It appears to be a bbregister error:
bbregister --s APOE.269 --init-fsl --dti --mov
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/dwi.nii.gz --reg
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/xfms/anatorig2diff.bbr.dat --fslmat
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/xfms/diff2anatorig.bbr.mat
Make sure that SUBJECTS_DIR is correct in the config file. If the problem
persists, please email about the bbregister problem separately and perhaps Doug
can assist you. Note that I'll be traveling and may not be responding to email
in the next 10 days.
a.y
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow
<ddcc2...@gmail.com>
Sent: Thursday, October 10, 2019 9:20 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA error - MRISread could not open file
External Email - Use Caution
Hello,
It isn't an error with recon-all, at least I don't think it is. Recon-all ran
without error and the file that Tracula is trying to access seems to be where
it is supposed to be. It seems like Tracula is having an issue opening the
lh.white file. I just included the recon-all log for that subject to show that
recon-all hadn't had any issues. Do you still think it would have to do with
recon-all? It seems to have to do with the way Tracula is trying to read the
file?
Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
On Thu, Oct 10, 2019 at 9:14 AM Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula error"
in the subject line if you want the developers of the structural stream to look
into it.
a.y
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Daniel Callow <ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>>
Sent: Thursday, October 10, 2019 9:01:25 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA error - MRISread could not open file
External Email - Use Caution
Hello,
I am running tracula on some of my DTI data and have had no issues for most of
my subjects. However, for one of them I get the following error after mri_segreg
MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not open
file
Loading mov
Extracting frame 0
Projecting LH Surfs
Loading lh.white surf
No such file or directory
It doesn't make sense that I am getting this error because when looking in that
exact folder I see the following
[255a-280:freesurfer_pin/APOE.269/surf] amos% ls
lh.area lh.smoothwm.FI.crv rh.area rh.smoothwm.FI.crv
lh.curv lh.smoothwm.H.crv rh.curv rh.smoothwm.H.crv
lh.defect_borders lh.smoothwm.K.crv rh.defect_borders rh.smoothwm.K.crv
lh.defect_chull lh.smoothwm.K1.crv rh.defect_chull rh.smoothwm.K1.crv
lh.defect_labels lh.smoothwm.K2.crv rh.defect_labels rh.smoothwm.K2.crv
lh.inflated lh.smoothwm.S.crv rh.inflated rh.smoothwm.S.crv
lh.inflated.H lh.smoothwm.nofix rh.inflated.H rh.smoothwm.nofix
lh.inflated.K lh.sphere rh.inflated.K rh.sphere
lh.inflated.nofix lh.sphere.reg rh.inflated.nofix rh.sulc
lh.orig lh.sulc rh.orig rh.white.H
lh.orig.nofix lh.white.H rh.orig.nofix rh.white.K
lh.qsphere.nofix lh.white.K rh.qsphere.nofix rh.white.preaparc
lh.smoothwm lh.white.preaparc rh.smoothwm rh.white.preaparc.H
lh.smoothwm.BE.crv lh.white.preaparc.H rh.smoothwm.BE.crv rh.white.preaparc.K
lh.smoothwm.C.crv lh.white.preaparc.K rh.smoothwm.C.crv
It looks like the file it can't open is there? I have attached the log file for
recon-all and trac-all the subject in case it might help.
Thank you,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
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