Hi Saad, Thank you very much for your help! I've got better understanding of this issue thanks to your papers. Can I use the ball and stick model using a gamma distribution of diffusivities with FSL?
Best regards, Sol On 18 October 2014 14:05, Saad Jbabdi <[email protected]> wrote: > Hi Sol > I would recommend that you use the b=1000 shell and run dtifit. > You can extract the b=1000 shell from the data using fslsplit and > fslmerge. We will soon release a tool (fslselectvols) which should make > this more straightforward. > > Cheers > Saad. > > > > On 17 Oct 2014, at 15:34, 임솔 <[email protected]> wrote: > > Thank you so much for your helpful replies! > > While waiting for comments from Oxford, what do you recommend for tensor > fitting? > > Many thanks, > Sol > > On 16 October 2014 18:19, Harms, Michael <[email protected]> wrote: > >> >> Note though that you'll want to consider whether to use all the shells >> if computing a standard tensor fit because the assumption of Gaussian >> diffusion and mono exponential decay starts to break down for b>1500 or so. >> >> Perhaps someone from Oxford will chime in with more detailed thoughts >> on that issue. >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> ----------------------------------------------------------- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave. Tel: 314-747-6173 >> St. Louis, MO 63110 Email: [email protected] >> >> From: <House>, Matthew House <[email protected]> >> Date: Thursday, October 16, 2014 12:11 PM >> To: 임솔 <[email protected]>, "[email protected]" < >> [email protected]> >> Subject: Re: [HCP-Users] How I can use grad_dev file for tensor fitting >> using FSL dtifit? >> >> Hi, Sol. There is a hidden option of ‘--gradnonlin’ in the dtifit >> command to enable this function. Below is an example command that I used >> in a script to loop over the HCP DTI data. >> >> >> >> dtifit -k data.nii.gz -r bvecs -b bvals -m nodif_brain_mask.nii.gz -o >> $OUTDIR/$SUBJECT/dti --gradnonlin=grad_dev.nii.gz >> >> >> >> ~Matt >> >> >> >> *From:* [email protected] [ >> mailto:[email protected] >> <[email protected]>] *On Behalf Of *?? >> *Sent:* Thursday, October 16, 2014 12:06 PM >> *To:* [email protected] >> *Subject:* [HCP-Users] How I can use grad_dev file for tensor fitting >> using FSL dtifit? >> >> >> >> Dear all, >> >> >> >> I'm trying to fit the diffusion tensor model using FSL dtifit but I do >> not know how to include gradient correction using grad_dev file. There is >> an option flag '-gradadj' in Camino to do it. What would be the >> equivalent argument for FSL dtifit? Many thanks. >> >> >> >> Best, >> >> Sol >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> ------------------------------ >> >> The material in this message is private and may contain Protected >> Healthcare Information (PHI). If you are not the intended recipient, be >> advised that any unauthorized use, disclosure, copying or the taking of any >> action in reliance on the contents of this information is strictly >> prohibited. If you have received this email in error, please immediately >> notify the sender via telephone or return mail. >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> ------------------------------ >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------------------------------------------ > Saad Jbabdi, PhD > MRC Career Development Fellow & > University Research Lecturer > > FMRIB Centre, University of Oxford, > John Radcliffe Hospital, Oxford, OX3 9DU, UK. > tel (+44)1865-222466 (fax 717) > www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > > > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
