You could register another subject's segmentation to your subjects, but having
the individual segmentations is ideal.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Renew Andrade
<andradere...@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
External Email - Use Caution
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.edu<http://nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu>> on behalf
of Renew Andrade
<andradere...@yahoo.com<http://yahoo.com>>
Sent: Friday, October 18, 2019 5:02:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto: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 Caution
>
> Dear 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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