'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 <[email protected]> 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: [email protected]
>
>
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>
> <ours.png><hcp.png>
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