OK, then the question is why kvlQuantifyPosteriorProbabilityImages is
producing an empty file....
I think the problem is that
kvlQuantifyHippocampalSubfieldSegmentations.sh behaves in a different
way depending on the number arguments, etc. I would suggest that you go
back to the original version of the script, and use it the way it's
described in
http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation,
that is, setting the environment variable SUBJECTS_DIR and calling the
script without arguments.
Kind regards,
/Eugenio
On 07/17/2013 11:46 AM, Jasmeet Hayes wrote:
Hi Eugenio,
We are using version 5.1. I attached our script. We added to line 60,
setting the subject directory. We also changed the statFileName (see
line 291 on the attached script). I should also note that the
volumeStats_left and right text files within each subject's mri folder
is empty. Thanks for your help.
On Wed, Jul 17, 2013 at 11:16 AM, Juan Eugenio Iglesias
<igles...@nmr.mgh.harvard.edu <mailto:igles...@nmr.mgh.harvard.edu>>
wrote:
Hi Jasmeet,
what modification did you exactly make? Whih version of FreeSurfer
is this?
Cheers,
/Eugenio
On 07/17/2013 10:22 AM, Jasmeet Hayes wrote:
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 ..
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igles...@nmr.mgh.harvard.edu <mailto:igles...@nmr.mgh.harvard.edu>
Athinoula A. Martinos Center for Biomedical Imaging
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-------------------------------------------------------------------------------------
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.
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