hi stam, quick follow up here: does the current bedpostx_gpu (under 5.0.7/8) not support these flags?
a previous discussion on the fsl mailing list suggested that it did. cheers, satra On Tue, Feb 17, 2015 at 10:26 AM, Stamatios Sotiropoulos < [email protected]> wrote: > Hi Derek > > In the HCP released data, there is a T1w/Diffusion directory. > > If you do > > bedpostx T1w/Diffusion -n 3 -model 2 -g —rician > > that should run fine. Notice that even if you run that on a big cluster, > it will take a significant amount of time to finish because of the > dimensions of the data. We use a version of bedpostx on a GPU cluster to > run this analysis and this is what we will release, hopefully in the near > future. > > Best > Stam > > > On 17 Feb 2015, at 15:20, Archer,Derek B <[email protected]> wrote: > > > Hi Matt and Stam, > > I seem to still be having some sort of issue running bedpostx. I’m > using: > > bedpostx <subject_directory> --cnonlinear --rician --model=2 --nf=3. > > (The –g option is not available in my version of FSL (5.0.5). I am on a > cluster environment.) > > So when I run this line of code, I get the following error: > ** ERROR: nifti_convert_nhdr2nim: bad dim[0] > ** ERROR: (nifti_image_read): cannot create nifty image from header > ‘data’ > ** ERROR: nifti_image_open (data): bad header info > ** ERROR: failed to open file data > > The error seems to be with data.nii.gz, but is there error actually > occurring because I am not feeding in grad_dev.nii.gz via the –g option? Do > I need a newer version of FSL? > > Thanks, > Derek Archer > > *From:* Stamatios Sotiropoulos [ > mailto:[email protected] > <[email protected]>] > *Sent:* Monday, February 16, 2015 12:48 PM > *To:* Archer,Derek B > *Cc:* [email protected] > > *Subject:* Re: [HCP-Users] Processing Diffusion MRI Data > > Hi Derek > > Please notice that model=3 is not officially released yet in FSL. Also, > there should be a future HCP release in the near future including bedpostx > results, with the optimal parameters. > > Stam > > > > On 16 Feb 2015, at 16:25, Archer,Derek B <[email protected]> wrote: > > > Matt, > > Thanks for the fast reply. I will use these three inputs in bedpostX. > > Derek > > *From:* Glasser, Matthew [mailto:[email protected] > <[email protected]>] > *Sent:* Monday, February 16, 2015 11:24 AM > *To:* Archer,Derek B; [email protected] > *Subject:* Re: [HCP-Users] Processing Diffusion MRI Data > > Why do you need to use FLIRT/FNIRT with already registered data? As > for the others and aside from the flags you already mention, I think the > recommendation for bedpostX will include these flags: > > -n 3 (for 3 fibers) > --cnonlinear > --rician > --model=3 > > Not all of this may yet be available in the public release (you might > need to use --model=2 for now). > > Peace, > > Matt. > > *From: *<Archer>, Derek B <[email protected]> > *Date: *Monday, February 16, 2015 at 9:16 AM > *To: *"[email protected]" <[email protected]> > *Subject: *[HCP-Users] Processing Diffusion MRI Data > > Hello, > > I am trying to analyze the preprocessed diffusion data, however, I am > having some difficulties. Is there some documentation that I could look at > that outlines how to use bedpostx, FLIRT/FNIRT, DTIFIT and probtrackx with > this data? > > From what I’ve found in the archives, I need to do the following: > > Bedpostx: include the –g option > FLIRT/FNIRT: do I include any extra options here? > DTIFIT: include the –gradnonlin option > > Is this all that needs to be done to have this data ready for > tractography? Or are there steps that I have missed? > > Please let me know if there is any documentation I have failed to > locate. > > Thanks, > Derek Archer > > > > > _______________________________________________ > 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 > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
