Re: [HCP-Users] T1UnwarpDir

[Glasser, Matthew]

Yes that is the failure if the HCP specific version is not used. Peace, Matt. From: <Harms>, Michael <mha...@wustl.edu> Date: Wednesday, October 29, 2014 at 9:52 PM To: Micah Chambers <micahc...@gmail.com>, "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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: mha...@wustl.edu From: Micah Chambers <micahc...@gmail.com> Date: Wednesday, October 29, 2014 5:29 PM To: "Harms, Michael" <mha...@wustl.edu> 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" <mha...@wustl.edu> 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: mha...@wustl.edu From: Micah Chambers <micahc...@gmail.com> Date: Tuesday, October 28, 2014 3:03 AM To: Gordon Xu <junqian...@mssm.edu> Cc: HCP Users <hcp-users@humanconnectome.org> 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 <junqian...@mssm.edu> wrote: On Oct 26, 2014, at 9:21 AM, Glasser, Matthew <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> 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> 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> 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org 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: mica...@ucla.edu _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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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