Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files
Thank you for your email. Just to follow up, the rh and lh hippocampal hippoSfVolumes-T1.v10.txt files are present, but for a large number of cases, only the lh hippoSfVolumes-T1.long.v10.txt files are present. I reran the exact same recon-all -long command for all the cases, and I reran them after your suggestion, but there is no change in the number of missing rh.hippoSfVolumes-T1.long.v10.txt files. The log file for the longitudinal processing for recon-all says the process completed with no errors.
Is there anything else I should check?
Thanks!
On Fri, Apr 14, 2017 at 3:54 AM Alan Francis alandarkenergy@gmail.com wrote:
Hi Salil:
It could be that the HSF script may have `errored out' mid way through the analysis. If you go through the recon processing steps which are one of the output files, you will see exactly where the error occurred. Just reprocess that brain and see if that happens again.
Hope this helps,
best,
Alan
On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman sal@jhu.edu wrote:
Hi,
I have run a number of cases through the FS6 hippocampal longitudinal processing steps listed at https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
It seems that all steps completed, but when it came time to collect the results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67) than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what I may be doing incorrectly?
Thanks!
Salil Soman
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*Alan N. Francis PhD* Regional Sales Manager/ Application specialist Nordic Neurolab Boston. alan@nordicneurolab.com
*Previously:* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu
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Not sure what is going on, maybe Eugenio knows.
On 04/27/2017 10:29 PM, Salil Soman wrote:
Thank you for your email. Just to follow up, the rh and lh hippocampal hippoSfVolumes-T1.v10.txt files are present, but for a large number of cases, only the lh hippoSfVolumes-T1.long.v10.txt files are present. I reran the exact same recon-all -long command for all the cases, and I reran them after your suggestion, but there is no change in the number of missing rh.hippoSfVolumes-T1.long.v10.txt files. The log file for the longitudinal processing for recon-all says the process completed with no errors.
Is there anything else I should check?
Thanks!
On Fri, Apr 14, 2017 at 3:54 AM Alan Francis <alandarkenergy@gmail.com mailto:alandarkenergy@gmail.com> wrote:
Hi Salil: It could be that the HSF script may have `errored out' mid way through the analysis. If you go through the recon processing steps which are one of the output files, you will see exactly where the error occurred. Just reprocess that brain and see if that happens again. Hope this helps, best, Alan On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman <sal@jhu.edu <mailto:sal@jhu.edu>> wrote: Hi, I have run a number of cases through the FS6 hippocampal longitudinal processing steps listed at https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing It seems that all steps completed, but when it came time to collect the results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67) than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what I may be doing incorrectly? Thanks! Salil Soman _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| * Alan N. Francis PhD* Regional Sales Manager/ Application specialist Nordic Neurolab Boston. alan@nordicneurolab.com <mailto:alan@nordicneurolab.com> *Previously:* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu <mailto:ezra_wegbreit@brown.edu> afrancis@mclean.harvard.edu <mailto:afrancis@mclean.harvard.edu> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Alan, Can you please send me the log file for the longitudinal subfields? Cheers, /Eugenio
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 3 May 2017, at 14:11, Martin Reuter <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> wrote:
Not sure what is going on, maybe Eugenio knows.
On 04/27/2017 10:29 PM, Salil Soman wrote: Thank you for your email. Just to follow up, the rh and lh hippocampal hippoSfVolumes-T1.v10.txt files are present, but for a large number of cases, only the lh hippoSfVolumes-T1.long.v10.txt files are present. I reran the exact same recon-all -long command for all the cases, and I reran them after your suggestion, but there is no change in the number of missing rh.hippoSfVolumes-T1.long.v10.txt files. The log file for the longitudinal processing for recon-all says the process completed with no errors.
Is there anything else I should check?
Thanks!
On Fri, Apr 14, 2017 at 3:54 AM Alan Francis <alandarkenergy@gmail.commailto:alandarkenergy@gmail.com> wrote: Hi Salil:
It could be that the HSF script may have `errored out' mid way through the analysis. If you go through the recon processing steps which are one of the output files, you will see exactly where the error occurred. Just reprocess that brain and see if that happens again.
Hope this helps,
best,
Alan
On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman <sal@jhu.edumailto:sal@jhu.edu> wrote: Hi,
I have run a number of cases through the FS6 hippocampal longitudinal processing steps listed at https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
It seems that all steps completed, but when it came time to collect the results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67) than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what I may be doing incorrectly?
Thanks!
Salil Soman
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD Regional Sales Manager/ Application specialist Nordic Neurolab Boston. alan@nordicneurolab.commailto:alan@nordicneurolab.com
Previously: Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edumailto:ezra_wegbreit@brown.edu afrancis@mclean.harvard.edumailto:afrancis@mclean.harvard.edu
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
freesurfer@nmr.mgh.harvard.edu
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Iglesias Gonzalez, Eugenio -
Martin Reuter -
Salil Soman