[Freesurfer] funcroi-table-sess: how to specify frames for multi-band data

[Keishi NOMURA]

Hi all,

I’m using : freesurfer-Darwin-lion-stable-pub-v5.3.0

I’d like to plot HRF for each condition for each subject, using data acquired 
by multi-band EPI.
Here are the commands I used:


funcroi-config -roi rh.V1.roicfg -label rh.V1.label -analysis RH_fwhm8 -force 
funcroi-sess -s ORI01 -roi rh.V1.roicfg -df sessdirfile

# m: frames

foreach m ( 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 )
  funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis 
RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame 
$m
end


Then I got an error like “Error: input frame = 2, input volume only has 1 
frames”.

I referred to the related questions:
  https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15883.html
  https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017958.html
It seems that there is nothing wrong with these commands, except for specifying 
the frames.
One possibility is that using multi-band data is somehow causing trouble.
I’m now using multi-band factor = 8 and TR = 0.8 sec, so then I set the frames 
to multiple number of TR = 0.8, and ran the commands again:


foreach m ( 0.8 1.6 2.4 3.2 4.0 4.8 5.6 6.4 7.2 8.0 8.8 9.6 10.4 11.2 12.0 12.8 
13.6 14.4 15.2 16 )
  funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis 
RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame 
$m
end


But still I get errors like “Error: input frame = 2, input volume only has 1 
frames”. (when I used frame = 2.4. Hence, it seems that we cannot use 
non-integral inputs)
So, my question is:
(1) How should I specify frames when I use multi-band data?
(2) Regarding (1), what temporal resolution do I get when I use TR = 0.8? (for 
example, TER = 0.8/20 = 0.04 or anything like that)
(3) Or, is there anything wrong with my commands other than frames?

Thank you,
Keishi



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Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

[Carissa Nicole Weis]

My mistake. It was acquired that way.

Also, after running my subjects through the -bedp step several times I’ve now 
only got one subject who is lingering there, but some subjects had to run 7+ 
times through bedp before finishing properly. I do have another dataset to 
analyze that was acquired with the same parameters so it’s quite possible this 
issue may arise again.

Thanks again for your help,

Carissa


From:  on behalf of "Yendiki, 
Anastasia" 
Reply-To: Freesurfer support list 
Date: Saturday, January 13, 2018 at 3:49 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?


Those are pretty standard dimensions, so memory is not likely to be a problem. 
Can you upload a zip file with this subject's entire TRACULA subject dir for me 
here: https://gate.nmr.mgh.harvard.edu/filedrop2/


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Carissa Nicole Weis 

Sent: Saturday, January 13, 2018 10:14:26 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?


How much memory would you recommend using? I’ve been using 8gb from our cluster 
for each step in TRACULA.



The diffusion images were acquired with fairly common parameters: 3 B=0 images, 
35 different gradient directions at B=800 with 70 slices per direction at a 
voxel size of 2x2x2mm for a 128x128 matrix.



Thanks for your help!



Carissa



From:  on behalf of "Yendiki, 
Anastasia" 
Reply-To: Freesurfer support list 
Date: Friday, January 12, 2018 at 2:15 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?



Hi Carissa - One possibility is that you may be running out of memory. What are 
the dimensions of your diffusion images?



a.y



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Carissa Nicole Weis 

Sent: Thursday, January 11, 2018 4:55:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?



Hello Anastasia!



I’ve since tried to rerun –bedp with this same subject and the output still did 
not indicate it had completed.



Thanks for your help!



Carissa



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Thursday, January 11, 2018 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of 
bedpostx?



Hi Carissa - It loks like bedpost ran fine. Can you please attach your entire 
log file (scripts/trac-all.log)? It's hard to tell what went wrong just from 
the end of it.



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Carissa Nicole Weis >
Sent: Tuesday, January 9, 2018 11:42:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?



Hello all,



I’ve been running trac-all from the command line without the configuration file 
since I’m not changing any defaults. I’ve successfully run several subjects 
through the trac-all –prep stage, and the –bedp stage. **Although I never got 
the “trac-all –bedp finished without error” prompt in the -bedp terminal output 
and usually just get something that says at the end:



../freesurfer_6.0/bin/bedpost_mgh: line 440: 46773 Terminated   
${subjdir}.bedpostX/monitor



OR it’ll make it to something like…



37 slices processed

38 slices processed

Queuing post processing stage

46 slices processed



…and that’s as far as the output in the terminal goes.



It appears all the expected files have been created in dmri.bedpostx/ so I was 
assuming this step had been completed. However, when I go to run the –paths 
step I get an error that says:



Loading DWIs from 
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/dmri/dwi.nii.gz

Loading mask from 
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dlabel/diff/aparc+aseg_mask.bbr.nii.gz

Loading BEDPOST parameter samples from 
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri.bedpostX

Loading b-values from 

Re: [Freesurfer] tracula flags

[Yendiki, Anastasia]

Hi - Is this the only output that you get? This is the first line of text that 
you see when you run trac-all? To figure this out we'll need the full terminal 
output (which is also saved in scripts/trac-all.log), as well as your config 
file.


Thanks,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Renew Andrade 

Sent: Sunday, January 28, 2018 3:02:23 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] tracula flags

Hello everyone!
I have this problem with TRACULA. When I go to the second part of the tutorial 
I can´t keep going. I acknowledge that during the first part I have switch from 
tcsh to bash depending on errors but I’m not sure if that is normal or a 
mistake. The error is for example:
trac-all -prep -c home/andraderenew/Downloads/freesurfer data 
tutorial/diffusion_tutorial/dmrirc.tutorial
if: Expression Syntax
Thanks!
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The information in this e-mail is intended only for the person to whom it is
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[Freesurfer] tracula flags

[Renew Andrade]

Hello everyone!
I have this problem with TRACULA. When I go to the second part of the tutorial 
I can´t keep going. I acknowledge that during the first part I have switch from 
tcsh to bash depending on errors but I’m not sure if that is normal or a 
mistake. The error is for example:
trac-all -prep -c home/andraderenew/Downloads/freesurfer data 
tutorial/diffusion_tutorial/dmrirc.tutorial
if: Expression Syntax
Thanks!
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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.