On Sep 30, 2021, at 12:52 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

What happens when you convert run 12, which has 70 volumes?

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edu>
Sent: Thursday, September 30, 2021 12:41 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] unpacking Diffusion data

 

Hi,

The data was collected in MGH main campus, with Siemens Skyra. 

When I look at the data in PACS system, I see that runs 13, 14, 15, 16 have full volumes (74 volumes) and I can go through all the slices of the brain. However, when I look at the unpacked data, it only has one volume, The scan info I sent you, is acquired with "unpacksdcmdir -src  -targ . -scanonly scan.info” command in Freesurfer. I think it hasn’t been able to unpack the data properly, and that’s why when I look at the data in freeview, I don’t see all the volumes.

Thanks,

Mona

Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow

Department of Psychiatry | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

On Sep 30, 2021, at 12:27 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

Hi Zahra - What scanner/sequence was this scan collected with? From your scan info below, it looks like run IM01113 has dimensions: 110 x 110 x 74 x 1. This means only 1 volume, so it's not a full diffusion series. What does it look like when you open it in a viewer, like freeview?

Anastasia.

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edu>
Sent: Wednesday, September 8, 2021 12:46 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] unpacking Diffusion data

 

Hello Freesurfers,

I have  6 runs of DTI data per subject in a sample of 50, and I want to unpack the dicoms, so it outputs the bval bvec values, to use in dt_recon.

I realized I can use either dcm2nii or mri_convert to do this.

Could you please let me know what the command should be? and also should I do it separately for each run? subject’s scan info is attached.

I used the below command in dev environment but didn’t get any bval bvec values. 

mri_convert /${subj}/IMAGES/IM01113 /${subj}/DTI/IM_13.nii

Appreciate your help.

Mona

1            Localizer  ok  512 512  13   1 IM00269

  2      SagT2FLAIRSPACE  ok  512 512 176   1 IM00273

  3      SagT2FLAIRSPACE  ok  512 512 171   1 IM02084

  4 SagT1MPRAGE1mmiso_P3  ok  256 256 176   1 IM00449

  5      SagT2FLAIRSPACE  ok  512 512 227   1 IM02311

  6 SagT1MPRAGE1mmiso_P3  ok  256 256 171   1 IM02482

  7 SagT1MPRAGE1mmiso_P3  ok  256 256 239   1 IM02721

  8            AxWaveSWI  ok  288 252  88   1 IM00793

  9            AxWaveSWI  ok  288 252  88   1 IM00881

 10            AxWaveSWI  ok  288 252  81   1 IM00705

 11            AxWaveSWI  ok  288 252  88   1 IM00969

 12            Diffusion  ok  990 990   1  70 IM00970

 13            Diffusion  ok  110 110  74   1 IM01113

 14            Diffusion  ok  110 110  74   1 IM01187

 15            Diffusion  ok  110 110  74   1 IM01261

 16            Diffusion  ok  110 110  74   1 IM01335

 17            Diffusion  ok  110 110   1  74 IM01336

Zahra (Mona) Nasiriavanaki, M.D.

Postdoctoral Research Fellow

Department of Psychiatry | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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