Hi Derek, Did you or the administrators change something in bedpostx script ?
I cannot find these error messages in FSL 5.0.8. Moises. On 3 April 2015 at 01:27, Archer,Derek B <arche...@ad.ufl.edu> wrote: > Hi Stam, > > > I got the FSL version updated (5.0.8) on the cluster, and am attempting > to process this data, however, I am getting an error. > > > *Line of code:* > > *bedpostx <subject_dir> --cnonlinear -model 2 --rician -g * > > > *The error is as follows: * > > *"Checking **for slices to be processed.* > > *All slices have been previously processed. Skipping slice processing stage."* > > I have not run bedpostx before today on this subject, so I'm confused why > this is occurring. Is there something I'm missing? > > Thanks, > > Derek > > > ------------------------------ > *From:* Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk> > *Sent:* Friday, February 27, 2015 10:45 AM > > *To:* Archer,Derek B > *Cc:* hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] Processing Diffusion MRI Data > > Hi Derek > > With the default burn-in period (b=1000 iterations), on a CPU cluster > you should expect ~10 hours per subject. We are using a GPU cluster, so it > takes us much less than that. > > It’s unrealistic to proceed without any parallelisation or GPU > acceleration (you would be looking into many days per subject). > > Cheers > Stam > > > > > On 27 Feb 2015, at 15:38, Archer,Derek B <arche...@ad.ufl.edu> wrote: > > Hi Matt, > > What computational time do you typically expect for bedpostx to run on > the diffusion data? (With no parallelization.) > > Thanks, > Derek Archer > > *From:* Glasser, Matthew [mailto:glass...@wusm.wustl.edu > <glass...@wusm.wustl.edu>] > *Sent:* Tuesday, February 17, 2015 12:55 PM > *To:* Archer,Derek B; Stamatios Sotiropoulos; > hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] Processing Diffusion MRI Data > > Are you running the command on ${StudyFolder}/${Subject}/T1w/Diffusion ? > > You’ll need the latest version of FSL 5.0.8 on your cluster as well. > > Peace, > > Matt. > > *From: *<Archer>, Derek B <arche...@ad.ufl.edu> > *Date: *Tuesday, February 17, 2015 at 11:53 AM > *To: *Matt Glasser <glass...@wusm.wustl.edu>, Stamatios Sotiropoulos < > stamatios.sotiropou...@ndcn.ox.ac.uk>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > *Subject: *RE: [HCP-Users] Processing Diffusion MRI Data > > Hi Matt, > > The exact command I’m using locally is (I tried this from Stam’s input): > > bedpostx <subject directory> –n 3 –model 2 –g –rician > > Subject directory contents: > bvals > bvecs > data.nii.gz > nodif_brain_mask.nii.gz > grad_dev.nii.gz > > This works. How long do you estimate this will take? Because the –g > option is not available on the cluster I am working on (not sure why this > is the case..), and I think that may be causing the issue. > > Thanks, > Derek > *From:* Glasser, Matthew [mailto:glass...@wusm.wustl.edu > <glass...@wusm.wustl.edu>] > *Sent:* Tuesday, February 17, 2015 12:47 PM > *To:* Archer,Derek B; Stamatios Sotiropoulos; > hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] Processing Diffusion MRI Data > > How about posting the exact command line you are using and a listing of > the contents of <subject_directory> > > Peace, > > Matt. > > *From: *<Archer>, Derek B <arche...@ad.ufl.edu> > *Date: *Tuesday, February 17, 2015 at 9:20 AM > *To: *Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk>, " > hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *Re: [HCP-Users] Processing Diffusion MRI Data > > > 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:stamatios.sotiropou...@ndcn.ox.ac.uk > <stamatios.sotiropou...@ndcn.ox.ac.uk>] > *Sent:* Monday, February 16, 2015 12:48 PM > *To:* Archer,Derek B > *Cc:* hcp-users@humanconnectome.org > *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 <arche...@ad.ufl.edu> wrote: > > > > > Matt, > > Thanks for the fast reply. I will use these three inputs in bedpostX. > > Derek > > *From:* Glasser, Matthew [mailto:glass...@wusm.wustl.edu > <glass...@wusm.wustl.edu>] > *Sent:* Monday, February 16, 2015 11:24 AM > *To:* Archer,Derek B; hcp-users@humanconnectome.org > *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 <arche...@ad.ufl.edu> > *Date: *Monday, February 16, 2015 at 9:16 AM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *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 > HCP-Users@humanconnectome.org > 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. 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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. > > ------------------------------ > 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. 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