nucleus. The three methods were relatively equivalent in terms of mean and median kappa values, suggesting they perform similarly in producing the automated segmentation of deep brain structures.

Differences between the three methods were observed only for some of the structures, which mean there was, in fact, very little dissimilarity. However, when applied to a new patient, the patch-based method is notably more efficient than the other two methods, as it avoids the lengthy time-consuming non-linear registration step to achieve segmentation.

Moreover, considering the resulting high inter-rater variability in our study, the automatic segmentation was as variable as another expert rater but was not subject to intra-rater variability. The patch-based segmentation method may improve the surgical workflow by quickly and automatically identifying the STN on the preoperative MRI data of new patients, thus reducing part of the preoperative planning time in STN targeting. In clinical practice, the patch-based method is not yet applicable because it requires an engineer.

From a point of view of a neurosurgeon, the three methods of segmentation were accurate enough to visualize the STN or the thalamus and to be applicable to new patients. More work is needed to have a software solution that is usable by the clinicians without supervision of the engineers.

We assessed that the intra-rater variability between the manual segmentations was lower than the inter-rater variability. Although template-based approaches are the most frequently used techniques to warp basal ganglia segmentation onto MR images, we found that the patch-based method provides similar results and is much less time consuming. The authors thank Amanda Leonard for her help with the English language. National Center for Biotechnology Information , U.

Author manuscript; available in PMC Aug 5. Author information Copyright and License information Disclaimer. Copyright notice. See other articles in PMC that cite the published article. Abstract Purpose Template-based segmentation techniques have been developed to facilitate the accurate targeting of deep brain structures in patients with movement disorders.

Conclusion Although template-based approaches are the most used techniques to segment basal ganglia by warping onto MR images, we found that the patch-based method provided similar results and was less-time consuming. Open in a separate window. Fig 4. Patch-based segmentation method In addition to the registration-based methods, we also evaluated a novel patch-based method using anatomical information derived from manual segmentations by experts, as described in detail in Coupe et al.

Data analysis The resulting kappa values were not Gaussian distributed; therefore, a nonparametric Friedman test for paired data was used to compare the kappa values obtained with ANIMAL and SyN and with the patch-based method. Results The results of intra- and inter-rater variability of manual segmentation are presented in Table 2.

Table 3 Mean distances and standard deviation SD in mm between the center of gravity positions between manually segmented deep brain structures, and the automatically segmented labels from the 3 different methods: ANIMAL, SyN and the patch-based. Fig 5. Patch-based method The median kappa values computed between the labels obtained with the patch-based method and the manual labels were greater than 0. Fig 6. Discussion The template-based segmentation approach is one method that has been developed to assist neurosurgeons in the target planning step of deep brain stimulation procedures.

Acknowledgments The authors thank Amanda Leonard for her help with the English language. References 1. Lancet Neurol. Deep brain stimulation of the Vim nucleus of the thalamus for the treatment of tremor. Magnetic resonance imaging stereotactic target localization for deep brain stimulation in dystonic children. J Neurosurg. Their advertising sizzle had more substance than their steak. Viking, sadly, fell far short. This was the first cruise that either me or my husband have ever taken and we were pleasantly surprised as to the product we received.

I made our reservations fairly late in the process I believe only 5 months before we left. We chose to make our own flights and chose to do Lisbon on our own rather than take advantage of Viking's pre-cruise offering in Lisbon. Quite frankly, I did not find it very cost effective and we were able to stay and do twice as much for half the cost, for comparable accommodations.

As we were already in Lisbon, we did not get to the ship until our room was available - which for us turned out to be a smart idea. We missed a lot of the crowd of boarding, so it was fairly easy getting on board around 4 pm, without hassle or waiting in line. Our luggage was almost immediately available after we got to our room, which was nice.

The room was spacious, as far as cruise rooms run. It turned out being an excellent choice for us. The bedding was wonderful, the bathroom and its heated floors generous and the bed very comfortable. In the evenings, I spent the better part of the time wrapped up in the cashmere blanket at the bottom of the bed, and wound up buying one of these to take home. I think it made a nice souvenir of our trip, and will get a lot of use. It was not inexpensive though.

We chose not to take advantage of the drink package offered. Neither my husband, nor myself drink to excess and found the wine available at lunch and dinner usually sufficient. We did find that it was of variable, in that some nights it was excellent and others not so much.

We ate most of our meals at World Cafe, and found the food there very good. It was nice that the meat and the vegetables were not cooked within an inch of their lives! The fruit found on the breakfast bar each morning was excellent, I've not managed to get such good tasting fruit that tastes like fruit as consistently as I found on this cruise. My only objection would be that it would have been nice if there had been a large salad bar available at lunch each day in the cafe.

I normally don't eat a large lunch like this, and like having a salad along with dinner. However, this isn't enough to to knock Viking about. The staff on the Viking Sun was phenomenal and made our trip very enjoyable, from the waitstaff to our cabin steward to guest services.

No complaints here. We did not take advantage of the tours offered, other than those that were free. The bus trip in the Azores was a bust - only because the weather was so lousy and the cloud cover so low that when we got to our destination were were actually in the clouds! I can't complain that the weather was Viking's fault. In Bermuda, we received a bus pass for our tour, and took the bus to the end of the island and back - then did some shopping in Hamilton.

It was a nice day, but it would have been nice if we stayed longer in port. I believe we had to be back on the ship at 3, to leave at 4. If I had a single complaint about the cruise, it would have to be on our docking in Miami.

Info from the waitstaff, apparently half the staff got detained by immigrations in Miami and did not get back in time for breakfast. As everyone had to be out of our staterooms at 8 am, and off the boat by 9 am, breakfast was an absolute madhouse. Tables were not cleared, and it was difficult getting service.

Everyone had to be on the second and first deck by 9, to leave the ship. My husband and I were in the first group called to exit and we did not get off the ship until I am not sure why things were so disorganized that last morning, considering after how smoothly everything else was run. That disembarkation was such a mess.

I can't see how the ship was unloaded before 11, considering what time we got off and how many people were behind us. I really felt for some of the elderly passengers, as seating in the area was at a premium and there was barely room to turn around. I'm already looking at booking our next cruise. I see there have been many negative reviews of the Viking river cruises on the Danube - most arising from the lower water levels in the river over the summer causing changes to the itinerary and how this was handled by the company and staff.

We sailed from Budapest to Nuremburg in December - exactly as planned. Throughout we found the ship comfortable and all the staff attentive and helpful. There was nothing to fault. It was a great experience and we would happily sail with the company again. If you are considering this cruise, please read this letter that we wrote to Viking after our cruise: We are writing to express our disappointment in the recent cruise that we took July aboard the Viking Tor.

The cruising was cut short due to low water levels on the Danube River between Passau and Regensburg and the supposed grounding of a barge in that stretch. Let me provide a timeline of events. Late in the afternoon of July 3 almost exactly 48 hours before our departure from the US , we received an email from Viking advising us that, due to low water levels, we may have to endure a ship swap during our cruise.

July 6, Cruise Day 1, Budapest: Five star experience. After boarding, we were advised by the front desk that there was a high likelihood that we would endure a ship swap and that it was probably best not to fully unpack our luggage as it was likely that we would have to pack again in just a few days. July 7, Cruise Day 2, Budapest: Five star experience July 8, Cruise Day 3, Vienna: Five star experience July 9, Cruise Day 4, Krems: We were advised that the boat with which we would have done a ship swap had made it through the stretch of river in question and that the news was both good news in that the water levels had risen and bad news in that there was no longer a boat for us to conduct a swap.

If river conditions remained as they were, we would be bussed to Regensburg on July 12 for a total of 3 hours in a coach. Given the time that would be spent on the bus, plus the shortened time for the excursion in Nuremberg, we elected not to go to Nuremberg and to get a refund on the optional WWII excursion that we had booked.

This is a shame because of the rich architectural, historical, and transportation aspects of the city — but a 4. July 11, Cruise Day 6, Scheduled city Regensburg, Actual city Passau: We woke up at an industrial docking station see attached pictures with no easy access to Passau and the news that two shuttle busses in the morning and two shuttle busses in the afternoon would bring passengers to and from Passau for those who wished not to endure the long ride to Nuremberg. The industrial docking station was equipped with a crane and stationary containers for loading and unloading barges and had a constant stench of what smelled like sewage.

As we left for the coach to Passau, the crew was loading pallets worth of provisions on the boat. We took a morning coach into Passau and an afternoon coach back from Passau. After returning from Passau, we decided to make the best of a bad situation, got ourselves a couple of drinks from the bar, went up to the upper deck of the ship with our reading material, arranged two lounge chairs such that we were facing away from the industrial dock so that we could see the distant spires of Passau, and sat down with our novels to read.

After a few minutes, we determined that the limited view from the industrial facility where we were docked was not worth the stench and retreated to a lower deck. July 12, Cruise Day 7, Scheduled city Nuremburg, Actual city: Passau with excursion to Regensburg: We went on the rescheduled excursion from Passau to Regensburg which now required 3 hours in a coach for the round trip via land. In contrast to a typical excursion to Regensburg from a dock in the Altstadt, our free time to explore the city after the formal tour was reduced by several hours due to both the need to allow time for the bus ride and to ensure we were not late getting to the bus for our scheduled departure.

It is hard to believe that docking the boat for three days amidst the stench of sewage was the best that Viking could do. We are left to wonder several things: Did Viking do all that it could to minimize the draft of the ship in order to negotiate the low river level for example pumping out the various tanks that affect the draft of the ship and unloading passengers, nonessential crew members, and luggage and transporting them up river via roads? We think not, given that the crew loaded the ship on July 11 with provisions while docked in Passau.

Was there really a barge that ran aground and prevented the ship from passing? Despite multiple internet searches, we found no reference to any such events in the location and timeframe of our trip. Viking could have offered alternate day trips instead of just bussing passengers into Passau for another day for those who wished not to endure the six hour round trip to Nuremburg.

For example, Viking could have orchestrated a trip to Salzburg on July 11 for those who had not taken part in the add-on trip on July Viking could have found a way to keep the boat in the original docking location in Passau, or sailed back to Melk for a day instead of holding us for three nights in the industrial docking facility that reeked of sewage.

These are just some of the options that seem obvious for us, two people who are experts in neither the region nor the cruise industry. For us to take advantage of your future discount, we would be forced to book with Viking for a second cruise, and our first Viking experience does not warrant a second cruise.

Knowing that we had been looking forward to our trip, many people has asked us how our cruise was. Instead we say in a nutshell: It was a 5 star experience for the first four nights. After that, it was a disaster that made the whole experience a star experience. How a company deals with bad situations really defines who they are as a company. While it may be possible that so many ships — Viking and others — were adversely affected by the water levels that acceptable workaround were not possible for so many ships, a saturated market does not make it acceptable to dock us for three nights in stench.

We are shocked that a company whose on-boat personnel are so customer oriented can have its corporate decision makers display such little customer orientation. Based on where things are now, these four points will be the core of our on-line reviews that we will be publishing shortly. Took the Rhine tour in August on the Viking Kara. Here's the honest truth. The ships cater to old folks, but oddly they don't do it very well. It seems if that is your target market they would be better prepared with comforts and care for the elderly.

For example, they bus you to a walking tour which is only a 1-mile walk but there are 5 flights of rustic euro stairs to climb if you want to get on the bus. I'm 47 years old and 5 flights of stairs are no fun for me but a do-able huff- I saw elderly people just standing looking at the stairs and turning back to the ship.

Average walking is 5 miles per day as per my I-watch- so just be prepared for 5 flights and 5 miles daily if you can't do it there is no assistance I saw, no scooters or bikes just stay on the boat dying of boredom and low bandwidth wi-fi or hike for it, grandma.

And there is no REAL bar - a cocktail hour exists before and after dinner I guess they don't want grandma falling down so it shuts down pretty fast. Bartenders are never behind the bar, always vacuuming or setting up for something and don't keep the bar open late at all so if you have a wild night So the people that spent money on that were annoyed I heard them grumbling, one even starting serving himself and became an add lib bartender for the guests.

Wine is available only with your meal and it's like pulling teeth to get that 2nd 3rd glass, the pours are short and the wine is just OK. All from Argentina screw top stuff. Forget drinking regional wines, if you are in France- so what it's South America for you! Very marginal small portions ribeyes are slim cuts, like breakfast steak and filet mignon is a 4 oz cut in half.

So 2 oz of filet strips displayed on a sad mash of potato. The food was always just hmmm Desserts even missed the mark so snicker chocolate thing with lemon yogurt?? Aquavit terrace for lunch and dinner has outdoor dining but it is very sad. There are some yogurts, sad pastries and muslix and breads in the morning- with nobody there to attend to you. Courtyard Marriott or Hampton Inn does it better. Of course, if you want to eat in the dining room there is an omelet station and everything is good for that meal as breakfast is cheap.

Interestingly, German night when all the crew dressed up German, oddly it was the night in France, couldn't they have served a French meal? Instead, a sloppy German buffet which may sound cool, but really Bet when Germans spend this type of money they expect French chefs and American portions.

For those that don't make the formal dining. No pizza station or vending area even. My mom was feeling exhausted and it was like pulling teeth to get the kitchen to give me soup to take to the room. It's like room service is a completely foreign word here. So if you miss dinner grandma Tic - Toc.

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It was at this moment that the hotel staff accepted that they had made a mistake and let us check in. We had another unpleasant experience when dining in the roof-top restaurant on the night of the National Day. The wonderful fireworks dinner was spoilt by another hotel staff named Didier who took ages to split the bill between 2 rooms. He just spilt the bill as he wanted without clarifying with us how to split and was rude and dismissive during the whole process.

He did not even have the basic courtesy to inform us after the correct split was made and kept us standing and waiting at the cashier when it was already close to midnight at the time. Also, when we went to the reception to ask for an extra pair of slippers following the dinner, we were told that the housekeeping room was locked and they could NOT provide us with a single pair of slippers. I wonder if their housekeepers bring the keys home.

I could not hold my laugh next to him. I never know it was that hard to get a pair of slippers in a 4-star hotel and I should have got back to this atrocious hotel in the afternoon to ask for a pair of slippers. The standard and ability of the staff are unbelievably and consistently low, not to mention the computer system. I bet the lack of ability and courtesy is the key criteria to get hired by this horrendous hotel.

I cannot see why this ghastly hotel is ranked 4-star. This is the worst hotel I have ever been to and would never stay at any "Mercure Hotel" in my life. There are many hotels nearby. I bet they cannot be worse. We stayed here for five days and enjoyed it. We joined their club and got an upgraded room which included an espresso machine and refrigerator stocked with water and soft drinks which were replenished daily. We figured this was a value of roughly 15 euros per day.

We also signed up for the breakfast, which was quite good. It's right across the street from a mall and roughly 2 blocks from a tram stop. It's roughly a 15 minute walk to the old city and 20 minutes to the river. My biggest complaint is that there was no drawer space at all--and the room was a little too small to simply leave your suitcase open on the floor to use. But the staff is extremely friendly and all spoke excellent English.

We'd go back. Skip to main content. Log in to get trip updates and message other travelers. Lowest prices for your stay. Guests 1 room , 2 adults , 0 children Guests 1 2. Show Prices. Like saving money? We search up to sites for the lowest prices. Good base for city break. More Show less. Date of stay: August Trip type: Traveled as a couple. Report response as inappropriate Thank you.

We appreciate your input. See all 1, reviews. Nearby Hotels. Hotel Mercure Bordeaux Cite Mondiale. View Hotel. Hotel Notre-Dame. Free Wifi. Hotel des Quinconces. Room service. Taking safety measures. Hotel de Seze. Hotel de Normandie. Hotel Majestic. Hotel des 4 Soeurs. Hotel de L'Opera. Hotel Choiseul. Hotel de Tourny. View more hotels in Bordeaux. Reviews 1, Write a review. Filter reviews. Traveler rating.

Excellent Very good Average Poor Terrible Traveler type. Time of year. Language All languages. All languages. English French Spanish More languages. Italian German Portuguese Dutch A weight, proportional to the neighbourhood similarity between the image and the templates, is computed and used as a label voting mechanism to achieve segmentation. Here, the gold standard labels are used to define the template library, and experiments are completed in a leave-one-out fashion i.

For each patient, the patch-based method was used to obtain the same labels as those identified manually for the gold standard. We first processed the method on the T1w images of the 10 patients, but the substantia nigra, red nuclei, and STN were only visualized on the T2w sequences. For these six labels, the patch-based method was applied to the T2w images using the T2w data from the gold standard template library.

Finally, the eight labels obtained from the T1w patch-based procedure and those obtained from the T2w patch-based procedure were combined to complete the patch-based segmentation for each patient. Figure 4 presents a view of the different labels obtained with the patch-based method.

The kappa was measured as follows:. K takes on a value between 0 and 1. Before the kappa metric is used to evaluate the automated methods, it was first used to estimate intra- and inter-rater variability of manual structure segmentation to establish a baseline for comparison. The center of gravity was estimated for each segmented structure obtained with the 3 methods, the ANIMAL and SyN registrations and the patch-based method.

The Euclidean co-ordinates of the center of gravity were used to estimate a distance between the automatic segmentations and their respective gold standard. A p -value of less than 0. We also computed the center-of-gravity values between the repeated manual segmentations of the two experts, to estimate inter-rater variability. The resulting kappa values were not Gaussian distributed; therefore, a nonparametric Friedman test for paired data was used to compare the kappa values obtained with ANIMAL and SyN and with the patch-based method.

When a significant difference was detected by the Friedman test, a nonparametric post-hoc multicomparison test was used to determine which pair of methods was significantly different. The results of intra- and inter-rater variability of manual segmentation are presented in Table 2. The results of the center-of-gravity values between the deep brain structures obtained with 2 registration methods and the patch-based method are presented in Table 3.

Mean distances and standard deviation SD in mm between the center of gravity positions between manually segmented deep brain structures, and the automatically segmented labels from the 3 different methods: ANIMAL, SyN and the patch-based. The mean distances measured between the repeated segmentations of the two experts were 0. The kappa index values obtained with the three methods are presented in Table 4 and Figure 5. Box plots of the kappa index distribution for ANIMAL registration top row , SyN registration second row , and patch-based method of segmentation bottom row.

Boxes represent the lower quartile, median red line , and upper quartile of the kappa index distribution. Whiskers show the most extreme values within 1. The median kappa values computed between the labels obtained with the patch-based method and the manual labels were greater than 0.

The template-based segmentation approach is one method that has been developed to assist neurosurgeons in the target planning step of deep brain stimulation procedures. For example, Bardinet et al. This process allowed us to obtain T1w and T2w templates with a high degree of anatomical detail for deep brain structures and the cerebral cortex. In contrast to the atlases of Bardinet et al. One of the limits of our study was that the segmentation used during methods comparison was performed by only one expert.

However, the segmentation quality was verified by a second expert, Xavier Morandi and two experts Claire Heagelen and D. The intra-rater segmentation reliability was quite high with values above 0. The inter-rater segmentation variability was slighty higher than the intra-rater for putamen and SN while significantly higher for STN. In the literature, many segmentation methods [ 18 , 29 , 34 , 36 ] are first tested on lateral ventricles, hippocampus or amygdala, structures for which the boundaries and limits are better defined.

In our opinion, these facts explain why in our study the STN had higher inter-rater variability compare to other reports of automatic segmentation techniques. Considering these manual segmentation difficulties, our results should be taken with the caveat that the inter-rater variability is relatively high.

Nevertheless, the mean distances between centers of gravity were not different in the two sets of manual segmentations, and these distances were lower in labels obtained with the patch-based method than with the two registration methods. Overall, the mean distance of 1. Furthermore, the mean Dice Kappa values for inter-rater segmentation are at approximately the same level as the mean Dice Kappa values comparing the manual labels and those generated by the three automatic techniques.

In the future, we will investigate the effect of consensus segmentations from multiple experts. We applied two nonlinear registration-based segmentation tools to MR images, as nonlinear registration has been shown to perform better than linear registration for the automated identification of subcortical targets [ 30 — 32 ]. The accuracy of the automated segmentation depends on the accuracy of registration. In Klein et al. SyN was one of the methods that reached top rank for all label sets [ 33 ].

In our case, the two nonlinear registrations were quite similar for all the structures, even for the smallest ones, except for the left thalamus and red nucleus, for which ANIMAL performed better than SyN. The advantage of this type of segmentation approach is that the manual segmentation is performed on a high-contrast image i. However, the difficulty is then in registering the template with an individual MR image because of inter-subject variability.

Instead, nonlinear transformations are needed to address this issue. By using nonlinear transformations, we obtained a more accurate segmentation result; however, the nonlinear registration of the template to the patient MR image is time consuming, taking in our case from thirty minutes to one hour per patient for ANIMAL and from one to three hours per patient for SyN.

Another way to obtain better segmentation accuracy than by registering images to a single labelled template is to fuse several labelled images [ 34 ]. Fusing the labelled images in the training library can be done by nonlinear registration [ 34 — 35 ] or patch comparison [ 18 ]. The advantage of label fusion approaches is that they can handle inter-subject variability correctly by aggregating labels from several images. The patch-based label fusion approach evaluated here is also less time consuming than nonlinear registration, since it required only one minute of processing.

The difficulty with the patch-based label fusion approach is that it requires manual segmentation of structures on the MR images of several subjects to form the library. While the overall segmentation quality was similar for the patch-based and registration-based methods, there was more variability in the segmentation quality of the patch-based approach see Fig. As shown in Coupe et al.

During our leave-one-out experiment, only nine templates were used to segment the subject under study. This number of training templates is small compared with what is suggested in Coupe et al. By increasing the number of training templates, the segmentation quality is expected to increase and the robustness of the segmentation to improve.

The kappa metric is often used to compare the agreement between structures in the literature [ 18 , 32 , 34 — 36 ]. The kappa metric depends on the surface-to-volume ratio of the structure, with decreasing kappa values in small structures for which the ratio increases. We found lower kappa values for the hippocampus than what is reported in Coupe et al.

As mentioned, this lower segmentation quality may be due to the smaller number of training subjects used in our segmentation procedure. Patenaude et al. They found that the best structures in terms of kappa values were the thalamus and putamen with a median kappa as high as 0.

We also found lower median kappa values for the smallest structures, the STN and substantia nigra, but not for the red nucleus. The three methods were relatively equivalent in terms of mean and median kappa values, suggesting they perform similarly in producing the automated segmentation of deep brain structures.

Differences between the three methods were observed only for some of the structures, which mean there was, in fact, very little dissimilarity. However, when applied to a new patient, the patch-based method is notably more efficient than the other two methods, as it avoids the lengthy time-consuming non-linear registration step to achieve segmentation. Moreover, considering the resulting high inter-rater variability in our study, the automatic segmentation was as variable as another expert rater but was not subject to intra-rater variability.

The patch-based segmentation method may improve the surgical workflow by quickly and automatically identifying the STN on the preoperative MRI data of new patients, thus reducing part of the preoperative planning time in STN targeting. In clinical practice, the patch-based method is not yet applicable because it requires an engineer. From a point of view of a neurosurgeon, the three methods of segmentation were accurate enough to visualize the STN or the thalamus and to be applicable to new patients.

More work is needed to have a software solution that is usable by the clinicians without supervision of the engineers. We assessed that the intra-rater variability between the manual segmentations was lower than the inter-rater variability. Although template-based approaches are the most frequently used techniques to warp basal ganglia segmentation onto MR images, we found that the patch-based method provides similar results and is much less time consuming.

The authors thank Amanda Leonard for her help with the English language. National Center for Biotechnology Information , U. Author manuscript; available in PMC Aug 5. Author information Copyright and License information Disclaimer.

Copyright notice. See other articles in PMC that cite the published article. Abstract Purpose Template-based segmentation techniques have been developed to facilitate the accurate targeting of deep brain structures in patients with movement disorders. Conclusion Although template-based approaches are the most used techniques to segment basal ganglia by warping onto MR images, we found that the patch-based method provided similar results and was less-time consuming.

Open in a separate window. Fig 4. Patch-based segmentation method In addition to the registration-based methods, we also evaluated a novel patch-based method using anatomical information derived from manual segmentations by experts, as described in detail in Coupe et al. Data analysis The resulting kappa values were not Gaussian distributed; therefore, a nonparametric Friedman test for paired data was used to compare the kappa values obtained with ANIMAL and SyN and with the patch-based method.

Results The results of intra- and inter-rater variability of manual segmentation are presented in Table 2. Table 3 Mean distances and standard deviation SD in mm between the center of gravity positions between manually segmented deep brain structures, and the automatically segmented labels from the 3 different methods: ANIMAL, SyN and the patch-based. Fig 5. Patch-based method The median kappa values computed between the labels obtained with the patch-based method and the manual labels were greater than 0.

Fig 6. Discussion The template-based segmentation approach is one method that has been developed to assist neurosurgeons in the target planning step of deep brain stimulation procedures. Acknowledgments The authors thank Amanda Leonard for her help with the English language. References 1. Lancet Neurol. Deep brain stimulation of the Vim nucleus of the thalamus for the treatment of tremor. Magnetic resonance imaging stereotactic target localization for deep brain stimulation in dystonic children.

J Neurosurg. Relationship between neuropsychological outcome and DBS surgical trajectory and electrode location.

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