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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.
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Sorry, you will have to figure this out for yourself.
On 10/18/2019 5:02 PM, Renew Andrade wrote:
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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list 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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Renew Andrade andraderenew@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
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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
Renew Andrade -
Yendiki, Anastasia