Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

ab blocked design analysis
by Tom Bayer 22 May '06

22 May '06

to analyze an ab blocked experiment, is it appropriate to run selfreqavg? I am analyzing data from a somatopy experiment, so the stimulus is not expanding or rotating but it is phasic. I analyzed it as an eccentric stimulus with positive value. Is this an appropriate choice? -tom

6 10

FreeSurfe NIFTI
by Doug Greve 19 May '06

19 May '06

I just wanted to let you know that I've modified the way FreeSurfer stores NIFTI1 files (these are the single .nii and .nii.gz files). The change is somewhat esoteric: the vox_offset is now 352 instead of 348. 352 is the NIFTI spec, so we were technically out of compliance before, though AFNI, FSL, and SPM did not seem to have a problem with it. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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retinotopy starting with blanks
by Dahlia Sharon 18 May '06

18 May '06

Hi, I'm analyzing a retinotopy data-set in which each scan started with 2 TRs of a blank screen, and then proceeded to 8 cycles as usual. Is there any possibility to tell a retinotopy analysis to ignore these 2 TRs? Thanks! Dahlia. PS - I can't answer as to why these 2 blank TRs were put there.

2 1

FreeSurfer algorithms
by anthony gallo 18 May '06

18 May '06

Surfers, Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data.......maybe there are some papers that talk about this?? Anthony

4 3

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…

3 2

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

3 2

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

2 1

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

4 3

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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