On Oct 26, 2014, at 9:21 AM, Glasser, Matthew <glass...@wusm.wustl.edu<mailto:glass...@wusm.wustl.edu>> wrote:
That note in the pipeline example code was put there because I donąt know how to tell what readout direction was used from the DICOMs and z seems to be the Siemens default. If someone else does, I’d be interested in what field(s) they used. It may take some deductive work. Mike Harms once figured out the phase encoding direction from the DICOM header. We just need to find the corresponding code of slice direction in the DICOM header. The one left is the readout direction. However, to be completely sure about the sign would be tough or might be impossible from the DICOM header alone. Gordon, I’d be a bit surprised here if the shim mattered given how small the correction is already and the fact that the bulk of the correction is likely to be the same from one shim to another. I agree that the bulk of the correction is not likely to change between re-shims. However, I assume the main reason to do readout distortion correction is for regions close to sinuses, where local fields could vary substantially between re-shims with global (whole brain) optimization. I don’t think it’s likely to be made worse by reshiming, just won’t be quite as precise of a correction. I agree that no matter what it is a “small” effect. However I don’t completely agree it can’t be made worse by a wrong fieldmap due to re-shimming. I think we can do an experiment of: Fieldmap - Structural - re-shim - wrong Fieldmap, to evaluate. Gordon Peace, Matt. On 10/24/14, 10:33 PM, "Xu, Junqian" <junqian...@mssm.edu<mailto:junqian...@mssm.edu>> wrote: As for importance, it depends on your application but readout distortion is typically quite small. Btw, weąve 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<mailto:junqian...@mssm.edu>> wrote: 'Unwarp Dirą should correspond to the Readout (frequency encoding) direction for the ŚPreFreeSurferPipeline', 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 whatąs 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<mailto: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. 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