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 ..