External Email - Use Caution
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. <DGREVE@mgh.harvard.edu
> <mailto:DGREVE@mgh.harvard.edu>> 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.
> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
> 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.
> >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
> <mailto:DGREVE@mgh.harvard.edu <mailto: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
> <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.
> >>> <DGREVE@mgh.harvard.edu
> <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
> <mailto: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:
> >>>>
> >>>> 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/search?l=freesurfer@nmr.mgh.harvard.edu&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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