Ok I got through the svreg pipeline without error. I have also run my test subject through the thicknessPVC.sh pipeline.
I tried to run through the generate_stats_xls_manual file and it works, but I’m not really sure what I should be feeding it.
subbasename=’/Storage/session_1/anat_1/mprage’;
vol_label_file=’/Storage/1_LH_V1.label.nii’; % binary volume file registered to .bfc
ROI_IDs= [1];
surf_ext=’svreg.dfs’; %[subbasename,’.left.mid.cortex.’,surf_ext]
output_ext=’testout’; %[subbasename,’.roiwise.’,output_ext,’.stats.txt’]
generate_stats_xls_manual(subbasename,vol_label_file,ROI_IDs,surf_ext,output_ext);
I’m not really sure what I should be putting for ROI_IDS. I’ve tried several different combinations of numbers. I thought 1 would be correct as the mask is binary. For ROI_IDs = 1 I get:
ROI_ID Mean_Thickness(mm) GM_Volume(mm^3) CSF_Volume(mm^3) WM_Volume(mm^3) Total_Volume(GM+WM)(mm^3) Cortical_Area_mid(mm^2) Cortical_Area_inner(mm^2) Cortical_Area_pial(mm^2)
1 NaN 219.089869 7.097567 9.160284 228.250153 0.000000 0.000000 0.000000
So it has a GM volume, but no thickness value?
Should I be setting my binary mask not equal to 1? I had a look around the xml file with ROI Ids but I don’t really know what I should be setting it to.
Thanks for the help,
Wes
