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 ------------------------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
