Re: [Freesurfer] error while running dt-recon all

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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> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
>jalves@usc.edu <mailto:jalves@usc.edu> <mailto:jalves@usc.edu
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--
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greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

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

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