Hi Moe
Could you send us the data ( sig.nii .. directly to my email if it's
not big enough ). What steps do you take so that I can mimic the crash
here?
Thanks
Krish
On Nov 25, 2008, at 3:01 PM, Zeidan, Mohamed A. wrote:
Hi Everyone,
I'm trying to create a label but as I'm highlighting the area of
interest in
tkmedit, the window closes out and I get the following message:
ERROR: A segfault has occurred. This is not your fault,
: but is most likely an unrecoverable error and has
: made the program unstable.
:
: Please send the contents of the file .xdebug_tkmedit
: that should be in this directory to [EMAIL PROTECTED]
:
: Now exiting...
This has happened four times so far. Furthermore,
the .xdebug_tkmedit file is
nowhere to be found (I checked the directory from which I opened
tkmedit). My
command line was:
tkmedit fsaverage orig.mgz -aux brain.mgz -bc-main .33 7 -overlay
$SUBJECTS_DIR/Recall_vol_m_vs_f/Recall/CS+EevsCS-/tal.rfx.m_vs_f/
double/sig.nii
-fthresh 1.3 -fmax 3
Anyone else have this problem or have thoughts as to why it's
happening?
Thanks so much,
Moe
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Scott Gorlin
Sent: Tue 11/25/2008 2:57 PM
To: Doug Greve
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fs-fast smoothing
Thanks Doug, though I'm still a bit confused:
I'd like to see the smoothed results on the individuals, not just the
group - so it seems isxconcat-sess wouldn't be appropriate.
Are you suggesting running mri_surf2surf directly on the contrast
sig.nii files? Is smoothing a significance map the equivalent of
smoothing the data, then recreating the significance in the sphere
space? This didn't seem true to me, which is why I tried to recreate
the significance maps as below.
Thanks,
-S
Doug Greve wrote:
Hi Scott, you should skip steps 2-6 (that is the old stream).
Instead,
run isxconcat-sess after #1, then smooth on the surface either in
isxconcat-sess or with mri_surf2surf before running mri_glmfit.
doug
Scott Gorlin wrote:
Hi,
I'd like some clarification on the recommended procedure for
smoothing functional data across the cortical surface in FS-FAST.
I've managed to get it working using the following procedure:
1) analyze my data using selxavg3-sess in the native space, without
smoothing
2) resample the averages into the spherical space using func2sph-
sess
3) smooth these averages using sphsmooth-sess (which required
several
edits to work with .nii files)
4) recreate the contrasts in the smoothed sph space with
stxgrinder-sess
5) paint the analysis onto the surface with paint-sess (which also
required edits for .niis)
6) view with surf-sess (which I had to edit to read the subject
properly)
Surely there's a simpler way to accomplish this? I'm particularly
confused because the online documentation says that selxavg3
replaces
stxgrinder, but it seems stxgrinder has to be called to make
contrasts in non-native space (and uses different code to produce
the
contrasts than selxavg). Plus, the revision date for stxgrinder is
more recent!
Then, it seems odd that isxconcat will reproject the data for a
group
analysis if it's already sampled on the surface via func2sph.
Thanks,
Scott
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