[Freesurfer] corpus callosum mask
Dear FreeSurfer Experts, I wonder if Freesurfer saves the mask of corpus callosum or not. If so, could you please tell me where it is saved or how can I get a cc mask? Many thanks Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] corpus callosum mask
Hi Ali, yes, we segment the cc and save it in the aseg.mgz divided into 5 parts anterior/posterior. cheers, Bruce On Tue, 24 Mar 2009, Al-Radaideh Ali wrote: Dear FreeSurfer Experts, I wonder if Freesurfer saves the mask of corpus callosum or not. If so, could you please tell me where it is saved or how can I get a cc mask? Many thanks Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FDR correction
Hi, I have done an analysis involving three groups, so there are three pairwise comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple comparisons (across the vertices), so I use FDR. But since FDR determines the threshold basd on the actual p-values, I get 6 different tresholds: comparison 1: lh and rh, 0.016 and 0.028 (I can choose .01) comparison 2: lh and rh, 0.01 and 0.001 (I can choose.001) comparison 3 lh and rh, 0.001 and 0.0001 (I can choose .0001) There are lots of significant vertices in comparison 1 and nothing significant, after correction, in comparison 3. Is there anything wrong with using different tresholds here, and concluding that in comparison 1 there were extensive differences between the groups, whereas in comparison 3 there were none? I'm not sure if this is a problem, but I'm afraid some reviewers might have an issue with it. Across the hemispheres, I can choose a conservative threshold which covers both hemispheres, i.e. lower than both the FDR-adjusted treshold for lh and rh. But between the comparisons the tresholds differ even more, by a factor of 10 and 100. And if I choose the most conservative of all the adjusted thresholds, I'm afraid that I'll make a type II error in comparison 1. >From what I understand, the adjusted threshold for comparison 3 is more conservative because of the actual empirical data (the distribution of p-values), so that's an empirical argument for using a more conservative threshold there. And: What if I pooled all thre p-maps (sig.mgh) and did an FDR on the whole thing, would that be a better approach? And does Freesurfer use the Benjamini algorithm, and if you do, can I use Tom Nichols' matlab function for FDR (http://www.sph.umich.edu/~nichols/FDR/FDR.m) for pooling all three p-maps? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FDR correction
Some links that may be helpful: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis http://surfer.nmr.mgh.harvard.edu/fswiki/MultipleComparisons Hope it helps. PPJ --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom On Tue, Mar 24, 2009 at 12:38, Lars M. Rimol wrote: > Hi, > I have done an analysis involving three groups, so there are three pairwise > comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple > comparisons (across the vertices), so I use FDR. But since FDR determines > the threshold basd on the actual p-values, I get 6 different tresholds: > > comparison 1: lh and rh, 0.016 and 0.028 (I can choose .01) > comparison 2: lh and rh, 0.01 and 0.001 (I can choose.001) > comparison 3 lh and rh, 0.001 and 0.0001 (I can choose .0001) > > There are lots of significant vertices in comparison 1 and nothing > significant, after correction, in comparison 3. Is there anything wrong with > using different tresholds here, and concluding that in comparison 1 there > were extensive differences between the groups, whereas in comparison 3 there > were none? I'm not sure if this is a problem, but I'm afraid some reviewers > might have an issue with it. Across the hemispheres, I can choose a > conservative threshold which covers both hemispheres, i.e. lower than both > the FDR-adjusted treshold for lh and rh. But between the comparisons the > tresholds differ even more, by a factor of 10 and 100. And if I choose the > most conservative of all the adjusted thresholds, I'm afraid that I'll make > a type II error in comparison 1. > > From what I understand, the adjusted threshold for comparison 3 is more > conservative because of the actual empirical data (the distribution of > p-values), so that's an empirical argument for using a more conservative > threshold there. > > > And: What if I pooled all thre p-maps (sig.mgh) and did an FDR on the whole > thing, would that be a better approach? And does Freesurfer use the > Benjamini algorithm, and if you do, can I use Tom Nichols' matlab function > for FDR (http://www.sph.umich.edu/~nichols/FDR/FDR.m) for pooling all > three p-maps? > > Thank you! > > -- > yours, > LMR > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] FDR correction
Well, I believe there is a problem in principle here. FDR deals with multiple comparisons across the surface (or brain volume), but how do you deal with a series of such analyses? Of course, if you use a different method of correction you avoid this problem but that's not the point. LMR Date: Tue, 24 Mar 2009 14:03:46 -0300 Subject: Re: [Freesurfer] FDR correction From: p...@netfilter.com.br To: lari...@gmail.com CC: freesurfer@nmr.mgh.harvard.edu Some links that may be helpful: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysishttp://surfer.nmr.mgh.harvard.edu/fswiki/MultipleComparisons Hope it helps. PPJ--- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom On Tue, Mar 24, 2009 at 12:38, Lars M. Rimol wrote: Hi, I have done an analysis involving three groups, so there are three pairwise comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple comparisons (across the vertices), so I use FDR. But since FDR determines the threshold basd on the actual p-values, I get 6 different tresholds: comparison 1: lh and rh, 0.016 and 0.028 (I can choose .01) comparison 2: lh and rh, 0.01 and 0.001 (I can choose.001) comparison 3 lh and rh, 0.001 and 0.0001 (I can choose .0001) There are lots of significant vertices in comparison 1 and nothing significant, after correction, in comparison 3. Is there anything wrong with using different tresholds here, and concluding that in comparison 1 there were extensive differences between the groups, whereas in comparison 3 there were none? I'm not sure if this is a problem, but I'm afraid some reviewers might have an issue with it. Across the hemispheres, I can choose a conservative threshold which covers both hemispheres, i.e. lower than both the FDR-adjusted treshold for lh and rh. But between the comparisons the tresholds differ even more, by a factor of 10 and 100. And if I choose the most conservative of all the adjusted thresholds, I'm afraid that I'll make a type II error in comparison 1. >From what I understand, the adjusted threshold for comparison 3 is more >conservative because of the actual empirical data (the distribution of >p-values), so that's an empirical argument for using a more conservative >threshold there. And: What if I pooled all thre p-maps (sig.mgh) and did an FDR on the whole thing, would that be a better approach? And does Freesurfer use the Benjamini algorithm, and if you do, can I use Tom Nichols' matlab function for FDR (http://www.sph.umich.edu/~nichols/FDR/FDR.m) for pooling all three p-maps? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?
Hi FreeSurfers, After a months of QC'ing FreeSurfer results, my team and I are now working toward end stage analysis of our cortical thickness data. All along, we have been aiming to make improvements in the wm.mgz volume so that we can assure that the white matter and gray matter surfaces are as accurate as possible. This was under the assumption that if the white matter and gray matter surfaces are accurate, then the voxel-wise representation of the white and gray matter in the aparc+aseg.mgz file would be accurate. However, in almost all of our cases, the aparc+aseg.mgz segmentation looks very bad. The bad aparc+aseg.mgz representation of what seem to be accurate white and gray matter segmentations in the wm.mgz file is leading us to believe that the cortical correspondences created after template mapping are wrong. Does anyone else have an explanation for such a discrepancy? Is this a common problem and if so, is there any way to remedy this situation? Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?
Hi Ryan, what version are you using? And when you say "bad" what exactly do you mean? Can you send some snapshots? If you're doing a thickness study the aparc+aseg is irrelevant - just the white and pial surfaces matter (and the spherical registration of course) cheers Bruce On Tue, 24 Mar 2009, Ryan Scotton wrote: Hi FreeSurfers, After a months of QC'ing FreeSurfer results, my team and I are now working toward end stage analysis of our cortical thickness data. All along, we have been aiming to make improvements in the wm.mgz volume so that we can assure that the white matter and gray matter surfaces are as accurate as possible. This was under the assumption that if the white matter and gray matter surfaces are accurate, then the voxel-wise representation of the white and gray matter in the aparc+aseg.mgz file would be accurate. However, in almost all of our cases, the aparc+aseg.mgz segmentation looks very bad. The bad aparc+aseg.mgz representation of what seem to be accurate white and gray matter segmentations in the wm.mgz file is leading us to believe that the cortical correspondences created after template mapping are wrong. Does anyone else have an explanation for such a discrepancy? Is this a common problem and if so, is there any way to remedy this situation? Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] New Tutorial Attachments
Hello, I wanted to review the FreeSurfer attachments on the wiki's tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Whenever I try to click on an attachment, it brings me to a page and says: Attached FilesNo attachments stored for FsTutorial/April2009CourseSchedule You are not allowed to attach a file to this page. I see the page was recently updated for the new class. Are the powerpoints still available to view somewhere? Mahalo, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] New Tutorial Attachments
Jeff, We haven't yet uploaded the latest slides for a course we are running in April, which the main FsTutorial page points at. You can get slides and wiki links from our most recent course here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/BrazilCourseSchedule Nick On Tue, 2009-03-24 at 17:42 -0600, Jeff Sadino wrote: > Hello, > > I wanted to review the FreeSurfer attachments on the wiki's tutorial > page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Whenever I > try to click on an attachment, it brings me to a page and says: > > Attached Files > No attachments stored for FsTutorial/April2009CourseSchedule > You are not allowed to attach a file to this page. > I see the page was recently updated for the new class. Are the > powerpoints still available to view somewhere? > > Mahalo, > Jeff Sadino > > > > > > __ > Hotmail® is up to 70% faster. Now good news travels really fast. Find > out more. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
