Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Gyral region centroids?
by Dankner, Nathan (NIH/NIMH) [F] 26 May '10

26 May '10

Hi all, I am looking to get the centroids of the Desikan parcellation gyral regions to calculate distance. Any ideas on how to go about doing this? Thanks, Nathan

2 1

Recon failing during topology correction
by Michael Waskom 26 May '10

26 May '10

Hi, all, We have a recon that is failing during topology correction. Here's the history or what's happened: --first run through the recon-all -all pipeline went fine --control points were added and pial edits were made for quality control --a second recon was run with --autorecon3-cp --autorecon3 During the second recon, the process gets stuck for a long time in topology correction and eventually crashes. We've tried it twice, and it crashes on the same defect. Here's info from the bugr script: Debian version: 5.0 Kernel info: Linux 2.6.28-18-generic x86_64 recon-all log is attached. Any ideas? Thanks! Mike

2 1

missing gaussian curvature file
by Ana Catarino 26 May '10

26 May '10

Hello, I was trying to run a qdec analysis on Gaussian curvature and got the following error message: Error in Analyze: Couldn't open file $SUBJECTS_DIR/AS1/surf/lh.white.K.fwhm10.avgsubject.mgh I get the same error message on mean curvature analysis. Any ideas? Thanks, Ana Catarino

1 0

Doubt about GM and thickness
by Kelly Silva 26 May '10

26 May '10

Hello, I'm doing regression analyses with cortical thickness at the level of voxel. Should I correct the total GM volume by introducing this parameter as a confounding variable? Shoud I include the intracranial volume as an additional nuisance variable? If positive, I assume that these variables can only be introduced as covariates if they differ between groups. Am I correct? I saw in one message that we should not corret for thickness. Why not? Thanks in advance and best regards, Kelly

1 0

3mm slices?
by Mishkin Derakhshan 25 May '10

25 May '10

Hi, I'm wondering if anyone has looked at the accuracy/reproducibility of cortical thickness measurements using 3mm slice data. I found the Han 2006 paper in NeuroImage comparing different sequences, but it doesn't compare different slice thicknesses. If not, does anyone have anecdotal experience using 3mm slices? thanks, mishkin

2 1

brainmask and wm correction
by Deniz Ozgen 25 May '10

25 May '10

Hello all, I am new to FreeSurfer and still trying to understand how things work. I am currently trying to understand how the manual correction works. Following the online tutorials I was able to fix the brainmask and wm.mgz, and also add control points in the wm so that low intensity wm is also included in the segmentation. In the tutorials it is suggested to run the FreeSurfer after doing the brainmask correction by recon-all -autorecon2 -subjid <subject name> After the wm control point addition, the tutorial says that "run the program with -autorecon2-cp" Is it possible to do brainmask correction, white matter edits and control points in one session and run the FreeSurfer again to fix all this at once? Is there a different command for this? I apologize if this has been answered before. Thanks a lot. Deniz.

2 1

MNI305 to MNI152
by Yigal Agam 25 May '10

25 May '10

How do I convert between the two coordinate systems? Yigal

1 0

Error untarring fsfast tutorial
by Jesse Friedman 25 May '10

25 May '10

Hi, I'm following instructions from: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialData The anatomical data extracts successfully, but the functional data hangs on this command: tar xvfz fsfast-tutorial.tar.gz The process extracts files for a while and produces this output: ./fsfast-tutorial/ ./fsfast-tutorial/.xdebug_tkmedit ./fsfast-tutorial/run-fsfast-tut.log.bak ...More successful extractions... ./fsfast-tutorial/fb1-preproc-study/mgh-104.1/bold/007/f.nii ./fsfast-tutorial/fb1-preproc-study/mgh-104.1/bold/007/fmcsm5.nii tar: Skipping to next header tar: Archive contains obsolescent base-64 headers (process hangs here) Any help? I'm in /autofs/space/schnook_001/users/caitlin_tutorial/functional. bugr details are below. Thanks! Jesse FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: vantz SUBJECTS_DIR: /autofs/space/ventzl_001/users/SUBJECTS_DIR PWD: /space/schnook/1/users/caitlin_tutorial/functional ssh vantz setenv SUBJECTS_DIR /autofs/space/ventzl_001/users/SUBJECTS_DIR cd /space/schnook/1/users/caitlin_tutorial/functional

3 4

Getting Talairach Coordinates
by Yigal Agam 25 May '10

25 May '10

Hi, Is there a way to get the Tal and MNI coordinates of a given fsaverage vertex through matlab or the unix command line, without opening tksurfer? Thanks, Yigal

2 1

Fractional Anisotropy Command Question
by Weisinger, Brian (NIH/OD) [E] 25 May '10

25 May '10

Hello, I am trying to run the dt_recon with the fractional anisotropy to do a project with white matter. I am running into a problem actually getting the command to work. I am trying to follow the example online dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti But I am not sure where/what I am supposed to put after the -i. The other stuff I am pretty sure I know, --s = the subject folder --o = the folder I want the output to go in Can you fill me in on what I'm missing, I looked in the subjects output files and could not find anything that ended with .dcm. I was told that it is the input diffusion weighted time series. Is that something that would be different for everyone or something that would always be the same? If it is unique for each person where would I find that file so I can input the name of it? Thank you, Brian Weisinger

2 1

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