Re: [HCP-Users] missing _Atlas.dtseries.nii

[Glasser, Matthew]

Perhaps you should post your fMRIVolume and fMRISurface calls. Peace, Matt. From: <Book>, Gregory <gregory.b...@hhchealth.org> Date: Thursday, April 16, 2015 at 11:47 AM To: Matt Glasser <glass...@wusm.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: RE: [HCP-Users] missing _Atlas.dtseries.nii Yes, I ran that pipeline, but now I see that it also generated an error too! I hadn’t looked at the output from the pipeline, I was only using the fMRIVolume results.   START: SubcorticalProcessing While running '/opt/HCP/Pipelines-3.3.3/global/binaries/caret7/bin_rh_linux64/../exe_rh_linux64/wb_command -volume-parcel-resampling /home/pipeline/onrc/data/pipeline/S8560ORS/1/HCPfMRI-APPangry/analysis/MNINonLinear/Results/APPAngry/APPAngry.nii.gz /home/pipeline/onrc/data/pipeline/S8560ORS/1/HCPfMRI-APPangry/analysis/MNINonLinear/ROIs/ROIs.2.nii.gz /home/pipeline/onrc/data/pipeline/S8560ORS/1/HCPfMRI-APPangry/analysis/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz .84932180028801904272 /home/pipeline/onrc/data/pipeline/S8560ORS/1/HCPfMRI-APPangry/analysis/MNINonLinear/Results/APPAngry/APPAngry_AtlasSubcortical_s2.nii.gz -fix-zeros': ERROR: volume spacing or dimension mismatch set -- --path=/home/pipeline/onrc/data/pipeline/S8560ORS/1/HCPfMRI-APPangry       --subject=analysis       --fmriname=APPAngry       --lowresmesh=32       --fmrires=2       --smoothingFWHM=2       --grayordinatesres=2       --regname=FS . /opt/HCP/HCP/Examples/Scripts/SetUpHCPPipeline.sh   What might be the cause of the fMRISurface pipeline error? Thanks, -G   From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Thursday, April 16, 2015 12:20 PM To: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] missing _Atlas.dtseries.nii   Did you run the fMRISurface pipeline yet?  That file gets generated by that pipeline.   Peace,   Matt.   From: <Book>, Gregory <gregory.b...@hhchealth.org> Date: Thursday, April 16, 2015 at 9:30 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] missing _Atlas.dtseries.nii   I’m running the TaskfMRIAnalysisBatch script against data that was processed using the PreFS,FS,PostFS, and GenericfMRI batch scripts.   It doesn’t get far and gives an error that it can’t find _Atlas.dtseries.nii:   Wed Apr 15 16:38:04 EDT 2015 - TaskfMRILevel1.sh - Use wb_command to calculate TR_vol While running '/opt/HCP/Pipelines-3.3.3/global/binaries/caret7/bin_rh_linux64/../exe_rh_linux64/wb_command -file-information /home/pipeline/onrc/data/pipeline/S6221VDW/1/HCP_APPangry_stats/analysis/MNINonLinear/Results/APPAngry/APPAngry_Atlas.dtseries.nii -no-map-info -only-step-interval': ERROR: failed to open file '/home/pipeline/onrc/data/pipeline/S6221VDW/1/HCP_APPangry_stats/analysis/MNINonLinear/Results/APPAngry/APPAngry_Atlas.dtseries.nii'   I can’t find this file anywhere, so I don’t think it’s a path issue. Is this file supposed to be generated in another script? -Greg _________________________________________________ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 gregory.b...@hhchealth.org http://nidb.sourceforge.net   This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. _______________________________________________ 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.   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