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. < [email protected]> wrote: > 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 0 > > The output file subject.hemi.cluster.dat will have a row for each > subject and hemisphere (the order will be subject.lh, subject.rh, > nextsubject.lh, nextsubject.rh) and a column for each cluster. The > values will be the thickness. > > > > On 10/8/19 12:22 PM, Jose Graterol wrote: > > > > External Email - Use Caution > > > > Aha, yes. That is what I want. The original thickness values. > > > > Greve, Douglas N.,Ph.D. <[email protected] > > <mailto:[email protected]>> 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 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]> > > <mailto:[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]> > > <mailto:[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> > > >> <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]> <mailto:[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]> > > <mailto:[email protected] > > <mailto:[email protected]>> > > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> [email protected] > > <mailto:[email protected]> > > >>> <mailto:[email protected] > > <mailto:[email protected]>> > > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>> > > >>> > > >>> _______________________________________________ > > >>> Freesurfer mailing list > > >>> [email protected] > > <mailto:[email protected]> > > <mailto:[email protected] > > <mailto:[email protected]>> > > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> [email protected] > > <mailto:[email protected]> > > >> <mailto:[email protected] > > <mailto:[email protected]>> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> [email protected] > > <mailto:[email protected]> > > <mailto:[email protected] > > <mailto:[email protected]>> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > [email protected] > > <mailto:[email protected]> > > <mailto:[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
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