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In other words I cannot process TRACULA without the T1w images of my subjects? Because this Parkinson database is from NITRC and I only have the diffusion images not the T1. I can practice on other subjects that I have both the T1 and diffusion images but I was expecting on using this Parkinson tractography and do the analysis. In case you want to know is this https://www.nitrc.org/projects/parktdi/ https://www.nitrc.org/projects/parktdi/. Sincerely, Andrade.
Hi, you need to run recon-all on the T1, not on the diffusion scan. This will produce an anatomical segmentation of each subject based on the T1s, which TRACULA will then use to extract anatomical priors on white matter tracts, to aid tractography. When you run trac-all to do the actual tractography, then you run it on the diffusion scan. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Renew Andrade andradere...@yahoo.com Sent: Friday, October 18, 2019 5:02:35 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Learning dti processing tutorial
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I am using a database of NITRC repository https://www.nitrc.org/projects/parktdi/ https://www.nitrc.org/projects/parktdi/ . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don’t know if it is MPRAGE or not. Can you help me?
What is the input file that you are supplying? Often this happens when the input it a multi-echo MPRAGE. If so, you can run mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to recon-all
On 10/12/2019 4:48 PM, Renew Andrade wrote:
External Email - Use CautionDear freesurfer experts: I am trying to learn dti processing. For using Tracula it appears there is a need for running "recon-all -all -i -s” on every subject before starting to run Tracula. But there seems to be a problem. I have a Parkinson dwi images database and every subject gives me an error of the type “input(s) cannot have multiple frames!”. I am a little bit stuck on this step. Is it a problem of the file as input? Am I putting the wrong file? Can it be done a recon-all analysis to a dwi image? With trackvis I can obtain the results without any problem. My doubt comes from FreeSurfer only and may be my little knowledge about it. Thanks for your help! Sincerely, Andrade.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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You could register another subject's segmentation to your subjects, but having the individual segmentations is ideal. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Renew Andrade andraderenew@yahoo.com Sent: Thursday, October 24, 2019 9:53 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Learning dti processing tutorial
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In other words I cannot process TRACULA without the T1w images of my subjects? Because this Parkinson database is from NITRC and I only have the diffusion images not the T1. I can practice on other subjects that I have both the T1 and diffusion images but I was expecting on using this Parkinson tractography and do the analysis. In case you want to know is this https://www.nitrc.org/projects/parktdi/. Sincerely, Andrade.
Hi, you need to run recon-all on the T1, not on the diffusion scan. This will produce an anatomical segmentation of each subject based on the T1s, which TRACULA will then use to extract anatomical priors on white matter tracts, to aid tractography. When you run trac-all to do the actual tractography, then you run it on the diffusion scan. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.eduhttp://nmr.mgh.harvard.edu> on behalf of Renew Andrade <andradere...@yahoo.comhttp://yahoo.com> Sent: Friday, October 18, 2019 5:02:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Learning dti processing tutorial
External Email - Use Caution
I am using a database of NITRC repository https://www.nitrc.org/projects/parktdi/ . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don’t know if it is MPRAGE or not. Can you help me?
What is the input file that you are supplying? Often this happens when the input it a multi-echo MPRAGE. If so, you can run mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to recon-all
On 10/12/2019 4:48 PM, Renew Andrade wrote:
External Email - Use CautionDear freesurfer experts: I am trying to learn dti processing. For using Tracula it appears there is a need for running "recon-all -all -i -s” on every subject before starting to run Tracula. But there seems to be a problem. I have a Parkinson dwi images database and every subject gives me an error of the type “input(s) cannot have multiple frames!”. I am a little bit stuck on this step. Is it a problem of the file as input? Am I putting the wrong file? Can it be done a recon-all analysis to a dwi image? With trackvis I can obtain the results without any problem. My doubt comes from FreeSurfer only and may be my little knowledge about it. Thanks for your help! Sincerely, Andrade.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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