Try converting the cluster directly to the volume using mri_surf2vol. Run it with --help to get more info. Use method 2.
On 10/6/2023 7:43 PM, Tyler J Ward wrote:
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Hi FreeSurfer developers and community,
I have a template space statistical surface map that I want to extract cortical thickness and volume from several thousand MRIs with freesurfer parcellations.
I converted the map to a cortical label using /mri_surfcluster./
/mri_surfcluster --in sig.mgh --thmin 4 --sign neg --hemi lh --subject fsaverage --olab ./my_label --cortex/unnamed.pngunnamed2.png
I then converted these template space labels to subject space labels using mri_label2label.
/mri_label2label --srcsubject fsaverage --srclabel .///my_label//.label --trgsubject bert --trglabel .///burts_label//.label --regmethod surface --hemi lh /Lastly I extracted thickness and created volumes from these labels.
/mri_segstats --slabel bert lh //burts_label//.label --i $SUBJECTS_DIR/bert/surf/lh.thickness --nonempty --excludeid 0 --sum ./bert_thickness_table //mri_label2vol --o ./berts_mask.mgh --label .///berts_label//.label --temp $SUBJECTS_DIR/bert/mri/nu.mgz --subject bert --hemi lh --fillthresh 0.3 --proj frac 0 1 .1 --identity/The results look okay but the voxels are not as clean as other freesurfer volumes and ROIs. For example, the cortical masks created from the label have small holes inside the mask. 2023-10-06T16:24:00,146947999-07:00.png
I decided to smooth this by 3mm^3 fwhm and threshold by the left hemisphere cortical parcellation in aparc+aseg.mgz file to get a better looking ROI that is contained by and filled into the freesurfer cortical parcellation: 2023-10-06T16:23:51,051653286-07:00.png 2023-10-06T16:37:34,665543751-07:00.png
From this, I have a couple questions:
1.) Can I expect my custom ROI thickness to be comparable to the thickness values outputted by Freesurfer for the Deikan-Killiany atlas? 2.) Is there anything I can do to verify the accuracy of the cortical thickness within this ROI? 3.) How can I extract volume from this ROI (should I just count voxels?) and will it be valid to do a cross-sectional analysis of volume from a region derived from a surface label, just as we look at any other region (tiv adjusted hippocampal volume for example)? Thanks in advance for your time and advice, Tyler
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