Dear Group - I seem to have run into an issue when attempting to assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts.
The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation?
tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table
Hi Shashwath - It looks like you have modified the directory structure of the output files. Normally the dpath/ directory is right under the directory with subject's name. From your file of inputs, it looks like you've created some other subdirectories and now dpath/ is a few levels down the hierarchy. I'd recommend reverting to the original structure that the commands expect.
Best, a.y
On Fri, 10 Jun 2016, Shashwath Meda wrote:
Dear Group - I seem to have run into an issue when attempting to assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts. The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation?
tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table
-- Best, Shashwath
Hi Anastasia - Yes thats what i figured, however the way our pipeline system is setup this was the most straightfoward way of doing it. Anyways i did figure out how to extract the average values in a more convoluted fashion so we are all set with that. However, im trying to do the same with the trac-all -stat command now to extract pathbyvoxel stats and am having issues. I see that while assimilating group level info, the program automatically rejects or doesnt ouput a column for the subject that has failed, is there a quick and dirty fix to the code that will enable me to output all subjects data even if its failed (maybe replace the values with NaN or somethign similar for failed subjects?). Please let me know.
Thanks Shashwath
On Mon, Jul 4, 2016 at 3:25 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Shashwath - It looks like you have modified the directory structure of the output files. Normally the dpath/ directory is right under the directory with subject's name. From your file of inputs, it looks like you've created some other subdirectories and now dpath/ is a few levels down the hierarchy. I'd recommend reverting to the original structure that the commands expect.
Best, a.y
On Fri, 10 Jun 2016, Shashwath Meda wrote:
Dear Group - I seem to have run into an issue when attempting to
assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts. The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation?
tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table
-- Best, Shashwath
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Hi Shashwath - Unfortunately this is not possible right now, so you'd have to add those extra columns after you run it.
a.y
On Fri, 8 Jul 2016, Shashwath Meda wrote:
Hi Anastasia - Yes thats what i figured, however the way our pipeline system is setup this was the most straightfoward way of doing it. Anyways i did figure out how to extract the average values in a more convoluted fashion so we are all set with that. However, im trying to do the same with the trac-all -stat command now to extract pathbyvoxel stats and am having issues. I see that while assimilating group level info, the program automatically rejects or doesnt ouput a column for the subject that has failed, is there a quick and dirty fix to the code that will enable me to output all subjects data even if its failed (maybe replace the values with NaN or somethign similar for failed subjects?). Please let me know. Thanks Shashwath
On Mon, Jul 4, 2016 at 3:25 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Shashwath - It looks like you have modified the directory structure of the output files. Normally the dpath/ directory is right under the directory with subject's name. From your file of inputs, it looks like you've created some other subdirectories and now dpath/ is a few levels down the hierarchy. I'd recommend reverting to the original structure that the commands expect. Best, a.y On Fri, 10 Jun 2016, Shashwath Meda wrote: Dear Group - I seem to have run into an issue when attempting to assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts. The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation? tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table -- Best, Shashwath
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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.
-- Best, Shashwath
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Shashwath Meda