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=$(pwd)
dt_recon --b /path/to/bvals.txt /path/to/bvecs.txt--i /path/to/dti.mgz --s
andrade --o /path/to/desired/diffusion/output
Let me know if this works.
Best,
Bram
Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598
________________________________________
From: Renew Andrade <andradere...@yahoo.com>
Sent: Thursday, December 20, 2018 10:12:31 AM
To: Diamond, Bram Ryder
Subject: Re: FreeSurfer: trouble processing subjects
External Email - Use Caution
I don'tknow if I understand right. I don't have a dicom format file for
dtrecons. What I have is nii.gz all that I gave you. In case I need to do
dcmunpack either way I need to do dtrecons for each of those dcmunpack or just
the first one?
Sent from my iPhone
> On 20 Dec 2018, at 15:46, Diamond, Bram Ryder <brdiam...@mgh.harvard.edu>
> wrote:
>
> Hi Andrade,
>
> You should be submitting the IXI025-Guys-0852-T1.nii.gz for recon-all. This
> seems to be working fine with freesurfer v6.0 on my machine.
>
> cd /path/to/desired/subjects/dir
> export SUBJECTS_DIR=$(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 <andradere...@yahoo.com>
> Sent: Wednesday, December 19, 2018 3:13:18 PM
> To: Diamond, Bram Ryder
> Subject: Re: FreeSurfer: trouble processing subjects
>
> External Email - Use Caution
>
> I sent you the whole information but the problem rises in processing with
> recon-all the DTI files.
>
> Sent from my iPhone
>
>> On 19 Dec 2018, at 16:54, Diamond, Bram Ryder <brdiam...@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
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
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>>
>
>
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