Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

2013-06-25 Thread Juan Eugenio Iglesias 

Hi again,
Zoe, Marcos is right about the fact that the script fails if the 
posterior*.mgz are not found in any


1- Set your $SUBJECTS_DIR variable as another another path and move 
your subjects directories (and only these directories to this place) 
and run the same script you tried 
(kvlQuantifyHippocampalSubfieldSegmentations.sh)


Rather than moving the subjects, I'd create symbolic links, but this is 
certainly an option.


Another option is to modify 
kvlQuantifyHippocampalSubfieldSegmentations.sh, replacing the two 
instances of:


 doIt "kvlQuantifyPosteriorProbabilityImages $compre."

by

cmd="kvlQuantifyPosteriorProbabilityImages $compre."
eval "$cmd"

Cheers,

/Eugenio





Em Seg, 2013-06-24 às 16:00 -0400, Yang, Zoe escreveu:

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!




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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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Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

2013-06-25 Thread Marcos Martins da Silva 
Dear, Zoe
Usually after Freesurfer fresh install you will get a SUBJECTS_DIR with
several directories, including Bert. The script you used will scan all
directories under SUBJECTS_DIR and if it finds any directory without the
posterior*.mgz files it will fail. You can check if this is the problem
running one side from one patient like this:

cd $SUBJECTS_DIR/yoursubject/mri 

kvlQuantifyPosteriorProbabilityImages 
$FREESURFER_HOME/data/GEMS/compressionLookupTable.txt posterior_right_* 
posterior_Right-Hippocampus.mgz  


This will show the volume in voxels for each subfield. If it works, you
can try some alternatives:
1- Set your $SUBJECTS_DIR variable as another another path and move your
subjects directories (and only these directories to this place) and run
the same script you tried
(kvlQuantifyHippocampalSubfieldSegmentations.sh)
2- Make a little BASH script to process just your subjects. It requires
you keep your subjects in directories named following a rule you can use
make an iterative loop in your script. I use subject1, subject2 but you
can adapt to your needs. Something like the CalcHippoVol I attached.
Before using do any adaptation you may need and make it executable (for
example, with a chmod +x CalcHippoVol). Then just run from command
prompt from within the directory you saved the attachment typing:

./CalcHippoVol

This way, if all works you will get 2 files, LeftVol and a RightVol,
inside each of your subject/mri directory with the volumes you want.
Notice that:
1- the volumes are in voxels and, despite your original voxel volume,
the hippo-subfields processed by Freesurfer will be 0.5 x 0.5 x 0.5 mm.
So vol(mm3)=vol(voxels)/8.
2- it is difficult to determine the precise limits of each subfield in
the extreme end of the tail of the hippocampus, so the recon-all
-hippo-subfield processing pipeline group all remaining voxels in the
posterior_Left-Hippocampus.mgz for left hippocampus and
posterior_Right-Hippocampus.mgz for right one. So these last files does
not represent the whole hippocampi as the name could suggest. Check
details at Automated Segmentation of Hippocampal Subfields from
Ultra-High Resolution In Vivo MRI. 
Hi, Eugenio.
I would like to suggest a different name for this file. What do you
think about something like posterior_left_tail_complement.mgz and
posterior_right_tail_complement.mgz.
Cheers,
Marcos
 
Em Seg, 2013-06-24 às 16:00 -0400, Yang, Zoe escreveu:
> 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_l

Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

2013-06-25 Thread Juan Eugenio Iglesias 
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!




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--
-
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.



___
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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.

___

Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

2013-06-25 Thread Yang, Zoe 
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!





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--

-

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
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

2013-06-24 Thread Juan Eugenio Iglesias 

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!



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Freesurfer@nmr.mgh.harvard.edu
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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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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] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

2013-06-24 Thread Yang, Zoe 
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!

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