which ROIs are different?
On 2/22/19 5:39 PM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to read out GM and WM values from parcels (ROIs) but get a different amount of ROIs for GM and WM.
I use the following commands (embedded in a loop),
for GM
mris_anatomical_stats -mgz \
-cortex label/lh.cortex.label \
-f stats/lh.250.aparc.pial.stats \
-b -a 250.aparc \
-c label/colortable.ctab \
$subject lh pial
and for WM
mri_segstats \
--seg mri/vol250.lh.nii.gz \
--ctab ../fsaverage/colortable.ctab \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--empty \
--sum stats/${subj}_fa_lh.stats
where “../fsaverage/colortable.ctab” has 299 labels and “mri/vol250.lh.nii.gz” is the segmented image that was extended 2mm into the WM and registered to the DTI image.
Is it possible that these two commands read out different amounts of ROIs?
And is there a reason why the –c flag in mris_anatomical_stats doesn’t save the colortable for each subject?
I would be very grateful for some help!
Thanks,
Stephanie
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer