Re 1) If you are using a modern version of ‘dcm2niix’, then in the context of the T1 and T2 scans, the values for T1wSampleSpacing and T2wSampleSpacing are available as the “DwellTime” entry in the BIDS-style json sidecar files.
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 "Glasser, Matthew" <glass...@wustl.edu> Date: Thursday, February 7, 2019 at 7:09 AM To: Aaron C <aaroncr...@outlook.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Some questions about using HCP structural preprocessing pipeline 1. This depends on the acquisition parameters. You can find this in the DICOM header in the named fields. 2. How do the T2w data look in the T1w folder? That matters most. 3. You need to update Connectome Workbench. 4. Doesn’t matter. 5. I hope so. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>> Date: Wednesday, February 6, 2019 at 11:57 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Some questions about using HCP structural preprocessing pipeline Dear HCP experts, I have some questions about using the HCP structural preprocessing pipeline. 1. For the parameters “T1wSampleSpacing” and “T2wSampleSpacing”, are they the same across different Skyra scanners? Will this significantly affect preprocessing quality if setting them to “NONE”? 2. I noticed some cortical regions were excessively removed in the file “T2w_acpc_brain.nii.gz” in “T2w” folder. Would this indicate any problem of brain extraction? If so, would you please suggest how to fix this problem? 3. I received the error “Unexpected parameter: -local-affine-method” when using “PostFreeSurferPipelineBatch.sh”. It occurred when the script tried to call wb_command to do some operations with the flag “-local-affine-method”. Would you please suggest how to fix this error? 4. I received a lot of “name collision in input name” warnings. I guess these warnings does not matter? 5. Will the updated pipeline using FreeSurfer 6.0.0 possibly be available in the near future (sometime this month)? Thank you. _______________________________________________ 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 ________________________________ 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
