Hi Kristina - You can enter nifti DWI volumes in the configuration file (or any other format that mri_convert can recognize). You should do the entire processing from scratch (including bedpost) using the concatenated data.
Best, a.y On Fri, 20 May 2016, Kristina Jelinkova wrote: > Hi Anastasia, > > Thank you for your response. Yes, we have created the concatenated DWIs and > bvec/bval files that we have gotten after running each of the sequences > separately from trac-all. How can we run these concatenated nii.gz mages > through the ball-and-stick model fit (I'm assuming the configuration file > only looks for dcm images)? Would we also need to run bedpostX again > separately with the concatenated images? > > Thanks again for your help! > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki > <ayend...@nmr.mgh.harvard.edu> > Sent: Friday, May 20, 2016 3:52:02 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Mult-Shell Tracula Help > > Hi Kristina - I'm assuming the 2 data sets were acquired in the same > session and with the same acquisition parameters, other than the b-values? > Then you can just concatenate the DWIs from the 2 runs (e.g. with > mri_concat) and also concatenate the b-value and gradient vector tables > (and make sure the 2 runs are concatenated in the same order for each type > of file!) > > Best, > a.y > > On Fri, 20 May 2016, Kristina Jelinkova wrote: > >> >> Hello all, >> >> >> I had a question regarding the program Tracula. I have two different DTI >> sequences that I wish to run (b=900 and b=2000) but am unsure at which step I >> am suppose to merge the two sequences together. >> >> >> At this point, I have pre-processed each of the sequences separately using >> trac-all. Should I take each of the separate trac-all output >> data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick >> model fit on the new bedpostX output? Also, is there a way to use nii.gz >> files in the configuration file rather than a dcm list? >> >> >> Thank you in advance for your help! >> >> >> > > _______________________________________________ > 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.
