Ahh I see. I was using the one here: https://github.com/ksubramz/gradunwarp, which is listed in the SetUpHCPPipeline.sh script, line 35. That should probably be updated. Thanks for the help.
-Micah On Oct 29, 2014 9:38 PM, "Glasser, Matthew" <[email protected]> wrote: > Yes that is the failure if the HCP specific version is not used. > > Peace, > > Matt. > > From: <Harms>, Michael <[email protected]> > Date: Wednesday, October 29, 2014 at 9:52 PM > To: Micah Chambers <[email protected]>, "Harms, Michael" < > [email protected]>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] T1UnwarpDir > > > Please post to the list so that others can respond. I'm going to let > someone more familiar with gradient_unwarp.py handle that one. But, can > you confirm that you using the HCP specific version of gradient_unwarp.py? > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > From: Micah Chambers <[email protected]> > Date: Wednesday, October 29, 2014 5:29 PM > To: "Harms, Michael" <[email protected]> > Subject: Re: [HCP-Users] T1UnwarpDir > > Ah I see. I was not handling it. I have now acquired the spherical > harmonics file. > > > Now it seems like there is nothing that generates the file: > 'T1w/T1w1_GradientDistortionUnwarp/fullWarp_abs.nii.gz' (on line 88 of > global/scripts/GradientDistortionUnwarp.sh). The comments state that this > is an output of gradient_unwarp.py, although not a direct one (unlike > trilinear.nii.gz). I've grepped for that filename and it seems like nothing > generates explicitly, or at least puts it on the command-line. It is > successful generating trilinear.nii.gz, however. Any thoughts on where > fullWarp_abs should come from? > > Thanks, > > > -Micah > On Oct 28, 2014 8:56 AM, "Harms, Michael" <[email protected]> wrote: > >> >> Hi Micah, >> Since we aren't allowed to distribute the file with the spherical >> harmonics for the gradient nonlinearity correction, how did you handle >> that? Did you obtain a copy (from Siemens) of the coefficient file >> specific to the HCP Connectom scanner? (Note that those coefficients are >> NOT the same as a stock Skyra). >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> ----------------------------------------------------------- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave. Tel: 314-747-6173 >> St. Louis, MO 63110 Email: [email protected] >> >> From: Micah Chambers <[email protected]> >> Date: Tuesday, October 28, 2014 3:03 AM >> To: Gordon Xu <[email protected]> >> Cc: HCP Users <[email protected]> >> Subject: Re: [HCP-Users] T1UnwarpDir >> >> So I have run subject 101309 through the >> Examples/Scripts/PreFreeSurferPipelineBatch.sh script to check that we get >> the same output as the published data (because we would like to validate >> our environment) and I'm getting a definite difference. I've attached the >> output from the script and slices of the downloaded (from ConnectomeDB) and >> locally processed results. >> >> Have these scripts been tested in different environments? It seems like >> running the local example scripts should generate identical results to the >> ConnectomeDB data. The reason I asked about the unwarp direction is that I >> can't figure out what is causing this difference, and I thought that might >> be the answer. Would it be incorrect to assume that there should be no >> difference between a locally generated T1w_acpc_dc.nii.gz file and the one >> from ConnectomeDB? >> >> -Micah >> >> On Sun, Oct 26, 2014 at 7:56 PM, Xu, Junqian <[email protected]> wrote: >> >>> >>> On Oct 26, 2014, at 9:21 AM, Glasser, Matthew <[email protected]> >>> 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" <[email protected]> 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 <[email protected]> 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 <[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] >>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectom >>> e.org_mailman_listinfo_hcp-2Dusers&d=AAIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8 >>> m8VqTSNCjYLg1wNX4&r=3I6-yvEg8KFim9hIErhCvm3QH8yehzFWJ6HsWQoeUT8&m=UEyeqf >>> 3jP4WJpWQN5X0VinWErEJz5X0LwGv9I9bKTaE&s=VGju-usV7cI7ZgqageB_YKPSrZ9SFw22 >>> f0BHVq4UfxA&e= >>> >>> <ours.png><hcp.png> >>> >>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome >>> .org_mailman_listinfo_hcp-2Dusers&d=AAIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8 >>> VqTSNCjYLg1wNX4&r=3I6-yvEg8KFim9hIErhCvm3QH8yehzFWJ6HsWQoeUT8&m=UEyeqf3jP >>> 4WJpWQN5X0VinWErEJz5X0LwGv9I9bKTaE&s=VGju-usV7cI7ZgqageB_YKPSrZ9SFw22f0BH >>> Vq4UfxA&e= >>> >>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=AAIF-g&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=3I6-yvEg8KFim9hIErhCvm3QH8yehzFWJ6HsWQoeUT8&m=Ndo6LYlXhYJh0mP_opWcHgJS6UfGOPpHuKHY31h2zqI&s=M4nb7hZR-h8Ni-m55xVUAJbOh_sQ4HigNbY9QG-1GFM&e= >>> >>> >>> >>> >>> ________________________________ >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> >>> >>> >> >> >> -- >> >> 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] >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> ------------------------------ >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. 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