Freesurfer

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30057 discussions

want to view one segmented subcortical object at a time...
by Shahabuddin Ansari 20 Mar '06

20 Mar '06

Hello, I have segmented subcortical regions of the whole brain from Freesurfer. Can somebody help me how to view one object (say right hippocampus) at a time. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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'zero distance at v' printing associated with missing hemi.smoothwm files.
by Greg Harris 20 Mar '06

20 Mar '06

In a sample of 50 brains, I found two hemispheres that fail at autorecon3, printing a whole lot of this: zero distance at v 91420, n 0 (vn = 89897) zero distance at v 91420, n 1 (vn = 91419) zero distance at v 91420, n 2 (vn = 91421) zero distance at v 91420, n 3 (vn = 91402) zero distance at v 91420, n 4 (vn = 88463) zero distance at v 91420, n 5 (vn = 89896) zero distance at v 91420, n 6 (vn = 88475) zero distance at v 91420, n 7 (vn = 89912) zero distance at v 91420, n 8 (vn = 91401) zero distance at v 91420, n 9 (vn = 89913) zero distance at v 91420, n 10 (vn = 91438) zero distance at v 91420, n 11 (vn = 91404) zero distance at v 91420, n 12 (vn = 91422) zero distance at v 91420, n 13 (vn = 92898) zero distance at v 91420, n 14 (vn = 92899) zero distance at v 91420, n 15 (vn = 91384) zero distance at v 91420, n 16 (vn = 91385) zero distance at v 91420, n 17 (vn = 92900) zero distance at v 91420, n 18 (vn = 92900) zero distance at v 91420, n 19 (vn = 92900) zero distance at v 91420, n 20 (vn = 92898) zero distance at v 91420, n 21 (vn = 91439) zero distance at v 91420, n 22 (vn = 91384) zero distance at v 91420, n 23 (vn = 92881) zero distance at v 91420, n 24 (vn = 91404) zero distance at v 91420, n 25 (vn = 89899) zero distance at v 91420, n 26 (vn = 91400) zero distance at v 91420, n 27 (vn = 88462) zero distance at v 91420, n 28 (vn = 89882) zero distance at v 91420, n 29 (vn = 91440) zero distance at v 91420, n 30 (vn = 88485) zero distance at v 91420, n 31 (vn = 91385) zero distance at v 91420, n 32 (vn = 89884) zero distance at v 91420, n 33 (vn = 88474) zero distance at v 91420, n 34 (vn = 89928) zero distance at v 91420, n 35 (vn = 88449) zero distance at v 91420, n 36 (vn = 88496) zero distance at v 91420, n 37 (vn = 88486) zero distance at v 91420, n 38 (vn = 89885) zero distance at v 91420, n 39 (vn = 88450) zero distance at v 91420, n 40 (vn = 89869) zero distance at v 91420, n 41 (vn = 91474) zero distance at v 91420, n 42 (vn = 91441) zero distance at v 91420, n 43 (vn = 86953) zero distance at v 91420, n 44 (vn = 89852) zero distance at v 91420, n 45 (vn = 88451) zero distance at v 91420, n 46 (vn = 86952) zero distance at v 91420, n 47 (vn = 92853) zero distance at v 91420, n 48 (vn = 89942) zero distance at v 91420, n 49 (vn = 88414) zero distance at v 91420, n 50 (vn = 86929) zero distance at v 91420, n 51 (vn = 91473) zero distance at v 91420, n 52 (vn = 89867) zero distance at v 91420, n 53 (vn = 92928) zero distance at v 91420, n 54 (vn = 89939) zero distance at v 91420, n 55 (vn = 91443) zero distance at v 91420, n 56 (vn = 91476) zero distance at v 91420, n 57 (vn = 86928) zero distance at v 91420, n 58 (vn = 88494) zero distance at v 91420, n 59 (vn = 86973) zero distance at v 91421, n 0 (vn = 89898) zero distance at v 91421, n 1 (vn = 91420) etc. etc. Any idea where to look for the cause of this bug? I discovered it because these hemispheres are missing their [lr]h.smoothwm, although they have [lr]h.smoothwm.nofix files. ( for my reference, they are the left hemisphere of scan 0182497 and the right hemisphere of scan 0193095.) Greg Harris

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RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
by Goldman, Aaron (NIH/NIMH) [C] 20 Mar '06

20 Mar '06

Hi, I think I may have observed the same issue he's talking about. What I've attached is possibly an extreme example (I haven't inspected many yet, to be honest), but it seems typical for at least a bit of this to happen in our subjects. I was also curious if the black "unknown" label was expected to extend into the temporal lobe as it does here. Thanks, -Aaron- -----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Saturday, March 18, 2006 5:51 PM To: Greg Harris Cc: Freesurfer Mailing List; Karl Helmer Subject: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data Hi Greg, Could you send along jpegs or rgbs detailing what excactly the parcellation atlas is doing in the cingulate region? Also have you looked at both the white and pial surfaces in this area? Hope you are well othwerwise, Rahul On Sat, 18 Mar 2006, Greg Harris wrote: > Dear Karl, > > Has anybody had any success with the midline rois given by the atlas > curvature.buckner40.filled.desikan_killiany that is automatically applied > by autorecon3 under the newest stable release, version 3.0? > > Our trouble lies in the regions labeled corpuscallosum and > <anything>cingulate: this > atlas is giving us a corpus callosum that is exactly the ventral cingulate > sulcus, and the 4 > cingulate gyrus segments, which is what we are interested in in this case, > incorrectly > exclude their ventral portion. > > I presume this has been made to work at mgh, because Rahul Desikan's paper > contains > an illustration that is anatomically correctly labeled for these regions. > > We are providing an orig/001.mgz image to the autorecon1 step that is > talairach aligned, > skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed > 16-bit > T1-weighted MRI scan. We have thousands of them, collected over the past 15 > years. > We are writing a nifti .nii file, and converting it with > > mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 > /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii > /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz > > We actually mean to numerically measure the extent -- the area and thickness, > say -- of > anatomical regions of interest including <anything>cingulate and apply > statistical tests to > these data. A line of guff about Type I and Type II errors and what is only > presumable > when identifying anatomical rois would be of no interest, and considered > needlessly > defensive. After all, the other 29 regions of Desikan's really great atlas > are in working > order! > > Do we need to convince Rahul Desikan to release the "correct" > *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 > that correspond to his paper? > > Greg Harris > The University of Iowa College of Medicine > Psychiatry NeuroImaging Lab > > > -- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesufer] Problems with control points
by Martin Ystad 20 Mar '06

20 Mar '06

Hi, I have some problems with the white matter segmentation on some of my brains. the Main-surface cuts into the white matter in certain bright areas. I tried to fix this by adding control points to the area. Then I ran recon-all -autorecon2-cp again, but this didn't resolve the problem. Any Ideas ? I've attached a picture of the problem. Thanks, Martin Ystad University of Bergen, Norway.

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lh.curv versus lh.curv.pial
by Yuhong Jiang 19 Mar '06

19 Mar '06

Dear Bruce and others, We recently started using the newly released freesurfer stable version 3.0.1. After auto-recon2 a few files are saved, including lh.curv and lh.curv.pial. When lh.curv is loaded as the curvature, the output looks awful. But lh.curv.pial looks great. What's the difference between these two files? Which one should be used for curvature overlay? Thanks. --Yuhong ============================================================================= Yuhong Jiang yuhong(a)MIT.EDU 617-876-2054 http://web.mit.edu/yuhong/www =============================================================================

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How to display isolated segmented object in Freesurfer viewer
by Shahabuddin Ansari 19 Mar '06

19 Mar '06

Hello, Thanks for answering my previous querry. I have successfully segmented the subcortical regions of the brain. Now, my next simple question is how to display each segmented object separately? I think it is to do with masking, but not sure how to apply that in 3D. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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question about subcortical brain segmentation using Freesurfer...
by Shahabuddin Ansari 18 Mar '06

18 Mar '06

Hello, I am new Freesurfer user. I need to segment subcortical regions of brain and wondering that if there is any doc or tutorial on the subject. I appreciate your comments. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
by Greg Harris 18 Mar '06

18 Mar '06

Dear Karl, Has anybody had any success with the midline rois given by the atlas curvature.buckner40.filled.desikan_killiany that is automatically applied by autorecon3 under the newest stable release, version 3.0? Our trouble lies in the regions labeled corpuscallosum and <anything>cingulate: this atlas is giving us a corpus callosum that is exactly the ventral cingulate sulcus, and the 4 cingulate gyrus segments, which is what we are interested in in this case, incorrectly exclude their ventral portion. I presume this has been made to work at mgh, because Rahul Desikan's paper contains an illustration that is anatomically correctly labeled for these regions. We are providing an orig/001.mgz image to the autorecon1 step that is talairach aligned, skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed 16-bit T1-weighted MRI scan. We have thousands of them, collected over the past 15 years. We are writing a nifti .nii file, and converting it with mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz We actually mean to numerically measure the extent -- the area and thickness, say -- of anatomical regions of interest including <anything>cingulate and apply statistical tests to these data. A line of guff about Type I and Type II errors and what is only presumable when identifying anatomical rois would be of no interest, and considered needlessly defensive. After all, the other 29 regions of Desikan's really great atlas are in working order! Do we need to convince Rahul Desikan to release the "correct" *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 that correspond to his paper? Greg Harris The University of Iowa College of Medicine Psychiatry NeuroImaging Lab

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paint binary
by Nahab, Fatta (NIH/NINDS) [E] 17 Mar '06

17 Mar '06

I just installed the new stable release on OSX. Installation ran smoothly and I made the changes in .cshrc. On starting freesurfer ('csurf'), I receive the following error: These binaries used by csurf not found in /Applications/freesurfer/bin: paint This binary is not in the directory (it was on my prior install which is in a different directory) and freesurfer doesn't seem to be running anything after I click 'ok' on the dialog box. Thanks for your help, Fatta

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RE: [Freesurfer] New average subject and stable release, v3.0
by Goldman, Aaron (NIH/NIMH) [C] 16 Mar '06

16 Mar '06

Hi, Is the fsaverage folder used when I run recon-all -all? Thanks, -Aaron- -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 06, 2006 6:13 PM To: martinos-tech(a)yahoogroups.com; Freesurfer Mailing List Subject: [Freesurfer] New average subject and stable release, v3.0 Sorry in advance for the long email ... We have a new average subject that we are recommending that people use instead of "average7". This subject can also replace the "talairach" subject as well. The name of the "fsaverage", and it can be found in the distribution itself: $FREESURFER_HOME/subjects/fsaverage To set up a link in your SUBJECTS_DIR, do the following: cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage There is a README file in $FREESURFER_HOME/subjects/fsaverage that describes how this subject was created. IMPORTANT: Differences between average7 and fsaverage, and FIX_VERTEX_AREA with impacts on mri_surfcluster and mri_glmfit. As some people have noted, the total surface area of average7 was much less than that of a typical subject (by about 40%). This caused the areas of clusters as reported by mri_surfcluster to be too small. HOWEVER, a bug in the routine that computed the vertex area caused the clusters to be 50% too large. So, the net effect was that the clusters were about the right size :). Stay with me. The surface area of the new average subject (fsaverage) is that of a typical subject, SO, it is IMPORTANT that it be used in conjunction with the fixed vertex area. This affects only two programs: mri_surfcluster and mri_glmfit. After today (March 6, 2006), if you use average7 with mri_surfcluster or mri_glmfit, they will give the following error: ERROR: you have selected subject average7. It is recommended that you use the fsaverage subject in $FREESURFER_HOME/subjects. If you really want to use average7, re-run this program with --really-use-average7 as the first argument. If you chose to do so, then it will print out: INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release. The results should be the same as when you ran it prior to the stable3 release. If you have used average7 along with Monte Carlo or Permutation simulation, inferences based on those simulations should still be correct. The only problem will be that the cluster area might be a little different. If you have used a non-average subject as your common surface space or an average subject that you created prior to March 1, 2006, then the cluster sizes will appear to drop by a third the next time your run mri_glmfit or mri_surfcluster. Again, any mri_glmfit simulation results will still be valid. For backwards compatibility, you can add --no-fix-vertex area to either mri_surfcluster or mri_glmfit. The new versions of mri_surfcluster or mri_glmfit will include the following line in their summary/logfile output: # FixVertexAreaFlag 1 The value will either be 1 or 0 depending upon whether it was fixed or not fixed. Again, sorry for the long-winded email. I know this is pretty confusing, so don't hesitate to write with questions as we get this sorted out. PLEASE send questions to the group to help in this process. thanks doug Nick Schmansky wrote: >Freesurfer community, > >A new stable release, v3.0, is now available. >The Release Notes page describing what's new, >and a link to the download page, is here: > >http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > >All users, including those using prior 'dev' >releases, are encouraged to upgrade to this >release. > >Updates to the stable release will be issued >if major bugs are found (and fixed), and as >new features which do not affect existing >functionality become available. > >The Freesurfer development team > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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