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]<mailto:[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]<mailto:[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<tel:314-747-6173> St. Louis, MO 63110 Email: [email protected]<mailto:[email protected]> From: <House>, Matthew House <[email protected]<mailto:[email protected]>> Date: Thursday, October 16, 2014 12:11 PM To: 임솔 <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[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]> [mailto:[email protected]] On Behalf Of ?? Sent: Thursday, October 16, 2014 12:06 PM To: [email protected]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
