Hi Doug,
Thanks for the reply. Sure I will try this command. But as it is now, how will
mri_segstats know the order in the fsgd file? Also, this command needs to run
for each subject, right? Then, which input file should I use for the --i flag?
mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh--id 1
--avgwf y.label.dat
Thanks a lot!
Hamdi
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, November 03, 2015 2:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a ROI
On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote:
> Sorry, the figures I inserted in the text did not appear in the email.
> I attach them now.
>
> Best,
> Hamdi
>
> ------------------------------------------------------------------------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eryilmaz, H.
> Hamdi [hamdi.eryil...@mgh.harvard.edu]
> *Sent:* Friday, October 30, 2015 1:32 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] cortical thickness - comparing two groups
> within a ROI
>
> Dear FS experts,
>
> I have a question about extracting average cortical thickness from a
> manually created ROI. I am comparing 2 groups, namely PostFort and
> PreFort and my fsgd file appears as the following:
>
> GroupDescriptorFile 1
> Title PostPreFortification
> Class PostFort
> Class PreFort
>
> Input Subject1 PostFort
> Input Subject2 PostFort
> .
> .
> .
>
> The contrast that I use to compare these groups is [1 -1]. When I
> display the significance map for this contrast I get the following
> image on the left hemisphere:
>
>
>
>
> My first question is, those blue clusters represent regions, where
> thickness is greater in the PreFort group, don't they?
Correct
> Assuming this is correct, I created a label for this region (which
> contains about 3000 vertices) and extracted the thickness value from
> this region for each subject using the following commands. These
> commands are part of scripts in which $subject and $label are defined.
>
>
>
> _to make a label for each subject (the original label was created on
> fsaverage):_
> *mri_label2label* --srclabel $SUBJECTS_DIR/labels/${label}.label
> --srcsubject fsaverage --trglabel
> $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
> --regmethod surface --hemi lh
>
> _to create a stats file of this ROI containing several anatomical
> measures:_
> *mris_anatomical_stats* -f
> $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l
> $SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh
>
> _to compile thickness values from all subjects into one table: _
> *aparcstats2table* --hemi lh --subjectsfile
> $SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc
> NP_PostMINUSPre_IPS.label --meas thickness --tablefile
> $SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt
>
> This table displays the average thickness value of my ROI for each
> subject. Based on this table I calculated the mean thickness for each
> group, which is as the following:
>
> PostFort: 3.043
> PreFort: 2.842
>
> My question is: If this cluster appears blue in the Post>Pre map,
> shouldn't the thickness have been greater in the PreFort group? Or am
> I missing a step?
Not sure. The commands look right. Can you try something else?
mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh
--id 1 --avgwf y.label.dat
This should create a single column of numbers in y.label.dat that
correspond to the mean thickness in the label of each subject as
ordered in your fsgd file. See if you get similar numbers to your method
doug
>
> Many thanks in advance!
>
> Best,
> Hamdi
>
>
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>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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