Try making it executable with
chmod a+x $FREESURFER/bin/mri_glmfit-sim
On 1/27/2021 10:41 AM, Na, Xiaoxu wrote:
External Email - Use Caution
Hi Dr. Greve,
Thanks for your reply. However, it shows me the command line error
when I try to run it after having the file replaced. Please kindly see
below. Is there any other settings I should run before that? Even the
- -help can’t be passed. Thanks a lot!
$ mri_glmfit-sim --glmdir sAnalysis/lh.area.g2v2CSHQ.10.glmdir
--cache 4 neg --cwp 0.05 --2spaces --spatial-sum
: Command not found.
: Command not found.
: Command not found.
: Command not found.
set: Variable name must begin with a letter.
$mri_glmfit-sim --help
: Command not found.
: Command not found.
: Command not found.
: Command not found.
set: Variable name must begin with a letter.
Regards,
Xiaoxu
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve
*Sent:* Tuesday, January 26, 2021 6:08 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Unit of the Numbers in
cache.th40.neg.y.ocn.dat
By default, mri_glmfit-sim will compute a spatial average inside of a
cluster to create the OCN table, so the values do not agree with the
table below. In he case of area or volume inputs, it needs to compute
the sum instead of the average. I have just modified this program to
do this. I've attached this new version. Copy it to $FREESURFER/bin
To run, add --spatial-sum to the command line
On 1/26/2021 12:56 PM, Na, Xiaoxu wrote:
* External Email - Use Caution *
To make it clear, I would like to extract the area of each subject
in the cluster. May I know if this is the correct way? If not,
it’s appreciated if you would point it out. Thanks!
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Na,
Xiaoxu
*Sent:* Tuesday, January 26, 2021 11:44 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Unit of the Numbers in
cache.th40.neg.y.ocn.dat
* External Email - Use Caution *
Dear Freesurfer Experts,
As I’d like to extract the average value of each subject in the
cluster after running group analysis, may I know the unit of these
numbers?
Since the one I’m running is surface area, and the cluster is
444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is
in the range of [0.55 1.05], may I know if this is correct and if
so, how the unit is for those? Thanks a lot!
ClusterNo
Max
VtxMax
Size(mm^2)
MNIX
MNIY
MNIZ
CWP
CWPLow
CWPHi
NVtxs
WghtVtx
1
-4.8321
40067
444.11
-58.1
-16.6
-23.9
0.0002
0
0.0004
670
-2784.11
Regards,
Xiaoxu
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