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

[Chuck]

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 
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>
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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
>> Ejustin.chang at sydney.edu.au  <mailto:justin.chang at sydney.edu.au><mailto:justin.chang at sydney.edu.au> Whttp://sydney.edu.au<http://sydney.edu.au/>
>>
>> CRICOS 00026A
>> This email plus any attachments to it are confidential and are subject to a claim for privilege. Any unauthorised use is strictly prohibited.  If you receive this email in error, please delete it and any attachments.
>> Please think of our environment and only print this e-mail if necessary.
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-- 
Chuck Theobald
System Administrator
The Robert and Beverly Lewis Center for Neuroimaging
University of Oregon
P: 541-346-0343
F: 541-346-0345

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