Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30061 discussions

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.

4 3

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.

1 0

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

3 2

Re: [Freesurfer] load overlay in TkSurfer
by Joongnam Yang 17 Nov '04

17 Nov '04

Hi Bruce, I found the error messages in SUBJECTID/scripts/csurf.log The error was that there is no talairach.xfm in /mri/transorms directory. I though that using tkregister2 for co-registration would be enough. Would you let me know how to generate talairach.xfm? Nam.

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Re: [Freesurfer] load overlay in TkSurfer
by Joongnam Yang 17 Nov '04

17 Nov '04

The following is in .xdebug_tksurfer. Segfault xDebug stack (length: 1) 00: 00: Segfault Does it ring a bell, Bruce? Nam.

2 1

load overlay in TkSurfer
by Joongnam Yang 17 Nov '04

17 Nov '04

The "Load Overlay" window in TkSurfer is not working for me. The window has two fileds to fill in, "Load Overlay" and "User Registration". What's strange is that whatever I type in those two fields, TkSurfer doesn't complain. For example, if I type in "hello" and "abc.dat" literally for those two fields, TkSurfer doesn't complain. No error message. (This is why my functinoal overlay is not working, I guess.) Could someone give me a clue? Nam.

2 1

functional data not showing up
by Joongnam Yang 16 Nov '04

16 Nov '04

Hi All, I hope someone can locate the problem for me. Here is what I did. 1. clicked for "flattened" surface on csurf, which opens tksurfer (I see a flattened surface window) 2. clicked "load overlay" on tksurfer, which asks two inputs. For "Load overlay", I typed in XXX for XXX_000.bfloat Use registration, I used register.dat, which seems OK. 3. Then click OK 4. No functional overlay is made. I mean no functional data show up on the flattened surface. I looked at the XXX_000.bfloat, which is around 3 Megabytes. Question: 1. Is there a way that I can verify that *.bfloat is valid? (I used mri_convert XXX.img *.bfloat to create those files) 2. What is a way of creating *.w files from functional data? Any lead would be welcome. Thanks Nam.

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csurf version?
by Joongnam Yang 16 Nov '04

16 Nov '04

Hi all, SessionTools menu in my csurf has only one submenu "View Functional Data". In some web sources that I read, there are many other submenus under it, such as "Setup Align/Funct Scans", "Calculate 3D Fourier Stats", etc. Is this version of csurf OLD? This freesurfer was installed last August. Thanks. Nam.

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