[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
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvals
Loading gradients from
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvecs
INFO: Found 3 baseline images (b = 0) out of a total of 38 frames
Segmentation fault
Linux compute-026.mortimer 2.6.32-696.18.7.e16.x86_64 #1 SMP Thu Jan 4 17:31:22
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-paths exited with ERRORS at Tue Jan 9 09:34:58 CST 2018
I've checked the mask and it looks fine. I can't imagine the bvals and bvecs
files should be the issue since I already made it through the -prep stage. Is
it something with my bedpost outputs??
Thanks for your help!
Carissa
___
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] 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Carissa Nicole Weis mailto:cnw...@uwm.edu>>
Sent: Tuesday, January 9, 2018 11:42:07 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvals
Loading gradients from
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvecs
INFO: Found 3 baseline images (b = 0) out of a total of 38 frames
Segmentation fault
Linux compute-026.mortimer 2.6.32-696.18.7.e16.x86_64 #1 SMP Thu Jan 4 17:31:22
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-paths exited with ERRORS at Tue Jan 9 09:34:58 CST 2018
I’ve checked the mask and it looks fine. I can’t imagine the bvals and bvecs
files should be the issue since I already made it through the –prep stage. Is
it something with my bedpost outputs??
Thanks for your help!
Carissa
___
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] TRACULA path segmentation fault error because of bedpostx?
I've uploaded the data. Just want to confirm you received it.
Thanks,
Carissa
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Saturday, January 13, 2018 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Carissa Nicole Weis mailto:cnw...@uwm.edu>>
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:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Yendiki, Anastasia"
mailto:ayend...@mgh.harvard.edu>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, January 12, 2018 at 2:15 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Carissa Nicole Weis mailto:cnw...@uwm.edu>>
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>
[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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Carissa Nicole Weis mailto:cnw...@uwm.edu>>
Sent: Tuesday, January 9, 2018 11:42:07 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvals
Loading gradients from
/bigraid-03/LS/Ot
Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Carissa Nicole Weis mailto:cnw...@uwm.edu>>
Sent: Tuesday, January 9, 2018 11:42:07 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvals
Loading gradients from
/bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvecs
INFO: Found 3 baseline images (b = 0) out of a total of 38 frames
Segmentation fault
Linux compute-026.mortimer 2.6.32-696.18.7.e16.x86_64 #1 SMP Thu Jan 4 17:31:22
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-paths exited with ERRORS at
[Freesurfer] TRACULA -stat coord output file
Hello, Are the contents of the *.coords.mean.txt file generated from the trac-all -stat command, the average MNI coordinates along the tract across subjects? Or average coordinates in native space? Thanks! Carissa ___ 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.
[Freesurfer] -make all error
Hello, I am running recon-all for several subjects’ 7T data using Freesurfer version 6.0 and currently trying to ensure appropriate skull stripping and pial/wm surface generation. For a few participants that needed some control points added and for which I reran them through the –autorecon2-cp option, I was unable to open the pial surfaces for review. I’ve seen on some of the other posts that you guys recommend running “recon-all –make all” to rebuild the files. I’ve tried to run the -make all command but have been running into the same error in the “Jacobian white lh” step: #@# Jacobian white lh Wed Apr 4 12:07:37 CDT 2018 /bigraid-03/LS/Data/7T_fall2017/6315/6315_fs/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc… mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn’t match ../surf/lh.white.preaparc No such file or directory mrisReadTriangleFile failed. No such file or directory mris_jacobian: could not read target surface ../surf/lh.sphere.reg No such file or directory recon-all –s 6315_fs exited with ERRORS at Wed Apr 4 12:07:40 CDT 2018 All of the output in the log file up until this point appears to have finished without error. I can now open the surfaces for review, but am wondering what is affected by –make all not finishing completely. Carissa N. Weis, B.S. Graduate Student Affective Neuroscience Laboratory University of Wisconsin-Milwaukee cnw...@uwm.edu ___ 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.
[Freesurfer] longitudinal TRACULA -prep error
External Email - Use Caution Hello, I'm running into an error in the longitudinal TRACULA pipeline that I'm not sure how to resolve. I saw this error in the message board but there was no resolution to the problem so I thought I'd ask again. I've successfully run the recon-all longitudinal pipeline and am trying to run the trac-all -prep step with a longitudinal configuration file. Here's the error, it happens for both time points listed in my configuration file: #@# Image corrections Thu Sep 27 12:59:31 CDT 2018 mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1... crypt_gkey = *CyXds2s6sOqQ Starting DICOMRead2() dcmfile = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 dcmdir = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI Ref Series No = 6 Found 2666 files, checking for dicoms Found 2660 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 38 nslices = 70 ndcmfiles = 2660 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=1.00, TE=57.70, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz... crypt_gkey = *CyXds2s6sOqQ mri_probedicom --i /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 > /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dcminfo.dat cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals flip4fsl /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz x -y z /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvals /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals eddy_correct /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz 0 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0001 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0002 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0003 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0004 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0005 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0006 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0007 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0008 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0009 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0010 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0011 process
[Freesurfer] cross sectional vs longitudinal TRACULA reliability
External Email - Use Caution Hello, I’ve run both longitudinal and cross-sectional TRACULA pipelines on the same dataset, and I’ve found surprisingly low correlations of FA measurements for several tracts (as low as r= .1 in some cases). Which measurement should be considered more reliable? I’m having a hard time deciding which set of results to carry forward to group analysis. Thanks, Carissa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
