Hi,
Thank you for your response! I solve this problem of mris_preproc.
The next step is to do mri_glmfit.
And, when I type the following command:
mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd
dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir
You probably have an older version that does not recoginze --cortex. Try
--label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label instead
Feng-Xian wrote:
Hi,
Thank you for your response! I solve this problem of mris_preproc.
The next step is to do mri_glmfit.
And, when I type the
Hi,
I copied the default average subject from $FREESURFER_HOME/subjects dir
to my analysis dir.
Then, I make a FSGD file and some contrast matrices and put them into my
analysis dir.
After that, I start to run group analysis.
But, when I type the following commands:
mris_preproc
Is there a space between -- and hemi?
caching is just a way to speed some analyses by pre-smoothing and
sampling to the standard space.
doug
Feng-Xian wrote:
Hi,
I copied the default average subject from $FREESURFER_HOME/subjects dir
to my analysis dir.
Then, I make a FSGD file and
Hi,
I have a problem with make_average_subject.
After running all commands (including ln -s
$FREESURFER_HOME/subjects/fsaverage
and recon-all -s subjid -qcache for all my subjects) about running QDEC, I
found that QDEC could not analysis my group.
Because the group have 1 factor and
Feng-Xian,
It appears that you do not have permission on your system to change the
limits. So you will have to edit the scripts make_average_volume,
make_average_surface and make_average_subject to comment out the 'limit'
line, so that it looks like this:
#limit descriptors unlimited
Nick
Feng-xian,
I should also mention that i dont think creating your own average
subject will solve the problem you describe, where you need to work with
three levels in your group. for that, you wont be able to use qdec, but
will need to run things manually. these pages give examples:
You don't *have to* to run make_average_subject to do your analysis,
only if you want to view the results on a map with the curvature
patterns averaged over your subjects. As for the limit error, how old is
your version of freesurfer? That line was removed about 1.5 years ago...
doug
