Dear HCP team members, Thank you so much for your valuable inputs, the freesurfer analysis is up and running again! I did not know that I had to set up environment for freesurfer to run. Only made changes to the FreeSurferPipelineBatch.sh as directed by the installation and usage page. Thank you again for your time and patience.
Kind regards, Sampada On Tue, Feb 17, 2015 at 11:55 AM, <[email protected]> wrote: > Send HCP-Users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of HCP-Users digest..." > > > Today's Topics: > > 1. Re: Processing Diffusion MRI Data (Archer,Derek B) > 2. Regarding: FreeSurfer: recon-all: command not found > (Dr Sampada Sinha) > 3. Re: Regarding: FreeSurfer: recon-all: command not found > (Donna Dierker) > 4. Re: Processing Diffusion MRI Data (Glasser, Matthew) > 5. Re: Regarding: FreeSurfer: recon-all: command not found > (Glasser, Matthew) > 6. Re: Processing Diffusion MRI Data (Glasser, Matthew) > 7. Re: Processing Diffusion MRI Data (Archer,Derek B) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 17 Feb 2015 15:20:56 +0000 > From: "Archer,Derek B" <[email protected]> > Subject: Re: [HCP-Users] Processing Diffusion MRI Data > To: Stamatios Sotiropoulos <[email protected]>, > "[email protected]" <[email protected]> > Message-ID: > <ff208477c5853f498cf288adb02491a34d9af...@ufexch-mbxn03.ad.ufl.edu > > > Content-Type: text/plain; charset="us-ascii" > > > 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]] > 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]<mailto: > [email protected]>> wrote: > > > Matt, > > Thanks for the fast reply. I will use these three inputs in bedpostX. > > Derek > > From: Glasser, Matthew [mailto:[email protected]] > Sent: Monday, February 16, 2015 11:24 AM > To: Archer,Derek B; [email protected]<mailto: > [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]<mailto:[email protected]>> > Date: Monday, February 16, 2015 at 9:16 AM > To: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[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]<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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150217/db6c01a6/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Tue, 17 Feb 2015 11:14:49 -0600 > From: Dr Sampada Sinha <[email protected]> > Subject: [HCP-Users] Regarding: FreeSurfer: recon-all: command not > found > To: [email protected] > Message-ID: > <CADmLBZ3453mT40tMTMfu+= > [email protected]> > Content-Type: text/plain; charset="utf-8" > > Dear HCP team members, > > Sorry for bothering you all again. But this time the analysis got stuck in > its initial FreeSurfer processing with the following error: > > > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh: > line 78: recon-all: command not found. > > Ful details of the error is given below: > > xxx@ndy10 > [/xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/Examples/Scripts] % > ./FreeSurferPipelineBatch.shThis script must be SOURCED to correctly setup > the environment prior to running any of the other HCP scripts contained > here > > LS2001 > About to use fsl_sub to queue or run > > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh > > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh: > line 78: recon-all: command not found > set -- --subject=LS2001 > --subjectDIR=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w > --t1=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w/T1w_acpc_dc_restore.nii.gz > > --t1brain=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w/T1w_acpc_dc_restore_brain.nii.gz > --t2=/xxx/xxx/xxx/xxx/HCP_data/LS2001//T1w/T2w_acpc_dc_restore.nii.gz > --printcom= > . > > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/Examples/Scripts/SetUpHCPPipeline.sh > > *Also, will you please let me know if there are separate scripts for the > analysis of lifespan data without the gradient distortion correction. * > > Thank you so much for your patience and your time? > > With kind regards, > > Sampada > > -- > Sampada Sinha > Post-Doctoral Associate > University of Minnesota (East Bank) > Molecular and neuroimaging laboratory > Department of Psychiatry > Minneapolis-55415 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150217/4e2315f3/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Tue, 17 Feb 2015 11:47:28 -0600 > From: Donna Dierker <[email protected]> > Subject: Re: [HCP-Users] Regarding: FreeSurfer: recon-all: command not > found > To: Dr Sampada Sinha <[email protected]> > Cc: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=windows-1252 > > Sounds like it can't find the freesurfer executables. This page might > help: > > https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration > > > On Feb 17, 2015, at 11:14 AM, Dr Sampada Sinha <[email protected]> > wrote: > > > Dear HCP team members, > > > > Sorry for bothering you all again. But this time the analysis got stuck > in its initial FreeSurfer processing with the following error: > > > > > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh: > line 78: recon-all: command not found. > > > > Ful details of the error is given below: > > > > xxx@ndy10 > [/xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/Examples/Scripts] % > ./FreeSurferPipelineBatch.shThis script must be SOURCED to correctly setup > the environment prior to running any of the other HCP scripts contained here > > > > LS2001 > > About to use fsl_sub to queue or run > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh > > > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh: > line 78: recon-all: command not found > > set -- --subject=LS2001 > --subjectDIR=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w > --t1=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w/T1w_acpc_dc_restore.nii.gz > > --t1brain=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w/T1w_acpc_dc_restore_brain.nii.gz > --t2=/xxx/xxx/xxx/xxx/HCP_data/LS2001//T1w/T2w_acpc_dc_restore.nii.gz > --printcom= > > . > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/Examples/Scripts/SetUpHCPPipeline.sh > > > > Also, will you please let me know if there are separate scripts for the > analysis of lifespan data without the gradient distortion correction. > > > > Thank you so much for your patience and your time? > > > > With kind regards, > > > > Sampada > > > > -- > > Sampada Sinha > > Post-Doctoral Associate > > University of Minnesota (East Bank) > > Molecular and neuroimaging laboratory > > Department of Psychiatry > > Minneapolis-55415 > > > > > > > > > > > > > > > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > > ------------------------------ > > Message: 4 > Date: Tue, 17 Feb 2015 17:47:26 +0000 > From: "Glasser, Matthew" <[email protected]> > Subject: Re: [HCP-Users] Processing Diffusion MRI Data > To: "Archer,Derek B" <[email protected]>, Stamatios Sotiropoulos > <[email protected]>, > "[email protected]" <[email protected]> > Message-ID: <d108daaf.e7d30%[email protected]> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150217/701d8818/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Tue, 17 Feb 2015 17:49:09 +0000 > From: "Glasser, Matthew" <[email protected]> > Subject: Re: [HCP-Users] Regarding: FreeSurfer: recon-all: command not > found > To: Donna Dierker <[email protected]>, Dr Sampada Sinha > <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <d108db17.e7d3c%[email protected]> > Content-Type: text/plain; charset="Windows-1252" > > What are your environment variables immediately before calling the main > FreeSurfer.sh pipeline script? > > Peace, > > Matt. > > > On 2/17/15, 11:47 AM, "Donna Dierker" <[email protected]> wrote: > > >Sounds like it can't find the freesurfer executables. This page might > >help: > > > >https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration > > > > > >On Feb 17, 2015, at 11:14 AM, Dr Sampada Sinha <[email protected]> > >wrote: > > > >> Dear HCP team members, > >> > >> Sorry for bothering you all again. But this time the analysis got stuck > >>in its initial FreeSurfer processing with the following error: > >> > >> > >>/xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPi > >>peline.sh: line 78: recon-all: command not found. > >> > >> Ful details of the error is given below: > >> > >> xxx@ndy10 > >>[/xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/Examples/Scripts] % > >>./FreeSurferPipelineBatch.shThis script must be SOURCED to correctly > >>setup the environment prior to running any of the other HCP scripts > >>contained here > >> > >> LS2001 > >> About to use fsl_sub to queue or run > >>/xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPi > >>peline.sh > >> > >>/xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPi > >>peline.sh: line 78: recon-all: command not found > >> set -- --subject=LS2001 > >>--subjectDIR=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w > >>--t1=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w/T1w_acpc_dc_restore.nii.gz > >> > >>--t1brain=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w/T1w_acpc_dc_restore_brain. > >>nii.gz > >>--t2=/xxx/xxx/xxx/xxx/HCP_data/LS2001//T1w/T2w_acpc_dc_restore.nii.gz > >> --printcom= > >> . > >>/xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/Examples/Scripts/SetUpH > >>CPPipeline.sh > >> > >> Also, will you please let me know if there are separate scripts for the > >>analysis of lifespan data without the gradient distortion correction. > >> > >> Thank you so much for your patience and your time? > >> > >> With kind regards, > >> > >> Sampada > >> > >> -- > >> Sampada Sinha > >> Post-Doctoral Associate > >> University of Minnesota (East Bank) > >> Molecular and neuroimaging laboratory > >> Department of Psychiatry > >> Minneapolis-55415 > >> > >> > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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 > > > ________________________________ > 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. > > > > ------------------------------ > > Message: 6 > Date: Tue, 17 Feb 2015 17:55:24 +0000 > From: "Glasser, Matthew" <[email protected]> > Subject: Re: [HCP-Users] Processing Diffusion MRI Data > To: "Archer,Derek B" <[email protected]>, Stamatios Sotiropoulos > <[email protected]>, > "[email protected]" <[email protected]> > Message-ID: <d108dc7e.e7d55%[email protected]> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150217/a31d4f70/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Tue, 17 Feb 2015 17:53:56 +0000 > From: "Archer,Derek B" <[email protected]> > Subject: Re: [HCP-Users] Processing Diffusion MRI Data > To: "Glasser, Matthew" <[email protected]>, Stamatios > Sotiropoulos <[email protected]>, > "[email protected]" <[email protected]> > Message-ID: > <ff208477c5853f498cf288adb02491a34d9af...@ufexch-mbxn03.ad.ufl.edu > > > Content-Type: text/plain; charset="us-ascii" > > 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:[email protected]] > Sent: Tuesday, February 17, 2015 12:47 PM > To: Archer,Derek B; Stamatios Sotiropoulos; [email protected] > 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 <[email protected]<mailto:[email protected]>> > Date: Tuesday, February 17, 2015 at 9:20 AM > To: Stamatios Sotiropoulos <[email protected]<mailto: > [email protected]>>, "[email protected] > <mailto:[email protected]>" <[email protected] > <mailto:[email protected]>> > 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:[email protected]] > Sent: Monday, February 16, 2015 12:48 PM > To: Archer,Derek B > Cc: [email protected]<mailto:[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]<mailto: > [email protected]>> wrote: > > > > Matt, > > Thanks for the fast reply. I will use these three inputs in bedpostX. > > Derek > > From: Glasser, Matthew [mailto:[email protected]] > Sent: Monday, February 16, 2015 11:24 AM > To: Archer,Derek B; [email protected]<mailto: > [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]<mailto:[email protected]>> > Date: Monday, February 16, 2015 at 9:16 AM > To: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[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]<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 > > > _______________________________________________ > 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. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150217/0b76ea11/attachment.html > > ------------------------------ > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > End of HCP-Users Digest, Vol 27, Issue 28 > ***************************************** > -- Sampada Sinha Post-Doctoral Associate University of Minnesota (East Bank) Molecular and neuroimaging laboratory Department of Psychiatry Minneapolis-55415 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
