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

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> 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>>
>
>
>
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--
Douglas N. Greve, Ph.D.
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

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