Freesurfer May 2006

freesurfer@nmr.mgh.harvard.edu

50 participants
74 discussions

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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error on parcellate_subject
by tao＠ucsd.edu 16 May '06

16 May '06

1 0

nifti q-form
by Strien, N van 16 May '06

16 May '06

Hi Is the information concerning the q-form header field in Nifti-1 still accurate (in relation to freesurfer): please see: http://nifti.nimh.nih.gov/nifti-1/support/FreeSurferandNIfTI1/view?searchte… I am planning to update my data conversion code and include the q-form header field in a meaningful way. It would be nice if I could get it to work properly with both fsl and freesurfer. Kind regards, Niels van Strien

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aseg.stats question
by Sasha Wolosin 15 May '06

15 May '06

Dear all, I would like to know what some of the abbreviations of areas in the aseg.stats file stand for, in particular: Left-F3orb Left-lOg Left-aOg Left-mOg Left-pOg Left-Stellate Left-Porg Left-Aorg and "Right-Thalamus" vs "Right-Thalamus-Proper" Where may I find documentation on these names? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. 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 e-mail in error, please immediately notify the sender via telephone or return e-mail.

3 2

apar+aseg.mgz values
by Stefano Pellegrini 15 May '06

15 May '06

Hi all, I would like to use the aparc+aseg.mgz as a mask image. I am mainly interested in the cortex segmentation and if I am not wrong the [2000-2034] values corresponde to the 35 (34 + 1 unknown) values correspond to the 34 areas of the Desikan atlas for the right emisphere. Are these the values that are listed in the rh.aparc.stats file? Can I say that the value 2000 in the aparc+aseg.mgz correspond to the unclussified voxel of the cortex in the right emisphere? Thanks, -stefano

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Freesurfer May 2006