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 ..
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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 < iglesias@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.
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 <iglesias@nmr.mgh.harvard.edu mailto:iglesias@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 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 iglesias@nmr.mgh.harvard.edu <mailto:iglesias@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.
That worked, thanks for your help!
On Wed, Jul 17, 2013 at 12:00 PM, Juan Eugenio Iglesias < iglesias@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 < iglesias@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@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.comiglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
freesurfer@nmr.mgh.harvard.edu
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Jasmeet Hayes -
Juan Eugenio Iglesias