Hi Julien,
Just to test something out, can you try running this again after replacing the
flirt.fsl binary in your new 7.0 install with the flirt.fsl binary from 6.0?
i.e.
cp /path/to/freesurfer/6.0.0/bin/flirst.fsl
/path/to/freesurfer/7.0.0/bin/flirst.fsl
Let me know how that works.
Best
Andrew
On 5/7/20, 8:04 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
julienbesle" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
julienbe...@gmail.com> wrote:
External Email - Use Caution
Hi,
I just installed freesurfer v7 and I'm getting an error in a script that
calls bbregister with the --fslmat and --init-fsl options. This error
does not occur in freesurfer v6 even when using exactly the same data,
but it does also occur with a development version of freesurfer I
downloaded in Sept 2019 (exact same error).
The call is:
DEBUG : 2020-05-06 12:07:12,816 : runCmd : Running: bbregister
--s HLOSS_p5 --mov
/home/julien/data/HLOSS/pilot05_B/DWI/B0_corrected_mean_resampled_MPRAGE.nii
--reg
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.dat
--fslmat
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.mat
--init-fsl --dti
The error occurs when bbregister calls fsl.flirt:
INFO : 2020-05-06 12:08:24,560 : main : flirt.fsl -ref
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii
-in
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
-searchrz -90 90 -verbose 0 -omat
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat
-schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat0
INFO : 2020-05-06 12:08:55,102 : main : Wed May 6 12:08:54
EEST 2020
INFO : 2020-05-06 12:08:55,603 : main : /mnt/f/data/HLOSS
INFO : 2020-05-06 12:08:56,105 : main : flirt.fsl -ref
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii
-in
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
-searchrz -90 90 -verbose 0 -omat
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat
-init
/home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat
-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
INFO : 2020-05-06 12:09:15,632 : main : terminate called after
throwing an instance of 'NEWMAT::SingularException'
INFO : 2020-05-06 12:09:15,633 : main : Abort (core dumped)
INFO : 2020-05-06 12:09:15,634 : main : ERROR: flirt
CRITICAL : 2020-05-06 12:09:15,634 : runCmd : Return Value: 1
It looks like the first time flirt.fsl is called everything goes fine,
but the second time, the error occurs. Unfortunately this is not a
script I wrote myself, so I'm not sure what this particular call to
bbregister is supposed to achieve. I'm not sure the call to fsl.flirt
depends on which version of FSL I have installed, but just in case, I
used the FSL v6 and didn't change anything to the FSL installation
between trying Freesurfer v6, dev or v7. I run everything on Ubuntu
16.04 running on WSL on Windows 10.
Any idea what could be going wrong?
Thanks
Julien
--
-------------------------------------
Julien Besle
Lagos Center, Apt 9A
Sadat Street
Beirut
Lebanon
tel: +961 78 980 317
-------------------------------------
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