Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Electrode Placement
by Nick Collisson 13 Aug '13

13 Aug '13

Hi all, Are point sets and isosurfaces reported in different coordinate systems? Points that are located on the surface of the cortex in Freesurfer appear far away from the brain (rendered from the .vtk file of the saved isosurface) when I export them into MATLAB. Thanks, Nick

2 1

FS and FSL
by Alexopoulos, Dimitrios 13 Aug '13

13 Aug '13

A quick question. Do all versions of FS (even the older 4.4 version) require a full FSL install to run recon-all -all. Would the command run "without error" even if you don't have FSL installed. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

3 2

mris_thickness threshold
by Giusy Chinnici 13 Aug '13

13 Aug '13

Hi all, I'd like to understand the difference in using the default value for maximum threshold (5 mm) instead of a custom value in mris_thickness function. Is the map of cortical thickness the same in both cases and the difference resides in the saturation (all values above 5mm are cut to 5 mm) or do we have a completely different map (all values above 5 mm have their own value but saturated value is displayed from 5 mm and above)? please find in attachment an example of what I'm saying... I aspected to find same values for thickness within the threshold value, why this is not the case? Thanks cheers -- Giusy Chinnici

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Label corresponding to coordinate
by Martin Kavec 13 Aug '13

13 Aug '13

Hi all, Is there a command in Freesurfer, which would return to which label (e.g. superior frontal white matter left) a coordinate x,y,z belongs to? Thanks, Martin Sent from my iPad

2 1

mri_glmfit-sim
by joost janssen 13 Aug '13

13 Aug '13

Hi, Linux jjanssen 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux command: mri_glmfit-sim --glmdir lh.thickness.20 --cache 2.0 pos error: ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 i saw 1 prior email about this error message but no solution posted. i'm suing Ubuntu v12.04 thanks, -joost

2 2

hippocampal subfields question
by Salil Soman 12 Aug '13

12 Aug '13

Hi, I just wanted to confirm that label "hippocampus" in the hippocampal subfields segmentation is simply parts of the hippocampus that do not fall into one of the other major categories? Also, where can I find the units for the hippocampal subfields? I am seeing some discrepancy between the left and right hippocampal volumes generated by freesurfer and the summed areas generated by the hippocampal subfield analysis. Thank you, -Sal

2 1

funcroi-table-sess error
by Alexandra Tanner 12 Aug '13

12 Aug '13

Dear Doug and Freesurfers, I am attempting to run funcroi-table-sess on a set of subjects but keep getting an error message I've never seen before: funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -c Cond2vFix -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/18ActiveFolate_12Placebo_PreAndPost_7Tpost/ctx_lh_insula_aparc+aseg_2vFix log/funcroi-table-sess.log log/funcroi-table-sess.log: No such file or directory. Funcroi-sess ran without error, as did funcroi-config. I've run this analysis many times in the past and have never had this problem so I am at a loss as to what is going wrong. Any help would be greatly appreciated! Thanks, Alex

2 2

recon-all after manual edits
by Jason Tourville 12 Aug '13

12 Aug '13

Hi there, I am doing manual edits on the brainmask.mgz, wm.mgz, and brain.finalsurfs.manedit.mgz volumes and adding control points. What autorecon flag or from which stage of processing should I rerun recon-all such that all of these manual edits are respected? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Re: [Freesurfer] Error when using preproc-sess -per-session in FS-5.3
by Sepide Movaghati 12 Aug '13

12 Aug '13

Just an update! FS 5.3 gives me the same error even when running -per-run. Using FS 5.1, the same error pops up only in -per-session and -per-run works fine. Thank you in advance. ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Sepide Movaghati [sepide.movaghati(a)mail.mcgill.ca] Sent: Monday, August 12, 2013 11:31 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Error when using preproc-sess -per-session in FS-5.3 Hello, I am using freesurfer 5.3 and try to run: preproc-sess -s session1 -surface self lhrh -fsd bold -mni305 -fwhm 5 -per-session it gives me an error: 1/1 session1 1/1 session1 003 lh --------- Mon Aug 12 11:21:09 EDT 2013 ERROR: could not determine file for /export01/data/sepid/subjects/ZY/session1/bold/003/fmcpr however, it works fine when I use -per-run. I have attached complete terminal output. Thanks.

1 0

FreeSurfer version for subjects
by Alex Hanganu 12 Aug '13

12 Aug '13

Hello everyone, isthere a method to verify which was the last version of FreeSurfer that was used to perform the recon-all ? For. ex. in /subjects/subject_name/scripts/build-stamp.txt/I can see that this subject was registered the first time with FS version 5.0but after that, an additional recon-all was performed and all the pre-processing steps have been passed with FS version 5.3, and this is registered in /recon-all-status.log/. Yet, in this log the version of FS that was used - is not shown. Thanks, Alex.

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