Dear Freesurfer experts,
I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left & right stats) but the only information in the text files is the subject ID number.
However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script.
Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files).
We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet
cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz > volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd ..