Re: [Freesurfer] Mult-Shell Tracula Help
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.
Re: [Freesurfer] Mult-Shell Tracula Help
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 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.
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 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.
[Freesurfer] Mult-Shell Tracula Help
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 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.
