ok, I still don't know what is going on. Can you upload the glmdir and the
input to mri_glmfit (ie, the argument of the --y flag). You can upload it using
these instructions:
From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use your email address
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
put subject.tar.gz
Send an email that the file has been and the name of the file.
On 10/7/2019 11:53 AM, Jose Graterol wrote:
External Email - Use Caution
Hi Douglas,
thanks for you answer. I have attached the file to the email.
On Mon, Oct 7, 2019 at 5:24 PM Greve, Douglas N.,Ph.D.
<[email protected]<mailto:[email protected]>> wrote:
Let's backup a moment. Can you send the y.ocn.dat file that has problematic
values?
On 10/4/2019 4:58 AM, Jose Graterol wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I would appreciate your help. I will explain first what I have done and where
my problem is.
I want to measure the cortical thickness in stroke patients. Therefore I
followed Douglas' instructions provided in this link
<https://www.mail-archive.com/[email protected]&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+surface+data%22&o=newest&f=1>
to join both affected hemispheres (left or right, depending on the patient)
and to analyze them with xhemi.
After mri_glmfit and mri_glmfit-sim (--cwpvalthresh 0,05 --cache 4 abs/neg)
have run I obtained 2 significant clusters. One in the precentral area, which I
am interested in. When I check the *abs/neg.y.ocn.dat file the values are all
-0.XXXX. If I understood it correctly, those should be cortical thickness
values in mm, making those values implausible. For that reason I made a label
of that cluster using the autofill option from tksurfer. The idea was to obtain
the mean cortical thickness using mris_anatomical_stats after mapping the label
to the subjects.
Now my questions, what would be the best method to map the label created from
the fsaverage_sym space to the subject space? Or just simply, is this the right
way to do this? or should I check why I am obtaining those values in the
*y.ocn.dat file?
Thanks in advance.
Kind Regards
José Graterol
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