Hi Andrade,
I'm adding the FreeSurfer support list so other can benefit.
To answer your question, you would use the first dicom from the diffusion scan... but since you don't have the dicoms that won't work. You can combine all of the DTI nifty files into one multi-frame diffusion 4d volume using mri_concat.
mri_concat /path/to/all/IXI025-Guys-0852-DTI-??.nii.gz --o /output/path/dti.mgz
Then run dt_recon using dti.mgz as your input.
cd /path/to/desired/subjects/dir export SUBJECTS_DIR=$(pwd) dt_recon --b /path/to/bvals.txt /path/to/bvecs.txt--i /path/to/dti.mgz --s andrade --o /path/to/desired/diffusion/output
Let me know if this works.
Best, Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
________________________________________ From: Renew Andrade andraderenew@yahoo.com Sent: Thursday, December 20, 2018 10:12:31 AM To: Diamond, Bram Ryder Subject: Re: FreeSurfer: trouble processing subjects
External Email - Use Caution
I don'tknow if I understand right. I don't have a dicom format file for dtrecons. What I have is nii.gz all that I gave you. In case I need to do dcmunpack either way I need to do dtrecons for each of those dcmunpack or just the first one?
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On 20 Dec 2018, at 15:46, Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu wrote:
Hi Andrade,
You should be submitting the IXI025-Guys-0852-T1.nii.gz for recon-all. This seems to be working fine with freesurfer v6.0 on my machine.
cd /path/to/desired/subjects/dir export SUBJECTS_DIR=$(pwd) recon-all -i /path/to/IXI025-Guys-0852-T1.nii.gz -s andrade -all
For the diffusion scan, you will want to run it through dt_recon. If you have the raw dcms, it would easiest to use one of those as input rather than combine all of your directions into one multi-frame volume. You can run unpacksdcmdir to get the first dcm of the diffusion scan.
cd /path/to/desired/subjects/dir export SUBJECTS_DIR=$(pwd) unpacksdcmdir -src /path/to/dicom/dir -targ /path/to/desired/log/output/ -scanonly unpack.log dt_recon --b /path/to/bvals.txt /path/to/bvecs.txt--i path/to/first/diffusion/dicom.dcm --s andrade --o /path/to/desired/diffusion/output
I hope this helps.
Best, Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
From: Renew Andrade andraderenew@yahoo.com Sent: Wednesday, December 19, 2018 3:13:18 PM To: Diamond, Bram Ryder Subject: Re: FreeSurfer: trouble processing subjects
External Email - Use CautionI sent you the whole information but the problem rises in processing with recon-all the DTI files.
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On 19 Dec 2018, at 16:54, Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu wrote:
Good morning, Andrade.
I received a message from Bruce that suggests you are having trouble processing a few of your subjects. We received the following file from you via the Martinos Center FileDrop: IXI025-Guys-0852-DTI-16.nii.gz IXI025-Guys-0852-DTI-14.nii.gz IXI025-Guys-0852-DTI-15.nii.gz IXI025-Guys-0852-DTI-13.nii.gz IXI025-Guys-0852-DTI-12.nii.gz IXI025-Guys-0852-DTI-10.nii.gz IXI025-Guys-0852-DTI-09.nii.gz IXI025-Guys-0852-DTI-11.nii.gz IXI025-Guys-0852-DTI-08.nii.gz IXI025-Guys-0852-DTI-07.nii.gz IXI025-Guys-0852-DTI-05.nii.gz IXI025-Guys-0852-DTI-06.nii.gz IXI025-Guys-0852-DTI-04.nii.gz IXI025-Guys-0852-DTI-03.nii.gz IXI025-Guys-0852-DTI-02.nii.gz IXI025-Guys-0852-DTI-01.nii.gz IXI025-Guys-0852-DTI-00.nii.gz bvecs.txt bvals.txt IXI025-Guys-0852-T1.nii.gz
They seem to be a separated diffusion scan (along with bvec and bcal files), and a T1. In order for me to help you, I need to know what exactly you are having trouble with.
Thanks, Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
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