As for importance, it depends on your application but readout distortion is
typically quite small. Btw, we’ve observed that the scanner re-shimming often
happens between the fieldmap and the structural scans if the scanner operator
is not well-educated for the importance of preventing re-shimming. In such
cases, I think it is better to disable the readout distortion correction in the
PreFreeSurferPipeline.
Gordon
> On Oct 24, 2014, at 11:18 PM, Xu, Junqian <junqian...@mssm.edu> wrote:
>
> 'Unwarp Dir’ should correspond to the Readout (frequency encoding) direction
> for the ‘PreFreeSurferPipeline', in which case is the Z direction (Head -
> Foot) for the sagittal T1w/T2w HCP structural acquisitions. Not sure what you
> mean by "The only comment is that z appears best.” Below is what’s in
> PreFreeSurfer/PreFreeSurferPipeline.sh
>
> --unwarpdir={x, y, z} Readout direction of the T1w and T2w images
> (Used with either a regular field
> map or a spin
> echo field map)
>
>
>> On Oct 24, 2014, at 8:28 PM, Micah Chambers <micahc...@gmail.com> wrote:
>>
>> Could anyone provide a better explanation of the importance of Unwarp Dir in
>> the example file 'PreFreeSurferPipelineBatch.sh'? The only comment is that z
>> appears best. It seems like direction of warping should be a known value, is
>> that not the case.
>>
>> I don't know if this is related, but I have been testing the scripts with
>> HCP subject 901038 and I am finding that the outputs do not match up. There
>> is a slight tilt to the head. While not a big issue (the brain is still
>> labeled correctly), it makes validation of scripts harder. Has anyone else
>> had such an issue? I have included screenshots (ours.png is our local
>> version, hcp.png is the downloaded version). Note that this came from
>> '901038_3T_Structural_preproc.zip' and was downloaded about a month ago.
>>
>> Thanks
>>
>> -MIcah
>>
>> --
>> Micah Chambers, M.S.
>> Ahmanson-Lovelace Brain Mapping Center
>> University of California Los Angeles
>> 635 Charles E. Young Drive SW, Suite 225
>> Los Angeles, CA 90095-7334
>> 310-206-2101 (Office)
>> 310-206-5518 (Fax)
>> 703-307-7692 (Cell)
>> email: mica...@ucla.edu
>>
>>
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>>
>>
>> <ours.png><hcp.png>
>
>
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