Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

2013-07-17 Thread Jasmeet Hayes 
That worked, thanks for your help!


On Wed, Jul 17, 2013 at 12:00 PM, Juan Eugenio Iglesias <
igles...@nmr.mgh.harvard.edu> wrote:

>  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> 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 ..
>>
>>
>>  ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> -
>> Juan Eugenio Iglesias, 
>> PhDhttp://www.jeiglesias.comigles...@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.
>>
>
>
> --
> -
> Juan Eugenio Iglesias, 
> PhDhttp://www.jeiglesias.comigles...@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] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

2013-07-17 Thread Juan Eugenio Iglesias 
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 
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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-- 
-

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.

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.




--
-
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.

Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

2013-07-17 Thread Jasmeet Hayes 
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> 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 ..
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> -
> Juan Eugenio Iglesias, 
> PhDhttp://www.jeiglesias.comigles...@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.
>


kvlQuantifyHippocampalSubfieldSegmentations.sh
Description: Bourne shell script
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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
dispose of the e-mail.

Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

2013-07-17 Thread Juan Eugenio Iglesias 

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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--
-
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] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

2013-07-17 Thread Jasmeet Hayes 
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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contains patient information, please contact the Partners Compliance HelpLine at
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