So the dicom did not come from the scanner? You can use that nifti file as input instead, but you should view it in freeview to make sure it is oriented correctly

On 04/05/2018 03:46 PM, Kan Ding wrote:

The data has been analyzed. The scan information from corresponding NIFTI file as following:

nua502608:3T8619 kding$ mri_info 3T8619_T1.nii.gz Volume information for 3T8619_T1.nii.gz type: nii dimensions: 160 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 160.000 dof: 0 xstart: -80.0, xend: 80.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = 0.0107 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 7.8592 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -15.4014 Orientation : LPS Primary Slice Direction: axial

voxel to ras transform: -1.0000 -0.0000 -0.0000 80.0107 -0.0000 -1.0000 -0.0000 135.8592 0.0000 0.0000 1.0000 -143.4014 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 1

ras to voxel transform: -1.0000 0.0000 0.0000 80.0107 0.0000 -1.0000 0.0000 135.8592 0.0000 0.0000 1.0000 143.4014 0.0000 0.0000 0.0000 1.0000

Date: Thu, 5 Apr 2018 12:59:16 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] scan log generated by dcmunpack To: freesurfer@nmr.mgh.harvard.edu Message-ID: 22ecfa88-e463-169b-03c5-4c25ac2244db@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"; format=flowed

It looks like there is something wrong with that dicom file/series because the pixel spacing is "unknown". Where did the dicoms from from? Have they been anonymized?

On 04/05/2018 12:12 PM, Kan Ding wrote:

...

Hello:

I am trying to unpack my DICOM folder and run recon-all. After dcmunpack, I selected 301 to run recon-all. But the recon-all didn?t go through. Please see the attached scan.log, recon-all.log, error.log, and the pic of my DICOM folder.

Thank you so mch.

Kan Ding, MD

On 4/5/18, 3:21 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu" <reesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu> wrote:

...

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Today's Topics:

1. scan log generated by dcmunpack (Kan Ding)
2. Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (Bruce Fischl)
3. Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (srishti goel)
4. Qdec+Table format issue ????? (Dimitrios Trifonopoulos)
5. Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (Bruce Fischl)
6. Re: recon-all: exited with errors (whit matter peak at 110, cannot allocate memory) (srishti goel)
7. Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (Bruce Fischl)
8. Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (srishti goel)
9. Re: recon-all: exited with errors (white matterpeak at 110, cannot allocate memory) (Bruce Fischl)
10. Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (srishti goel)
11. Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (Bruce Fischl)
12. Re: mri_vol2surf: unable to compare volume maps (Douglas N. Greve)
13. Re: scan log generated by dcmunpack (Douglas N. Greve)
14. Time Series to Surface (Crawford, Anna)
15. Tracula - Could not find satisfactory control point fit (Lussier,Desiree)

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Message: 1 Date: Thu, 5 Ap 2018 16:12:43 +0000 From: Kan Ding Kan.Ding@utsouthwestern.edu Subject: [Freesurfer] scan log generated by dcmunpack To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: D6EBC339.10FF3%kan.ding@utsouthwestern.edu Contnt-Type: text/plain; charset="iso-8859-1"

Hello:

I am trying to unpack my DICOM folder and run recon-all. After dcmunpack, I selected 301 to run recon-all. But the recon-all didn't go through. Please see the attached scan.log, recon-all.log, error.log, and the pic of my DICOM folder.

Thank you so much. Kan Din, MD Assistant Professor- Department of Neurology and Neurotherapeutics UT Southwestern Medical Center at Dallas Tel: 214-648-9197 Fax: 214-648-6320

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