Hi Freesurfers,
Is there a minimum number of subjects that should be used in
isxconcat groups and subsequent glmfit analysis? I recently generated
activation maps from a group with only 2 subjects, but the resulting
image (too large to attach) is very strage. The activation patterns are
"whis
Hi Adam, it is necessary that the DOF be greater than 0, which means
that the number of subjects must be greater than the number of
regressors. For, OSGM, the number of regressors is 1, so you can run it
with 2. But being able to run it does not mean that you will get good
results out of it. T
Doug,
Thanks for your reply.
I recalculated the beta value and got the same results as the Matlab does,
but be different from the mri_glmfit's. I can not figure out where the
problem is.
Details following:
I use the command
mri_glmfit --table lh.volume.txt --fsgd volume.gender.fsgd
I think the problem may be that your data are "badly scaled" meaning
that one column is much greater than another column. Try dividing the
ICV by 1e6 and see if you get more similar results.
doug
soft.join Huang wrote:
> Doug,
>
> Thanks for your reply.
> I recalculated the beta value and got
Using QDec, I've created an ROI label (lh.G_cuneus.label) and a .stats
file (lh.G_cuneus.stats) that corresponds to this ROI for each participant
in my group. Is there a quick way to compile cortical thickness data for
this ROI from all participants? The manual suggests using aparcstats2table
but I
Hello,
I'm trying to get this ROI drawn on a brain surface.
http://www.sal.mvm.ed.ac.uk/images/MT_roi.png
To do this, I first ran a script (of the form)[1]:
mri_cor2label --i ~/roi.nii --l ~/roi.label --id 1
Then opened the new roi.label file in tksurfer:
:~$ tksurfer s01 lh orig
The ROI see
Dear experts,
I have been processing my data on FreeSurfer v4.5.0, 32 bits (SUSE).
Now we have changed our system to 64bits (UBUNTU) and we are planning to
install FreeSurfer v5.0.0, 64 bits.
Do I have to process my data again or can I carry on processing my new data
on v5.0.0, 64 bit
Hello,
I need assistance customizing the recommended FLASH acquisition protocol for
FreeSurfer for the scanner I'll be using. The document containing the
recommended morphometry protocols for use with FreeSurfer provided online
mentions that custom multiecho sequences for Siemens scanners are avail
Hi Daniel,
you should reprocess your data, which shouldn't involve much additional
manual intervention as the edits are propagated.
cheers
Bruce
On Mon, 2 May 2011, Daniel
Ferreira Padilla wrote:
> Dear experts,
>
>
>
> I have been processing my data on FreeSurfer v4.5.0, 32 bits (SUSE).
>
>
Hi Jennifer
Andre van der Kouwe (ccd) is the one who wrote the multi-echo FLASH (MEF)
sequence, although we recommend multi-echo mprage as a morphometry
sequence.
cheers
Bruce
On Mon, 2 May 2011,
Jennifer Addicks wrote:
> Hello,
> I need assistance customizing the recommended FLASH acquisiti
Hello,
I'm running a cortical thickness analysis using Qdec. When I do Find
Clusters and Go to Max, I obtain 9 clusters (min threshold 3, max threshold
5):
Generating cluster stats using min threshold of 3...
Found 9 clusters
Contrast: '
Don't use --thmax.
doug
Fernanda Palhano wrote:
> Hello,
>
> I'm running a cortical thickness analysis using Qdec. When I do Find
> Clusters and Go to Max, I obtain 9 clusters (min threshold 3, max
> threshold 5):
>
> Generating cluste
Hi Krista
If the directory tree is something like
$SUBJECTS_DIR
|
| P01
| |-- stats
| || lh.G_cuneus.stats
| P02
| |-- stats
| || lh.G_cuneus.stats
where P0? are the participants subjects directories.. U
Hi,
I am trying to use an annotation file that was created from a parcellation
scheme developed in my lab with mri_surfcluster. However, it's unclear to
me how I can set the corresponding color table for this annotation file
either locally or globally. mri_surfcluster doesn't seem to have a --cta
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