Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski
Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 7:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski
Yes I updated those and renamed them so that they'd be in the locations TRACULA expects.
Lauren
El may. 30, 2017, a las 8:12 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> escribió:
Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 7:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Just to double-check my methods, I ran:
bbregister --s pBECTS026 --init-fsl --dti --mov dwi.nii.gz --reg xfms/anatorig2diff.bbr.dat --fslmat xfms/diff2anatorig.bbr.mat
from the subject's dmri directory, then checked and edited the results with tkregisterfv and saved the registration. I then set bbregister to 0 in the configuration file, and ran trac-all -prep
Unfortunately the registration still looks off -
[cid:9e308e63-a0d4-4e03-aa4e-6ca0a8148043]
We appreciate any other tips you might have!
Thanks,
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 8:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Yes I updated those and renamed them so that they'd be in the locations TRACULA expects.
Lauren
El may. 30, 2017, a las 8:12 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> escribió:
Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 7:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Lauren - The command looks right at first glance. Did you save the .dat file, the .mat file, or both?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Just to double-check my methods, I ran:
bbregister --s pBECTS026 --init-fsl --dti --mov dwi.nii.gz --reg xfms/anatorig2diff.bbr.dat --fslmat xfms/diff2anatorig.bbr.mat
from the subject's dmri directory, then checked and edited the results with tkregisterfv and saved the registration. I then set bbregister to 0 in the configuration file, and ran trac-all -prep
Unfortunately the registration still looks off -
[cid:9e308e63-a0d4-4e03-aa4e-6ca0a8148043]
We appreciate any other tips you might have!
Thanks,
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 8:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Yes I updated those and renamed them so that they'd be in the locations TRACULA expects.
Lauren
El may. 30, 2017, a las 8:12 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> escribió:
Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 7:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I saved both, but to be honest not many edits were required to make the registration line up, making me wonder if the error is coming from somewhere else.
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 11:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - The command looks right at first glance. Did you save the .dat file, the .mat file, or both?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Just to double-check my methods, I ran:
bbregister --s pBECTS026 --init-fsl --dti --mov dwi.nii.gz --reg xfms/anatorig2diff.bbr.dat --fslmat xfms/diff2anatorig.bbr.mat
from the subject's dmri directory, then checked and edited the results with tkregisterfv and saved the registration. I then set bbregister to 0 in the configuration file, and ran trac-all -prep
Unfortunately the registration still looks off -
[cid:9e308e63-a0d4-4e03-aa4e-6ca0a8148043]
We appreciate any other tips you might have!
Thanks,
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 8:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Yes I updated those and renamed them so that they'd be in the locations TRACULA expects.
Lauren
El may. 30, 2017, a las 8:12 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> escribió:
Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 7:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The registration is the screenshots does look like it'd be the source of major issues. Can you please send me the old and new version of the .mat files, to get an idea of how different they are?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 12:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
I saved both, but to be honest not many edits were required to make the registration line up, making me wonder if the error is coming from somewhere else.
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 11:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - The command looks right at first glance. Did you save the .dat file, the .mat file, or both?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Just to double-check my methods, I ran:
bbregister --s pBECTS026 --init-fsl --dti --mov dwi.nii.gz --reg xfms/anatorig2diff.bbr.dat --fslmat xfms/diff2anatorig.bbr.mat
from the subject's dmri directory, then checked and edited the results with tkregisterfv and saved the registration. I then set bbregister to 0 in the configuration file, and ran trac-all -prep
Unfortunately the registration still looks off -
[cid:9e308e63-a0d4-4e03-aa4e-6ca0a8148043]
We appreciate any other tips you might have!
Thanks,
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 8:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Yes I updated those and renamed them so that they'd be in the locations TRACULA expects.
Lauren
El may. 30, 2017, a las 8:12 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> escribió:
Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 7:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It looks like TRACULA overwrote the.mat files when I re-ran the -prep step. I can run TRACULA again using its internal bbregister and store the results in a different directory, and then give you those .mat files to compare against the ones with my use of bbregister?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 12:25 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
The registration is the screenshots does look like it'd be the source of major issues. Can you please send me the old and new version of the .mat files, to get an idea of how different they are?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 12:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
I saved both, but to be honest not many edits were required to make the registration line up, making me wonder if the error is coming from somewhere else.
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 11:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - The command looks right at first glance. Did you save the .dat file, the .mat file, or both?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Just to double-check my methods, I ran:
bbregister --s pBECTS026 --init-fsl --dti --mov dwi.nii.gz --reg xfms/anatorig2diff.bbr.dat --fslmat xfms/diff2anatorig.bbr.mat
from the subject's dmri directory, then checked and edited the results with tkregisterfv and saved the registration. I then set bbregister to 0 in the configuration file, and ran trac-all -prep
Unfortunately the registration still looks off -
[cid:9e308e63-a0d4-4e03-aa4e-6ca0a8148043]
We appreciate any other tips you might have!
Thanks,
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 8:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Yes I updated those and renamed them so that they'd be in the locations TRACULA expects.
Lauren
El may. 30, 2017, a las 8:12 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> escribió:
Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 7:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Lauren - The problem is that when trac-all ran bbregister, it saved the transformation both as a .dat file and as a .mat file. When you save your new .dat file, the .mat file doesn't get updated. To update it, run this on your new .dat file:
lta_convert --inreg dmri/xfms/anatorig2diff.bbr.dat --outfsl dmri/xfms/diff2anatorig.bbr.mat --src dmri/lowb.nii.gz --trg dmri/brain_anat_orig.nii.gz
Then you can run the rest of the prep (with bbregister commented out as we talked about) and it should hopefully work.
Best, a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 1:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
It looks like TRACULA overwrote the.mat files when I re-ran the -prep step. I can run TRACULA again using its internal bbregister and store the results in a different directory, and then give you those .mat files to compare against the ones with my use of bbregister?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 12:25 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
The registration is the screenshots does look like it'd be the source of major issues. Can you please send me the old and new version of the .mat files, to get an idea of how different they are?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 12:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
I saved both, but to be honest not many edits were required to make the registration line up, making me wonder if the error is coming from somewhere else.
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 11:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - The command looks right at first glance. Did you save the .dat file, the .mat file, or both?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Just to double-check my methods, I ran:
bbregister --s pBECTS026 --init-fsl --dti --mov dwi.nii.gz --reg xfms/anatorig2diff.bbr.dat --fslmat xfms/diff2anatorig.bbr.mat
from the subject's dmri directory, then checked and edited the results with tkregisterfv and saved the registration. I then set bbregister to 0 in the configuration file, and ran trac-all -prep
Unfortunately the registration still looks off -
[cid:9e308e63-a0d4-4e03-aa4e-6ca0a8148043]
We appreciate any other tips you might have!
Thanks,
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 8:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Yes I updated those and renamed them so that they'd be in the locations TRACULA expects.
Lauren
El may. 30, 2017, a las 8:12 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> escribió:
Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 7:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Great! Thanks so much.
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Tuesday, June 06, 2017 9:17 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - The problem is that when trac-all ran bbregister, it saved the transformation both as a .dat file and as a .mat file. When you save your new .dat file, the .mat file doesn't get updated. To update it, run this on your new .dat file:
lta_convert --inreg dmri/xfms/anatorig2diff.bbr.dat --outfsl dmri/xfms/diff2anatorig.bbr.mat --src dmri/lowb.nii.gz --trg dmri/brain_anat_orig.nii.gz
Then you can run the rest of the prep (with bbregister commented out as we talked about) and it should hopefully work.
Best, a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 1:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
It looks like TRACULA overwrote the.mat files when I re-ran the -prep step. I can run TRACULA again using its internal bbregister and store the results in a different directory, and then give you those .mat files to compare against the ones with my use of bbregister?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 12:25 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
The registration is the screenshots does look like it'd be the source of major issues. Can you please send me the old and new version of the .mat files, to get an idea of how different they are?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 12:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
I saved both, but to be honest not many edits were required to make the registration line up, making me wonder if the error is coming from somewhere else.
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 11:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - The command looks right at first glance. Did you save the .dat file, the .mat file, or both?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Wednesday, May 31, 2017 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Just to double-check my methods, I ran:
bbregister --s pBECTS026 --init-fsl --dti --mov dwi.nii.gz --reg xfms/anatorig2diff.bbr.dat --fslmat xfms/diff2anatorig.bbr.mat
from the subject's dmri directory, then checked and edited the results with tkregisterfv and saved the registration. I then set bbregister to 0 in the configuration file, and ran trac-all -prep
Unfortunately the registration still looks off -
[cid:9e308e63-a0d4-4e03-aa4e-6ca0a8148043]
We appreciate any other tips you might have!
Thanks,
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 8:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Yes I updated those and renamed them so that they'd be in the locations TRACULA expects.
Lauren
El may. 30, 2017, a las 8:12 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> escribió:
Yes, this is what I suspected. The outputs of bbregister are anatorig2diff.bbr.dat and anatorig2diff.bbr.mat. Are these the ones that you updated? The other ones are generated by trac-all -intra.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 7:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
It looks as though some but now all have updated -
[franklin:xfms] (nmr-dev-env) ls -l total 152 -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat -rw-rw-r-- 1 lo941 megclin 328 May 30 15:07 anat2anatorig.dat~ -rw-rw-r-- 1 lo941 megclin 83 May 30 15:07 anat2anatorig.mat -rw-rw-r-- 1 lo941 megclin 197 May 25 11:04 anat2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 187 May 30 15:09 anat2mni.mat -rw-rw-r-- 1 lo941 megclin 228 May 30 15:07 anatorig2anat.mat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat -rw-rw-r-- 1 lo941 megclin 326 May 25 12:10 anatorig2diff.bbr.dat~ -rw-rw-r-- 1 lo941 megclin 31304 May 25 12:10 anatorig2diff.bbr.dat.log -rw-rw-r-- 1 lo941 megclin 37322 May 25 11:04 anatorig2diff.bbr.dat.log.old -rw-rw-r-- 1 lo941 megclin 42 May 25 12:10 anatorig2diff.bbr.dat.mincost -rw-rw-r-- 1 lo941 megclin 114 May 25 12:10 anatorig2diff.bbr.dat.param -rw-rw-r-- 1 lo941 megclin 4084 May 25 12:10 anatorig2diff.bbr.dat.sum -rw-rw-r-- 1 lo941 megclin 197 May 25 12:14 anatorig2diff.bbr.mat -rw-rw-r-- 1 lo941 megclin 188 May 30 15:09 anatorig2mni.mat -rw-rw-r-- 1 lo941 megclin 178 May 25 11:04 diff2anat.bbr.mat -rw-rw-r-- 1 lo941 megclin 228 May 25 12:10 diff2anatorig.bbr.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 diff2mni.bbr.mat -rw-rw-r-- 1 lo941 megclin 185 May 30 15:09 mni2anat.mat -rw-rw-r-- 1 lo941 megclin 189 May 30 15:09 mni2anatorig.mat -rw-rw-r-- 1 lo941 megclin 194 May 30 15:09 mni2diff.bbr.mat
Thanks, Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 6:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you run "ls -l" in this subject's dmri/xfms/ and check the creation dates of the files to see if they were updated?
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 3:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Anastasia,
I just re-ran the trac-preproc script with the bbregister command set to 0 in the configuration file, and I'm afraid I got the same erroneous result. Do you have any other ideas as to where the problem could be coming from?
Lauren
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister registration file. That's because the -intra step in TRACULA doesn't just run bbregister, but also does a bunch of other things with the output of bbregister, like transform, invert, and compose a bunch of registration files. Because you skipped the -intra step, these things were not updated. You can temporarily comment out the bbregister command in the trac-preproc script, and run the -intra step so that it updates all those other files.
Hope this helps!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ostrowski, Lauren [LOSTROWSKI@mgh.harvard.edumailto:LOSTROWSKI@mgh.harvard.edu] Sent: Tuesday, May 30, 2017 1:46 PM To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hello experts,
I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it?
Thanks, Lauren Ostrowski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Ostrowski, Lauren -
Ostrowski, Lauren
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Yendiki, Anastasia