Freesurfer

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Tutorial Files
by Yigal Agam 25 May '10

25 May '10

Hi, We're having problems untarring the tutorial data. Are the uncompressed data available anywhere? Thanks, Yigal

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mris_preproc thickness vs functional data
by ridatta＠mail.med.upenn.edu 25 May '10

25 May '10

Hello All, I have a question regarding the actual command issued under the mris_preproc wrapper. I noticed that when I ran the recon-all -qcache to resample the different anatomical measures like thickness etc to fsaverage, one of the step is the following - mri_surf2surf --srcsubject 068 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval 068.1.mgh --sval ./lh.thickness --sfmt curv --noreshape --no-cortex When I ran mris_preproc using the tutorial as specified here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup the step similar to the one above is the following mri_surf2surf --srcsubject 068 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval 068.1.mgh --sval ./rh.VisStimBoth_rb.mgh --noreshape --no-cortex" What does the "--sfmt curv" do ? What happens if its included in the resampling of the functional data ? Should I ? Please let me know. Thanks Ri

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error in simulation script
by johanna feiler 25 May '10

25 May '10

Dear FreeSurfer experts, I want to run the simulation script with qdec, but I always get the following error message: 'error in simulation script generation command failed: chmod u+x' and then the adress of the 'mri_glmfit-sim-mc-z.abs.2' - file. This it what the file contains: mri_glmfit-sim \ --glmdir /home/hiwibp14/smb4k/CORTICAL/fmrt/Studie43/freesurfer/qdec/Untitled \ --sim mc-z 10000 2 mc-z.abs.2 \ --sim-sign abs \ --overwrite What can I do to run my simulations? Any help is appreciated! Johanna Feiler ___________________________________________________________ GRATIS: Movie-Flat mit über 300 Top-Videos. Für WEB.DE Nutzer dauerhaft kostenlos! Jetzt freischalten unter http://movieflat.web.de

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question about using control points
by Mehul Sampat 24 May '10

24 May '10

Hi Folks, One of my colleagues had the following issue while using control points. He re-processed the case after adding some control points (shown in the first figure), but after doing so, the WM was still not included. Is this a typical case, where it would be better to edit wm.mgz instead of adding control points. Second question: we noticed that some WM was left out from the yellow surface. But when we look at wm.mgz these values of these voxels are in the range 80-95 (shown in the second figure) In such cases should we remove these voxels from wm.mgz (using the right click option) and then include them again ? That is, this would change the voxel values from 80-95 to 255.. I ask this because sometimes, we see that the yellow surface is clipped but there is nothing to include in the wm.mgz since the corresponding values do have some intensity values Please let me know if you need more information/clarfication about the second question. thanks Mehul

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question 2 about using control points
by Mehul Sampat 24 May '10

24 May '10

Hi Folks, We noticed that some WM was left out from the yellow surface. But when we look at wm.mgz these values of these voxels are in the range 80-95 (shown in the figure) In such cases should we remove these voxels from wm.mgz (using the right click option) and then include them again ? That is, this would change the voxel values from 80-95 to 255.. I ask this because sometimes, we see that the yellow surface is clipped but there is nothing to include in the wm.mgz since the corresponding voxels do have some intensity values in the range 75-90. Please let me know if you need more information/clarification about this question. thanks Mehul

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question 1 about using control points
by Mehul Sampat 24 May '10

24 May '10

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wm correction issues
by Ilana Hairston 24 May '10

24 May '10

Hi there. we have been doing some white matter corrections, based on the wiki instructions. After filling in some missing voxels we ran ...autorecon2-wm autorecon3 ... but it doesn't look like the white matter was corrected. See the attached to images with the wm.mgz and brainmask after the autorecon steps. the corrected area is marked with a red circle thanks ilana

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Error message in opening OSX 10.5 version image disk of FS
by Danilo Scelfo 24 May '10

24 May '10

Hi there, I'm using a Mac OS X 10.6.3. I tried to install the freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0-full.dmg but I'm not allowed/able to open it, getting the error message "invalid checksum". Is it something up to the image disk version (i.e. do I need to use a *v4.6.3-full.dmg image?) or is it something up to my Mac? Thanks for your interest. Sincerely, Danilo Scelfo.

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Creating annotation file for lobar regions...
by Rudolph Pienaar 24 May '10

24 May '10

Hi all -- Is there a simple way to create an annotation for frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot files in a FS 'label' dir? Ideally speaking, I'd like to have a ?h.lobar.annot with corresponding lobar.annot.ctab. Apologies if this question has come up before... a quick google didn't reveal anything. Many thanks -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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recon-all ERROR reading wm.seg.mgz when doing routine correction processing
by Stacey M Schaefer 24 May '10

24 May '10

Hello Freesurfer List Gurus, We're at the stage of making white matter edits and adding control points, but one of my subjects recently produced the following error: zcat: /study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz: unexpected end of file mghRead(/study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz): could not read 65536 bytes at slice 90 mri_segment: could not read file wm.seg.mgz to preserve edits Linux cashew.keck.waisman.wisc.edu 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 23:11:58 EST 2009 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue May 18 21:04:35 CDT 2010 Any suggestions on how to fix? This subject has already had a great deal of hands on processing in terms of adding control points, editing the white matter, and running recon_all to fix, with multiple passes to get it as perfect as possible. Also, I've TRIED just rerunning recon-all on it, but the errors persist. (Each time, we're running the following command: recon-all -autorecon2-cp -autorecon3 -subjid subject057) Any and all info on how to salvage this subject's data without have to start from scratch will be much appreciated! Thank you. Stacey Schaefer --------------------------------------------------- Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937

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