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-right and negated half of your subjects). Do you want the original thickness values?
On 10/8/19 11:14 AM, Jose Graterol wrote: > > 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 --xhemi --paired-diff > --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out > leftlesionsubjects.lh.lh-rh.thickness.sm00.mgh --s sub-xxx > > For the right-affected: > mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff > --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out > rightlesionsubjects.lh.lh-rh.thickness.sm00.mgh --s sub-xxx > > Then I changed the sign of the right-affected subjects: > fscalc rightlesionsubjects.lh.lh-rh.thickness.sm00.mgh mul -1 -o > rightlesionsubjects.lh.rh-lh.thickness.sm00.mgh > > Then I concatenated them: > > mri_concat leftlesionsubjects.lh.lh-rh.thickness.sm00.mgh > rightlesionsubjects.lh.rh-lh.thickness.sm00.mgh --o > allsubjects.lh.lesion-healthy.thickness.sm00.mgh > > Then I smoothed the file: > mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 10 > --i allsubjects.lh.lesion-healthy.thickness.sm00.mgh --o > allsubjects.lh.lesion-healthy.thickness.sm10.mgh > > Then glmfit: > mri_glmfit --y allsubjects.lh.lesion-healthy.thickness.sm10.mgh > --glmdir glmdir.allsubjects.lh.lesion-healthy.thickness.sm10 --osgm > --surf fsaverage_sym lh > > and finally the correction for multiple comparisons: > > mri_glmfit-sim --y allsubjects.lh.lesion-healthy.thickness.sm10.mgh > --glmdir glmdir.allsubjects.lh.lesion-healthy.thickness.sm10 > --cwpvalthresh 0.05 --cache 4 neg > > > Hopefully this helps. > > > > > On Tue, Oct 8, 2019 at 4:45 PM Greve, Douglas N.,Ph.D. > <[email protected] <mailto:[email protected]>> wrote: > > 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.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. >> <[email protected] <mailto:[email protected]>> 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 >> <http://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 >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> <mailto:[email protected]> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> <mailto:[email protected]> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> <mailto:[email protected]> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> <mailto:[email protected]> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] <mailto:[email protected]> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] <mailto:[email protected]> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
