Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

aparc2feat with custom annotation file
by Michelle Umali 24 Oct '11

24 Oct '11

Hi Freesurfers, I am trying to generate binary V1 and V2 masks based on my fieldsign results. We created a custom annotation file by adding the two new areas (muuV1 and muuV2, entries 36 and 37, resp., i.e., in Matlab in rows 37 and 38) to the aparc color table using Matlab and setting all labels to zero. Then we marked the areas in tksurfer (imported the annotation file, made closed paths around the vertices, and added it to the muuV1 or muuV2 label) and exported the annotation file. This worked fine, but when we used aparc2feat (on feat data previously registered with regfeat2anat) using the --annot <our_annot> option, only muuV1 (entry 36) was correctly extracted, and there were no entries for label 37 in the resulting volume. Do you have any idea what could have gone wrong? I attached our annotation file (gzipped) containing the marked areas muuV1 and muuV2. Thank you very much, Michelle

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roi analysis from label or annotation
by Knut J Bjuland 24 Oct '11

24 Oct '11

I am working on roi analysis. I have made a label using mri_surdcluster and used mri_label2label to copy the label from fsaverage to each individual subject. The next step would be to use mris_anatomical_stats to calculate stats for each subject. I used a Python to merge the txt file from mris_anatomical_stats. Is it possible to force mri_surfcluster to save the label another dir than fsaverage? Can I use convert roi label to annotation and then use aparc2stats or similar command to get group statics? Cheers Knut J

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mris_anatomical stats different thickness files
by krista kelly 24 Oct '11

24 Oct '11

I'm looking at both cortical thickness and surface area differences between two groups. I've been using mris_anatomical_stats to retrieve values but had a few questions: 1) Do I need to do separate mris_anatomical_stats using different thickness files (bolded below) to get cortical thickness and surface area measures. For example: cortical thickness - mris_anatomical_stats -l lh.v1.label -t *lh.thickness*-b -f BV01/stats/lh.v1.stats BV01 lh surface area - mris_anatomical_stats -l lh.v1.label -t *lh.area *-b -f BV01/stats/lh.v1.stats BV01 lh Or, since the output files include all of these measures, is it fine to just run one of the two? 2) The output files for both analyses run above (with different thickness files) have identical values for everything except for tray matter volume. Using lh.thickness file - grayvol = 8082; using lh.area file - grayvol = 4029. Can anyone clarify why this happens? 3) The default surface area values are for the white matter surface. How do I run mri_anatomical_stats to get the pial surface? I've tried mris_anatomical_stats -l lh.v1.label -t *lh.area.pial *-b -f BV01/stats/lh.v1.stats BV01 lh but I get identical values for everything (except grayvol). Thanks! Krista

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matlab script to convert array back to thickness file format?
by Lara Foland-Ross 24 Oct '11

24 Oct '11

Hi there, We're using load_mgh.m to load several individual (single subject) cortical thickness maps (each 1X163842) that we'll use to compute a group-level statistic in matlab. We're not changing the dimensionality or order of the information loaded and we would like to know if there is a matlab script we might use to convert our resulting (1X163842) array of statistical values back into a .mgh file that can be read on FreeSurfer. Thanks! Lara -- Lara Foland-Ross Postdoctoral Fellow Stanford Mood and Anxiety Disorders Laboratory Department of Psychology Stanford University 450 Serra Mall, Stanford, CA 94305 Jordan Hall, Building 420, Room 142

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cortical surface of individual subject: coordinates in individual's MNI space
by Nela Cicmil 24 Oct '11

24 Oct '11

Dear Freesurfer Developers and Users, I have two question(s) about Freesurfer and individual subject's MNI coordinates: (1) Having run recon-all to reconstruct the cortical surface for an individual subject in my study, is it possible to obtain the list of coordinates that describe the points in the individual subject's MNI space that comprise the cortical surface of that subject's brain? This is in order to run an MEG beamformer analysis (in matlab) in the subject's own MNI space, but restricted to those voxels that comprise the cortical surface for that subject, as calculated by Freesurfer. (2) Once I have obtained (in matlab), for a list of voxels that comprise the cortical surface, each of the their MNI coordinates and their associated activation value (e.g. tstat), is there a straightforward way to display this on the cortical surface of that subject in tksurfer, for example by converting to a simple wfile? I searched the archives but could not find information that explained this directly; apologies if this does already exist: if so, could you please point me towards it? Thank you so much for your help, Best wishes, Nela ---- Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy & Genetics University of Oxford Tel: 01865 282274 Internal: 82274

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gray matter/csf surface reconstruction
by Shani Ben Amitay 23 Oct '11

23 Oct '11

Dear freesurfers, In order to generate cortical vector normals connecting homologous vertices of the inner and outer surface, I would like to better understand how the gray matter/csf surface is reconstructed and how correspondence between inner and outer surfaces is achieved. Does anyone can explain or give a reference? Thanks , Shani

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Re: [Freesurfer] fsaverage rh to fsaverage_sym lh question
by Douglas N Greve 21 Oct '11

21 Oct '11

Oh, you should not be running xhemireg (or anything else) on fsaverage. doug Ritobrato Datta wrote: > it is where it is choking...saying nu.mgz and norm.mgz not found > > mri_convert fsaverage/mri/nu.mgz fsaverage/xhemi/mri/nu.mgz --left-right-reverse > mri_convert fsaverage/mri/norm.mgz fsaverage/xhemi/mri/norm.mgz --left-right-reverse > > > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: "Ritobrato Datta" <ridatta(a)mail.med.upenn.edu> > Sent: Friday, October 21, 2011 5:12:26 PM > Subject: Re: fsaverage rh to fsaverage_sym lh question > > what is it that needs those files? > > Ritobrato Datta wrote: > >> that ok but it cant find the nu.mgz and norm.mgz in fsaverage/mri >> >> it needs those files to flip them left right reverse. >> >> >> ----- Original Message ----- >> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >> To: "Ritobrato Datta" <ridatta(a)mail.med.upenn.edu>, "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >> Sent: Friday, October 21, 2011 4:44:29 PM >> Subject: Re: fsaverage rh to fsaverage_sym lh question >> >> I think it just needs something there to get the volume geometry from. >> Does orig.mgz exist? If not, re-download fsaverage_sym.tar.gz and >> re-install it (the new version has an orig.mgz). >> doug >> >> Ritobrato Datta wrote: >> >> >>> Hi Doug, >>> >>> I am trying to apply ur scripts to register fsaverage rh to fsaverage_sym lh and the script fails saying it cant find nu.mgz >>> >>> Looks like two files that are missing in >>> >>> fsaverage/mri >>> >>> are >>> >>> nu.mgz and norm.mgz >>> >>> How can I create them in fsaverage ? >>> >>> >>> or any other suggestions how to get fsaverage rh to fsaverage_sym lh ? >>> >>> Thanks a lot >>> >>> Rito >>> >>> >>> >>> >>> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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map of vertices (by number) within an R01
by Polly Dhond 21 Oct '11

21 Oct '11

Hi FS, Is there a way to map the loction of several vertices with (numbers as labels) in an ROI ? For example I have a small R0I with 30 vetices in it, i have their numbers as a list but i want to see how they map with respect to one another (all at once). thanks -- Rupali P. Dhond, Ph.D. Dept. of Radiology, MGH-HMS Martinos Center for Biomedical Imaging Rm 2301, Bldg 149, 13th Street Charlestown, MA 02129 e-mail: polly(a)nmr.mgh.harvard.edu phone: 617-726-6542

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Re: [Freesurfer] fsaverage rh to fsaverage_sym lh question
by Douglas N Greve 21 Oct '11

21 Oct '11

I think it just needs something there to get the volume geometry from. Does orig.mgz exist? If not, re-download fsaverage_sym.tar.gz and re-install it (the new version has an orig.mgz). doug Ritobrato Datta wrote: > Hi Doug, > > I am trying to apply ur scripts to register fsaverage rh to fsaverage_sym lh and the script fails saying it cant find nu.mgz > > Looks like two files that are missing in > > fsaverage/mri > > are > > nu.mgz and norm.mgz > > How can I create them in fsaverage ? > > > or any other suggestions how to get fsaverage rh to fsaverage_sym lh ? > > Thanks a lot > > Rito > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer Error Message in running autorecon2 & autorecon3
by Vy Dinh 21 Oct '11

21 Oct '11

Dear Experts, I ran the wm.mgz corrections and pial corrections using the command: -autorecon2 –autorecon3 –subjid sub2 However, Freesurfer exited the program with the following message: SUBJECTS_DIR /Users/subdir FREESURFER_HOME Applications/freesurfer Loading source label. No such file or directory fsaverage/label/lh.BA1.label ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label Darwin mso00820bg.rush.edu<http://mso00820bg.rush.edu> 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011. Can someone please explain what this error message means regarding whether I need to rerun the autorecon processes with the fsaverage folder within my current subjects folder? I copied fsaverage/ from freesurfer/ to my designated SUBJECTS_DIR but have not run the recon. It seems that the pial surfaces were regenerated while the white matter segment was not corrected for this one subject. I ran other subjects within this SUBJECTS_DIR (before I copied the fsaverage folder) but the white matter segment and pial surfaces were regenerated for them. Looking forward to your responses. Thank you, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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