Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution It worked as intended. Thank you very much. On Tue, Oct 8, 2019 at 6:43 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > In that case, run mris_preproc in the same way but don't include the > paired-diff. Concatenate the two groups togeth

Re: [Freesurfer] Label created in the symmetric space

In that case, run mris_preproc in the same way but don't include the paired-diff. Concatenate the two groups together to give you one file. Smooth as you did before. Now with that one file run mri_segstats --seg csdbase.sig.ocn.mgh --i youronefile.mgh --avgwf subject.hemi.cluster.dat --excludeid

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution Aha, yes. That is what I want. The original thickness values. Greve, Douglas N.,Ph.D. schrieb am Di., 8. Okt. 2019, 17:36: > That all looks fine, I'm just not sure what problem you want me to > solve. You said that the values in the y.ocn.dat file we

Re: [Freesurfer] Label created in the symmetric space

That all looks fine, I'm just not sure what problem you want me to solve. You said that the values in the y.ocn.dat file were all negative, it has to be this way because you specified only negative values when you ran glmfit-sim (and negative values are possible because  you have computed left-

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution I will try to go back a bit, just to be sure I did not make a mistake. I registered both hemispheres of every subject (affected and non-affected) with xhemi. Then for the left-affected subjects I ran: mris_preproc --target fsaverage_sym --hemi lh --xhe

Re: [Freesurfer] Label created in the symmetric space

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: External Email - Use Caution Ok, I uploaded it with the name "glmdir.jg.allsubjects.tar

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution 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 yo

Re: [Freesurfer] Label created in the symmetric space

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 N

Re: [Freesurfer] Label created in the symmetric space

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. < dgr...@mgh.harvard.edu> wrote: > Let's backup a moment. Can you send the y.ocn.dat file that has > problematic values?

Re: [Freesurfer] Label created in the symmetric space

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

[Freesurfer] Label created in the symmetric space

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