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.infohttp://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.edumailto: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.

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

the unpacked run 12 has full volume and I can go through all the slices in freeview.

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 12:52 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

What happens when you convert run 12, which has 70 volumes? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Thursday, September 30, 2021 12:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.infohttp://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.edumailto: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.

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

_______________________________________________ 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

No, actually it has all the 74 slices.

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 3:00 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Just 1 volume? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Thursday, September 30, 2021 12:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] unpacking Diffusion data

the unpacked run 12 has full volume and I can go through all the slices in freeview.

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 12:52 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

What happens when you convert run 12, which has 70 volumes? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Thursday, September 30, 2021 12:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.infohttp://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.edumailto: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.

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

_______________________________________________ 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