Re: [Freesurfer] Fwd: TRACULA stat extraction issue

[Anastasia Yendiki]

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 
 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



___
Freesurfer mailing list
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.




--
Best,
Shashwath

___
Freesurfer mailing list
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.

Re: [Freesurfer] Fwd: TRACULA stat extraction issue

[Shashwath Meda]

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 <
ayend...@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
>>
>>
>>
> ___
> Freesurfer mailing list
> 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.
>
>


-- 
Best,

Shashwath
___
Freesurfer mailing list
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.

Re: [Freesurfer] Fwd: TRACULA stat extraction issue

[Anastasia Yendiki]

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


___
Freesurfer mailing list
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.