The input has both positives and negatives, so is is not surprising that the y.ocn.dat also has positive and negative. Not sure what is going wrong here ...

On 10/7/2019 5:48 PM, Jose Graterol wrote:

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Ok, I uploaded it with the name "glmdir.jg.allsubjects.tar.gz". I had to log in as anonymous and not with my email, otherwise it would throw an error (503 Login with USER first. Login failed.). The mgh file is inside the gz file too. Thanks again for your time and help.

On Mon, Oct 7, 2019 at 7:06 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

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:

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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. <DGREVE@mgh.harvard.edu> 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:

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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 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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