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> 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 > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Keith > Jamison <kjami...@umn.edu> > *Date: *Tuesday, April 23, 2019 at 3:59 PM > *To: *HCP Users <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 > 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 > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
