I have a perl script that converts a Siemens fMRI DICOM mosaic series to a single 4D file (Analyze format), suitable for running with FSL. Let me know if you are interested.
Robert
----- Original Message ----
From: Najmeh Khalili M. <[log in to unmask]>
To: [log in to unmask]
Sent: Sunday, August 27, 2006 4:33:38 PM
Subject: Re: [FSL] dicom to nifti converter
Hi,
Thanks for all suggestions.
mri_convert works well on T1 and DTI files but, on
interleaved_mosaic-bold files, it gives
WARNING: Proper slice order not detected! Suggestion: use -siemens_dicom flag instead of -dicom as such:
INFO: no Siemens slice order reversal detected (good!).
...
Using "-it siemens_dicom" does not remove the warning message.
Also, mri_convert fails on convertion the localizer scans.
The error follows.
Image information
RunNo 0
SeriesNo 1
ImageNo 2
NImageRows 512
NImageCols 512
NFrames 1
SliceArraylSize 3
IsMosaic 0
ImgPos 141.3174 16.0232 142.4734
VolRes 0.5469 0.5469 12.0000
VolDim 512 512 3
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -0.0000 -1.0000
Vs -1.0000 -0.0000 0.0000
VolCenter -16.6826 16.0232 2.4734
TransferSyntaxUID unknown
INFO: no Siemens slice order reversal detected (good!).
warning: output volume axes are not orthogonal:i_dot_j =
0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000
i_ras = (-1, -0, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
writing to local.nii...
bad orientation matrix (determinant = 0) in nifti1 file
No such file or directory
ERROR: failure writing local.nii
Thanks,
Naj
On Thu, 24 Aug 2006, Doug Greve wrote:
> Hi Naj,
>
> I've written a tool that comes with freesurfer that will do this for you. You
> can use either the mri_convert binary or the unpacksdcmdir script. If
> mri_convert, then run it something like:
>
> mri_convert onefilefromseries.dcm f.nii
>
> where onefilefromseries.dcm is one of the files from the series (it will find
> the rest). You can have one or more series in a directory, and it will still
> work correctly.
>
> unpacksdcmdir will unpack one or dicom series into a structured directory
> tree (all of the dicom files need to be in one directory). It is basically a
> front-end for mri_convert.
>
> good luck.
>
> doug
>
>
>
>
>
> Najneh Khalili-Mahani wrote:
>
>> Greetings,
>>
>> I was wondering if there exists a command-line (linux) tool for converting
>> DICOM files to nifti (or analyze.)
>>
>> I have over 8000 DICOM files (Siemens) per subject, comprising of
>> anatomical, fMRI (mosaic interleaved), and DTI data, and I would like to
>> analyse the lot using FSL.
>> Any suggestion is much appreciated.
>>
>> Best,
>> Naj
>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [log in to unmask]
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
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