Freesurfer November 2004

freesurfer@nmr.mgh.harvard.edu

22 participants
53 discussions

Re: [Freesurfer] thresh_zstat1.img
by Joongnam Yang 19 Nov '04

19 Nov '04

Thanks, Kevin > Have you tried changing the threshold parameters, in the > View->Configure->Overlay dialog box? The manual is very coarse on that. I've tried various combinations of the three parameters there. If you know the rule of combination, Please let me know. Nam.

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Re: [Freesurfer] thresh_zstat1.img
by Joongnam Yang 19 Nov '04

19 Nov '04

> Did you visually check the registration of the functional to the structural? The registration using tkregister2 produces three files func2struc.mat func2struc.hdr func2struc.img, I've tried to load func2struc.hdr in TkSurfer, but it crashes. Again, I don't understand what you do when you "visual check" registration. I am new to fMRI, please be more specific. Thanks. Nam.

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thresh_zstat1.img
by Joongnam Yang 19 Nov '04

19 Nov '04

Hi all, I did, (1) use mri_vol2surf to convert thresh_zstat*.img into thresh_zstat1-lh.w (2) use the *.w file to overlay it onto flattened surface. The resulting overlaid image (TkSurfer) doesn't show as much activation as that of thresh_zstat*.img (in FEAT). I see only a few tiny dots, not large areas of activation. Coud someone tell me in which direction I should explore it further? Nam.

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mri_vol2surf *.mat not found
by Joongnam Yang 18 Nov '04

18 Nov '04

For the mri_vol2surf, mri_vol2surf --src thresh_zstat1.img --src_type analyze --srcreg func2struc.dat --hemi lh --projfrac 0.5 --out ./thresh_zstat1-lh.w --out_type paint I got the following complaint. INFO: could not find XXX/XXX/thresh_zstat1.mat file for direction cosine info. Could someone tell me how to create *.mat for each statistical functional image? In other words, for each thresh_zstat*.mat? Thanks. Nam.

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Error in Sphere
by Calabrese Massimiliano 18 Nov '04

18 Nov '04

Hi everybody, does anyone give me an advice, please. I don't want to loose this subject at the end. Can I skip this step or can I try to fix it? Thanks a lot Massimiliano INFO: SUBJECTS_DIR is /net/apollo/nib/calabrem/freesurfer/subjects INFO: starting per-hemisphere operations ----- Starting Hemisphere lh -------- --------------------------------------------- Sphere lh Thu Nov 18 13:53:15 EST 2004 /net/apollo/nib/calabrem/freesurfer/subjects/gallagher/scripts mris_sphere -w 0 /net/apollo/nib/calabrem/freesurfer/subjects/gallagher/surf/lh.inflated /net/apollo/nib/calabrem/freesurfer/subjects/gallagher/surf/lh.sphere using write iterations = 0 Segmentation fault (core dumped) ERROR: mris_sphere exited with non-zero status

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mri_vol2surf warning seems serious
by Joongnam Yang 18 Nov '04

18 Nov '04

Hi, I would appreciate any comment on the following warning when I ran mri_vol2surf. At the end there is a warning, which might be serious. I ran lh and rh separately, and no warning message was issued for lh and the following warning was only issued for rh. . . . Done Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 144115/149534 Done mapping volume to surface Number of source voxels hit = 4441 Warning: all vertex values are zero

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Re: [Freesurfer] load overlay in TkSurfer
by Joongnam Yang 18 Nov '04

18 Nov '04

Thanks, Kevin So, I guess there is nothing special about retinotopy data, but the functionl overlay that I got doesn't look right. (not much activation) Here is the two steps that I've done for the functional data before I overlay it onto anatomical data. Any comments are appreciated. 1. use "mricro" to turn functional data into Analyze format (*.img and *.hdr). 2. use "mri_convert" to turn the Analyze format data into *.bfloat to use them in functional overlay. I guess that something is missing. That is I did not include anything about the experimental design, e.g., 1 2 1 2 1 2, or 1 2 3 4 1 2 3 4, etc. Where do I include such information in the analysis? I know where I put the design info in FSL, but not here in Freesurfer? Nam.

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Freesurfer RAS 2 TAL
by Darren Weber 17 Nov '04

17 Nov '04

Please find attached revised matlab functions for Freesurfer RAS to Talairach conversion. I found a problem with the input matrix orientation in the mni2tal function; it is now restricted to 3xN inputs (although there is still a potential problem for 3x3 input matrices if the XYZ values are row vectors rather column vectors). Now the freesurfer_surf2tal.m function does a little bit more transpose gymnastics.

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Error
by Calabrese Massimiliano 17 Nov '04

17 Nov '04

Hi everybody Does anyone know if there is something that I can do to fix the follow error occurred in stage1 of recon-all? Thnaks a lot Massimiliano Calabrese Imaging Group Neuroimmunology Branch NINDS, NIH. mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... find_cutting_plane:seed point not in structure! Searching neighborhood... ERROR: mri_fill exited with non-zero status ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on apollo.ninds.nih.gov:/arena3 1372150372 1218678884 83770268 94% /net/apollo ------------------------------------------ recon-all exited with errors at Mon Nov 15 14:25:03 EST 2004

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Freesurfer on Solaris
by Catherine Schevon 17 Nov '04

17 Nov '04

It says on the website that there is a version that will run on Solaris but it's untested...is there any experience with it or any more recent testing? Cathy

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Freesurfer November 2004