Also ReApplyFixMultiRunPipeline.sh is not affected at all by this bug. Matt.
From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, April 23, 2019 at 7:47 PM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: HCP Users <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects? This is a bug affecting the use of ReApplyFix to re-clean data using a hand classification instead of the original FIX classification (and does not affect the use of ReApplyFix in MSMAll). It has been present since the release of ReApplyFix and will affect the volume data of all HCP-YA subjects for which a hand classification was used (list will be forthcoming). The bug will be fixed in the next bugfix release of the HCP Pipelines and the data corrected. Sorry about this. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Tuesday, April 23, 2019 at 6:12 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: HCP Users <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects? Correction, the issue to follow is #107: https://github.com/Washington-University/HCPpipelines/issues/107 Tim On Tue, Apr 23, 2019 at 4:35 PM Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: For users that want to follow this, please see: https://github.com/Washington-University/HCPpipelines/issues/108 It has something to do with the fact that we needed to apply manual reclassification of the FIX output in that particular subject/run. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry 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<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Keith Jamison <kjami...@umn.edu<mailto:kjami...@umn.edu>> Date: Tuesday, April 23, 2019 at 3:59 PM To: HCP Users <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects? For subject 204218, both REST1_LR and REST1_RL, I noticed a linear trend in the *_hp2000_clean.nii.gz NIFTI time series, but the hp2000_clean.dtseries.nii CIFTI files do not have this trend. See attached figures showing this issue for both REST1_LR and REST1_RL for 204218. The overall mean time series has a negative trend for NIFTI, but in the voxel time series on the left you can see that some have positive trend and some have negative. To test, I did run fslmaths-based filtering on hp2000_clean.nii.gz and I no longer see any linear trend. I tried one scan in one additional subject, 102311 REST1_LR, and did not see this linear trend in either NIFTI or CIFTI (also attached). Note: I did remove the overall mean for each voxel timecourse before plotting, and for the NIFTI I'm only showing gray matter voxels, as determined by downsampling aparc+aseg.nii.gz and excluding labels for WM,CSF,ventricles, and a few misc. I also tried looking at all non-zero voxels, as well as only those marked in RibbonVolumeToSurfaceMapping/goodvoxels.nii.gz, but the issue of linear trends is the same. Any idea what might be going on with this subject? I haven't tried this in anyone other than 204218 (bad) and 102311 (good). -Keith _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
