Thanks very much. I just checked the multi-shell model option in BEDPOSTX. Best wishes, Sol
On 20 October 2014 09:48, Saad Jbabdi <[email protected]> wrote: > Hi > Yes you can, but not for calculating FA. We use the ball and stick model > to calculate orientations that we then use for tractography. > > Cheers > Saad > > On 18 Oct 2014, at 14:56, 임솔 <[email protected]> wrote: > > 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 >> >> >> >> > > ------------------------------------------------------------------ > 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
