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:
- scan log generated by dcmunpack (Kan Ding)
- Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (Bruce Fischl)
- Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (srishti goel)
- Qdec+Table format issue ????? (Dimitrios Trifonopoulos)
- Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (Bruce Fischl)
- Re: recon-all: exited with errors (whit matter peak at 110, cannot allocate memory) (srishti goel)
- Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (Bruce Fischl)
- Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (srishti goel)
- Re: recon-all: exited with errors (white matterpeak at 110, cannot allocate memory) (Bruce Fischl)
- Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (srishti goel)
- Re: recon-all: exited with errors (white matter peak at 110, cannot allocate memory) (Bruce Fischl)
- Re: mri_vol2surf: unable to compare volume maps (Douglas N. Greve)
- Re: scan log generated by dcmunpack (Douglas N. Greve)
- Time Series to Surface (Crawford, Anna)
- Tracula - Could not find satisfactory control point fit (Lussier,Desiree)
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
UT Southwestern
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