Can you send the full terminal output from when you run dt_recon with
the nifti as input?

On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> How was DTI.nii.gz created? DTI.nii.gz was converted from the raw
> dicom data using dcm2nii.
>
> Response for: "What happens if you run mri_info DTI.nii.gz"
>
> Volume information for DTI.nii.gz
>
>           type: nii
>
>     dimensions: 128 x 128 x 70 x 65
>
>    voxel sizes: 2.0000, 2.0000, 2.0000
>
>           type: FLOAT (3)
>
>            fov: 256.000
>
>            dof: 0
>
>         xstart: -128.0, xend: 128.0
>
>         ystart: -128.0, yend: 128.0
>
>         zstart: -70.0, zend: 70.0
>
>             TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> angle: 0.00 degrees
>
>        nframes: 65
>
>        PhEncDir: UNKNOWN
>
> ras xform present
>
>     xform info: x_r =  -0.9999, y_r =   0.0116, z_r =  -0.0028, c_r =
>   -0.4290
>
>               : x_a =   0.0116, y_a =   0.9999, z_a =  -0.0011, c_a =
>     4.1548
>
>               : x_s =  -0.0028, y_s =   0.0011, z_s =   1.0000, c_s =
>   30.9622
>
> Orientation   : LAS
>
> Primary Slice Direction: axial
>
> voxel to ras transform:
>
>                -1.9999   0.0232 -0.0057   126.2761
>
>                 0.0232   1.9999 -0.0021  -125.2474
>
>                -0.0057   0.0022 2.0000   -38.8153
>
>                 0.0000   0.0000 0.0000     1.0000
>
> voxel-to-ras determinant -8
>
> ras to voxel transform:
>
>                -0.5000   0.0058 -0.0014    63.8052
>
>                 0.0058   0.5000 0.0005    61.9083
>
>                -0.0014  -0.0005 0.5000    19.5206
>
>                 0.0000   0.0000 0.0000     1.0000
>
>
> On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve

> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>     How was DTI.nii.gz created? What happens if you run
>     mri_info DTI.nii.gz
>
>     If the DICOM is a siemens dicom but has been stripped of special
>     siemens
>     info, then we cannot unpack it
>
>
>     On 03/15/2016 02:02 PM, Jasmin Alves wrote:
>     >
>     > Still get the same error:
>     >
>     > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
>     > contain a Siemens ASCII header
>     >
>     > has this file been anonymized?
>     >
>     > ERROR: cannot unpack mosiacs without ASCII header
>     >
>     >
>     > The error I get when running in nifti format is actually found
>     in the
>     > log file.
>     >
>     >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a dicom
>     > file or some other problem
>     >
>     >
>     >
>     >
>     > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
>     > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu

>     <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>     >
>     >     if you run
>     >     mri_convert 00010001 deleteme.nii
>     >     what happens?
>     >
>     >     what is the error when running with nifti?
>     >
>     >
>     >     On 03/14/2016 05:59 PM, Jasmin Alves wrote:
>     >     >
>     >     > Dear Freesurfer experts,
>     >     >
>     >     > FREESURFER_HOME: /Applications/freesurfer
>     >     >
>     >     > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>     >     >
>     >     > Kernel info: Darwin 14.5.0 x86_64
>     >     >
>     >     >
>     >     > I received the following error while running the dt_recon --i
>     >     00010001
>     >     > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
>     >     >
>     >     > The participant is 40.
>     >     >
>     >     > And I received the following error:
>     >     >
>     >     > WARNING: file /Users/jasminalves/Desktop/data/40/00010001
>     does not
>     >     > contain a Siemens ASCII header has this file been anonymized?
>     >     >
>     >     > ERROR: cannot unpack mosiacs without ASCII header
>     >     >
>     >     >
>     >     > I did notice on previous threads this is a common error
>     that occurs,
>     >     > but the files I have were directly exported from our
>     siemens scanner
>     >     > via Osirix. I also tried running dt_recon using nifti
>     format but
>     >     that
>     >     > resulted in an error as well. Is there anything else I can do?
>     >     >
>     >     > Thanks,
>     >     >
>     >     > Jasmin
>     >     >
>     >     >
>     >     > --
>     >     > Jasmin Alves
>     >     > Predoctoral Student
>     >     > Medical Biology Graduate Program
>     >     > University of Southern California
>     >     > jalves@usc.edu <mailto:jalves@usc.edu>
>     <mailto:jalves@usc.edu <mailto:jalves@usc.edu>>
>     <mailto:jalves@usc.edu <mailto:jalves@usc.edu>

>     >     <mailto:jalves@usc.edu <mailto:jalves@usc.edu>>>
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>     >     MGH-NMR Center
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>     > --
>     > Jasmin Alves
>     > Predoctoral Student
>     > Medical Biology Graduate Program
>     > University of Southern California
>     >jalves@usc.edu <mailto:jalves@usc.edu> <mailto:jalves@usc.edu
>     <mailto:jalves@usc.edu>>
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