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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
