mriconvert: mcverter outputs are not the same as MRI Convert outputs

Tue May 13 14:03:48 PDT 2014

Thanks Chuck and Jolinda,

We are using fsl nifti. I changed –f nifty to –f fsl and the output is as expected.

Thanks again for your help

Kind regards
Justin

JUSTIN CHANG | Business Portfolio Manager Research
Information and Communications Technology

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From: Chuck <chuckt at uoregon.edu<mailto:chuckt at uoregon.edu>>
Date: Wednesday, 14 May 2014 1:23 am
To: MRIConvert user's list <mriconvert at lists.uoregon.edu<mailto:mriconvert at lists.uoregon.edu>>
Cc: Justin Chang <justin.chang at sydney.edu.au<mailto:justin.chang at sydney.edu.au>>
Subject: Re: mriconvert: mcverter outputs are not the same as MRI Convert outputs

Hi Justin,

In the list of GUI settings below, there is no mention of the setting for output target format. This is a drop-down selector between the input display and the output display, and, in fact, defaults to "FSL NIfTI". Your command-line argument specifies canonical NIfTI. If you did not change the GUI to output "NIfTI", this would explain the difference in alignment in your outputs.

Regards,
Chuck

On 05/13/2014 02:51 AM, Justin Chang wrote:
Hi Jolinda,

Good question, I'm not sure?

How do I check?

Regards
Justin

JUSTIN CHANG | Business Portfolio Manager Research | Information and Communications Technology

THE UNIVERSITY OF SYDNEY
Level 3 Services Building G12 | The University of Sydney | NSW | 2006
P +61 2 9114 0516
E justin.chang at sydney.edu.au<mailto:justin.chang at sydney.edu.au>  | W  http://sydney.edu.au

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On 13 May 2014, at 7:18 pm, "jolinda at uoregon.edu<mailto:jolinda at uoregon.edu>" <jolinda at uoregon.edu<mailto:jolinda at uoregon.edu>> wrote:

Are you using the same output format in both cases, or fsl nifti in one case and vanilla nifti in the other?

Sent from my HTC

----- Reply message -----
From: "Justin Chang" <justin.chang at sydney.edu.au<mailto:justin.chang at sydney.edu.au>>
To: "mriconvert at lists.uoregon.edu<mailto:mriconvert at lists.uoregon.edu>" <mriconvert at lists.uoregon.edu<mailto:mriconvert at lists.uoregon.edu>>
Subject: mriconvert: mcverter outputs are not the same as MRI Convert outputs
Date: Tue, May 13, 2014 8:42 AM

Hi,

I have been comparing .nii outputs from mcverter and MRI Convert and I am unable to get mcverter outputs to match those produced using the MRI Convert GUI. It appears that mcverter is flipping the alignment .

The configurations I have been using for DICOM data (T1, T2 and DTI)

T1 GUI Configuration:
- Save each subject in a separate directory (unchecked)
- Save each series in a separate directory (unchecked)
- Save multivolume series as 4D files (unchecked)
- Skip volumes for multivolume series (0)
- Apply rescale slope and intercept to data (unchecked)
- save as .nii file (checked)

T1 Terminal
$ mcverter -o ~/Desktop/DICOM/T1 -f nifti -n ~/Desktop/NIFTI/

T2 GUI Configuration:
- Save each subject in a separate directory (unchecked)
- Save each series in a separate directory (unchecked)
- Save multivolume series as 4D files (checked)
- Skip volumes for multivolume series (0)
- Apply rescale slope and intercept to data (unchecked)
- save as .nii file (checked)

T2 Terminal
$ mcverter -o ~/Desktop/DICOM/T2 -f nifti -n -d ~/Desktop/NIFTI/

DTI GUI Configuration:
- Save each subject in a separate directory (unchecked)
- Save each series in a separate directory (unchecked)
- Save multivolume series as 4D files (checked)
- Skip volumes for multivolume series (0)
- Apply rescale slope and intercept to data (unchecked)
- save as .nii file (checked)

T2 Terminal
$ mcverter -o ~/Desktop/DICOM/DTI -f nifti -n -d –s 7 ~/Desktop/NIFTI/

Is there any errors in my terminal argument that could be causing this issue?

Kind regards
Justin

JUSTIN CHANG | Business Portfolio Manager Research
Information and Communications Technology

THE UNIVERSITY OF SYDNEY
Level 3 Services Building G12 | The University of Sydney | NSW | 2006
P +61 2 9114 0516  M +614 0039 4246
E justin.chang at sydney.edu.au<mailto:justin.chang at sydney.edu.au><mailto:justin.chang at sydney.edu.au> W  http://sydney.edu.au<http://sydney.edu.au/>

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Chuck Theobald
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The Robert and Beverly Lewis Center for Neuroimaging
University of Oregon
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