Best,
Hamdi
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Eryilmaz, H. Hamdi [hamdi.eryilmaz@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
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? 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?
Many thanks in advance!
Best,
Hamdi
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? 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?
Many thanks in advance!
Best,
Hamdi