Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Installation troubleshoot (Afni won't work)
by Dreyfuss Jeremie 18 May '06

18 May '06

Hello everyone, I'm new here to the freesurfer community, and i've install the latest package on my Linux.64 version. I've completed the installation stages described on MGH site and it all seemed to work quite well until I've tried to run the mc-sess routine. The error message I got was that AFNI's to3d routine couldn't be found. I then realised that in Freesurfer's package there wasn't any AFNI directory to be found. I've downloaded AFNI from their official site and put the extracted file in the directory $FREESURFER_HOME/afni/$os I've also modified the FreeSurferEnv.sch to include the following lines: setenv AFNI_DIR $FREESURFER_HOME/afni setenv AFNI_BIN $AFNI_DIR/$os where $os is Linux on my computer. Still mc-sess wouldn't work on my computer. Please if somebody can tell what I'm doing wrong it would be of great help. Thanks in advance. Jeremie DREYFUSS. -- _______________________________________________ Search for businesses by name, location, or phone number. -Lycos Yellow Pages http://r.lycos.com/r/yp_emailfooter/http://yellowpages.lycos.com/default.as…

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mri_normalize resampling my monkey data
by Mark Pinsk 18 May '06

18 May '06

Still working thru these steps with a 0.5 mm monkey volume... I've run mri_nu_correct with no problem, set my control points, and then I run mri_normalize as follows: mri_normalize –monkey –f control.dat -g 1 nu.mgz T1.mgz but I end up with a 1mm resampled volume with a poor normalization. anything I can try differently here? Thanks Mark

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(no subject)
by Mark Pinsk 18 May '06

18 May '06

I just installed the latest release on my mac ox 10.4 Trying to set control points on a monkey volume, and something wierd keeps happening... I will middle-click to set the control point, and the green cross will appear, but when I move to another location to set another control point, the first point disappears. Am I missing something here? Thanks Mark

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inflated images
by anthony gallo 18 May '06

18 May '06

Hello all, Can some one edify me regarding how FreeSurfer is able to maintain the same basic brain geometry (hemisphere shape) when it creates an inflated file image. I would figure that some areas (because of deeper sulci) would blow up (produce more inflated surface) much differently than others thus not maintaining the basic shape. I was thinking that maybe the program just flattens it all period, but then I wouldn't really be able to explain how you can still view the respective cortical thickness data because that too must correspond with all the nooks and crannies............. I appreciate your help, Anthony

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which script creates the design matrix?
by Lars M. Rimol 17 May '06

17 May '06

Hi, I am using FS v3.02. I am using the tutorial to figure out how to do group analysis with the new FS version but there is one step that is confusing. The tutorial says that I should first create a FSGDF (and run make_average-subject), and then it says that running mris_glm will create the design matrix. But further down on the page it says that that mri_glmfit is replacing mris_glm. So, does that mean that I no longer have to use mris_glm to create the design matrix, and that mri_glmfit will create it? So I should run 1) make_average_subject, 2) mri_preproc and mri_surf2surf, and 3) mri_glmfit? Or does it mean that I should run 1) make_average_subject, 2) glms_mri , 3) mri_preproc and mri_surf2surf, and 4) mri_glmfit? Thank you! -- yours, LMR

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mri_convert from img to mnc
by Stefano Pellegrini 17 May '06

17 May '06

Hi Everybody, I have a problem with mri_convert when I try to convert an image (a mask) from .img (analyze) to .mnc (minc). using the simple command mri_convert image.img image.mnc what I get is that the result (image.mnc is different from the original image). and if I make the diff of the mri_info's of the two output, this is what I get < Volume information for mask.img < type: analyze4d --- > Volume information for mask.mnc > type: MINC 6,9c6,9 < fov: 256.000 < xstart: -128.0, xend: 128.0 < ystart: -128.0, yend: 128.0 < zstart: -32.0, zend: 32.0 --- > fov: 240.000 > xstart: -120.0, xend: 120.0 > ystart: -120.0, yend: 120.0 > zstart: -64.0, zend: 64.0 What I don't understand is also why the analyze format has a zspace of 64 (I have 64 for slices with 2mm thickness, shouldn't it be 128?). Can anybody please suggest me where I can look for the reason of this problem? thanks, -stefano

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retinotopy and FsFast
by Jane Aspell 17 May '06

17 May '06

Hi Thanks for all your previous help with freesurfer. I am trying to use FsFast to do retinotopy analysis and have been following the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I come undone at the stage of running the actual analysis, where the command should be: >sfa-sess -s avdk -a rtopy what does 'avdk' refer to? when i run it i get: ERROR: could not find session avdk when i try it with the arguments: >sfa-sess -analysis rtopy -sf sessid which is similar to the arguments needed for 'selxavg-sess' i get a similar error of not been able to find my (particular subject's) session. i believe i have set up the all the directory structures etc correctly for the sessions format as previous steps worked fine. any ideas what's going wrong? thanks Jane Aspell

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TIV
by Lee HL 16 May '06

16 May '06

Hi, Pardon my ignorance. How does the program determine the volume for TIV? Thanks! Kind regards, HweeLing

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freesurfer installation problems
by Chacko Cherian 16 May '06

16 May '06

Hello all, I am having some trouble in using the freesurfer version I had downloaded.The FREESURFER_HOME file is missing and so I cannot source or setenv anytime I want to use it.Do I need to tar and unzip again or is there any other way? Thanks in advance Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: Freesurfer Digest, Vol 27, Issue 13
by tao＠ucsd.edu 16 May '06

16 May '06

Hi: I have one question regarding the parcellate_subject and morph_subject After recon-all is complete, I setenv of CSURF_DIR to $FREESURFER_HOME, and then run parcellate_subject, got following error: reading atlas from /usr/pubsw/packages/freesurfer/average/lh.atlas2002_simple.gcs... GCSAread: couldn't allocate labels to -21852 Cannot allocate memory Does anyone can give me any hints? Thanks! Tao

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