Hi Greg,

You can do the following to skip eddy current correction and intra subject registration:

trac-all -inter -masks -tensor -prior -c /path/to/configurationfile/config_file

If you want to get tracula based files for the bbregister you've run with manual fixes, can you please let me know the command line you used for running bbregister?

This is what is typically used in tracula.

1. Set SUBJECTS_DIR variable

setenv SUBJECTS_DIR /path/to/recons/

2. Register low-b to Anatomical with bbregister

bbregister --s <SubjectID> --init-fsl --dti --mov <SubjectID>/dmri/dwi.nii.gz --reg <SubjectID>/dmri/xfms/anatorig2diff.bbr.dat --fslmat <SubjectID>/dmri/xfms/diff2anatorig.bbr.mat

After the bbregister step tracula expects, to find <SubjectID>/dmri/xfms/anatorig2diff.bbr.dat and <SubjectID>/dmri/xfms/diff2anatorig.bbr.mat in the tracula subject directory. Since you've already finished this step, you can probably rename your .dat and .mat files as above and proceed with the following steps[3-6].

3. Compute inverse

convert_xfm -omat <SubjectID>/dmri/xfms/anatorig2diff.bbr.mat -inverse <SubjectID>/dmri/xfms/diff2anatorig.bbr.mat

4. Compue Transformation beteween FSL's Flipped anatomical to low-b

convert_xfm -omat <SubjectID>/dmri/xfms/anat2diff.bbr.mat -concat <SubjectID>/dmri/xfms/anatorig2diff.bbr.mat <SubjectID>/dmri/xfms/anat2anatorig.mat

5. Compute inverse between low-b and fsl's flipped anatomical

convert_xfm -omat <SubjectID>/dmri/xfms/diff2anat.bbr.mat -inverse <SubjectID>/dmri/xfms/anat2diff.bbr.mat

6. Skip Eddy current and Intra Subject registration and run the rest of the steps in tracula as you've got all the registration files from the intra subject registration

trac-all -inter -masks -tensor -prior -c /path/to/configurationfile/config_file

To do it for all 17 subjects you can just create a shell script to run the steps 3-5 for all the subjects and then run trac-all to do the rest of the processing.

If you have any questions about the outputs from tracula or the files it creates/expects after every stage, please refer to the following page:

http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all

Let us know if you have any questions.

-Priti

Hi, I processed about 80 subjects with -prep stage and then checked the

bbregister registrations with

tkregister2 --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/dwi.nii.gz

--reg

/study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/xfms/anatorig2diff.bbr.dat

--surf

found 17 subjects with bad registrations, as always because the fsl

registration initialization was bad.

so now i manually fix the registeration and use the manual fix for the

initialization and rerun bbregister and get a good registration.

so now i need to rerun -prep phase but have it use the good registration

instead of computing a new

bbregister registration.

will trac-all -prep -nointra -c configfile accomplish this or do i need to get in and tinker with the scripts to make it run

everything including computing new fsl and inverse registration matricies

but using my bbregister good registration.

thanks

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