What was the exact call? Did you try setting SUBJECTS_DIR to the
directory at hand and running the command without arguments?
Cheers,
/Eugenio
On 06/25/2013 09:06 AM, Yang, Zoe wrote:
Dear Eugenio,
Thanks for the reply. Yes, we created a test directory containing two
subjects that have been reconed with the --hippo-subfields flag. Both
of them have 20 output files.
Cheers,
Zoe
*From:*Juan Eugenio Iglesias [mailto:igles...@nmr.mgh.harvard.edu]
*Sent:* Monday, June 24, 2013 5:03 PM
*To:* Yang, Zoe
*Cc:* 'Freesurfer@nmr.mgh.harvard.edu'
*Subject:* Re: [Freesurfer] Question about running
kvlQuantifyHippocampalSubfieldSegmentations.sh
Dear Zoe,
have you checked whether all directories within your subject directory
correspond to subjects which have been reconed with the
-hippo-subfields flag?
Cheers,
/Eugenio
On 06/24/2013 04:00 PM, Yang, Zoe wrote:
Hi all,
I am getting error messages while running
kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the
error mentioned in an earlier
email
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html).
We did use the -hippo-subfields flag for all of our subjects
first, and the output was 20 left and right subfield mgz files (it
completed without any errors). The subjects had already undergone
the standard volumetric FreeSurfer pipeline and therefore we ran
the command: recon-all -s subjectID -hippo-subfields.
The error message for kvlQuantifyHippocampalSubfieldSegmentation
that I'm getting is:
resultsDirectory ***/HIPPOCAMPAL_TEST
cd ***/HIPPOCAMPAL_TEST
resultsDirectory ***/HIPPOCAMPAL_TEST
startIndex: 1
endIndex: 2
cd subjectID_recon/
Quantifying subject ID_recon left
Doing left side
cd left
cd segmentationWithoutPartialVolumingLog
kvlQuantifyPosteriorProbabilityImages
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt
posterior_Left-Hippocampus.mgz
posterior_left_presubiculum.mgz posterior_left_CA1.mgz
posterior_left_CA2-3.mgz posterior_left_fimbria.mgz
posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz
posterior_left_hippocampal_fissure.mgz >
volumeStats_left.txt
terminate called after throwing an instance of 'itk::ExceptionObject'
what(): itkMGHImageIO.cxx:216:
itk::ERROR: MGHImageIO(0x46b690): Can't find/open file:
posterior_Left-Hippocampus.mgz
kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 50779
Abort trap kvlQuantifyPosteriorProbabilityImages
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt
posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz
posterior_left_CA1.mgz posterior_left_CA2-3.mgz
posterior_left_fimbria.mgz posterior_left_subiculum.mgz
posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz >
volumeStats_left.txt
failed to do kvlQuantifyPosteriorProbabilityImages
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt
posterior_Left-Hippocampus.mgz
posterior_left_presubiculum.mgz posterior_left_CA1.mgz
posterior_left_CA2-3.mgz posterior_left_fimbria.mgz
posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz
posterior_left_hippocampal_fissure.mgz >
volumeStats_left.txt
Is there anything else that we are missing and should run?
Thanks!
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
-------------------------------------------------------------------------------------
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu <mailto:igles...@nmr.mgh.harvard.edu>
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
-------------------------------------------------------------------------------------
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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
