Freesurfer September 2006

freesurfer@nmr.mgh.harvard.edu

37 participants
45 discussions

tkmedit problem, crash on loading aseg
by Johannes Klein 05 Sep '06

05 Sep '06

Hi everyone, I have a rather obscure problem. There are some subjects whose aseg subcortical parcellations will not load up in tkmedit, causing it to crash. This happens when using a Mac with X11 to view them, not on my Linux machine. Interestingly though, this does not happen for all subjects, some do get displayed correctly on the Mac, too. Here's what I do: tkmedit mysubj T1.mgz Then, use tkmedit's File-Load Segmentation There, select aseg.mgz and tkmeditColorsCMA tkmedit then crashes, producing the following log: tkmedit started: Tue Sep 5 17:26:20 2006 tkmedit PAT_XXXX T1.mgz lh.white -aux-surface rh.white $Id: tkmedit.c,v 1.274.2.1 2006/03/06 19:52:48 kteich Exp $ $Name: stable3 $ Set user home dir to /Volumes/JalapenoSAN/Scratch/XXXXXX/fs Set subject home dir to /Scratch/XXXXXX/fs/PAT_XXXX Using interface file /usr/local/freesurfer/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Error 1 in CLUT_GetLabel: Invalid pointer to object. I wonder if this is a known problem for Macs? Thanks, Johannes

2 1

newbie, white matter volumes
by Romke Rouw 05 Sep '06

05 Sep '06

Hi all, I would like to compare two groups of human subjects on volumetric measures of cerebral white matter. Does anyone know how to get more detailed information on white matter volumes ? (per brain region, or per white matter structure). Thanks! Romke

2 1

transform back to origin coordination ?
by tulu 05 Sep '06

05 Sep '06

Dear Freesurfer experts, I use freesurfer and when I finish recon-all autorecon1, I would like to transform Brainmask.mgz image back to origin coordination. How to do it ? Thank replay Kl chen

4 7

Mri convert
by Lee HL 04 Sep '06

04 Sep '06

Hi Bruce and all, I wish to convert the MGZ format image into ANALYZE format image. I used the command line to convert the MGZ format image: "mri_convert -i brainmask.mgz -o brainmask.img --out_type spm". When I display the image using SPM, the coordinate (0, 0, 0) appears at the posterior commissure. However, when I display the mgz format image using tkmedit, the coordinate (0, 0, 0) appears at the anterior commissure. Was I using the correct command line to convert the image? Thanks! Cheers, HweeLing

2 3

func2tal-sess question
by Cameron Ellis 01 Sep '06

01 Sep '06

Hi, Quick simple question I hope: does running func2tal-sess with two groups at once with a sessid that includes them both and running func2tal with each group separately result in any difference? And if you do need to resample your groups separately do you need to do this under 2 different analyses? Thanks, Cameron

2 1

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Freesurfer September 2006