For this task, there are only single runs. So, yes, I don't need to combine multiple runs. I was also planning to do second level stats outside of the HCP pipelines.
From: Glasser, Matthew [mailto:[email protected]] Sent: Friday, April 17, 2015 1:06 PM To: Book, Gregory; [email protected] Subject: Re: [HCP-Users] missing _Atlas.dtseries.nii You don't want to do level 2 stats because you don't have multiple tfMRI runs? Peace, Matt. From: <Book>, Gregory <[email protected]<mailto:[email protected]>> Date: Friday, April 17, 2015 at 12:04 PM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: [HCP-Users] missing _Atlas.dtseries.nii Yup, that was the problem. There was a mismatch between the volume and surface resolutions. I set them to be same and it processes now. Thanks! Back to the taskFMRIbatch. If I don't want to do level 2 stats, is there a way to turn it off so it only does level 1? From: Glasser, Matthew [mailto:[email protected]] Sent: Thursday, April 16, 2015 12:56 PM To: Book, Gregory; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] missing _Atlas.dtseries.nii Perhaps you should post your fMRIVolume and fMRISurface calls. Peace, Matt. From: <Book>, Gregory <[email protected]<mailto:[email protected]>> Date: Thursday, April 16, 2015 at 11:47 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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:[email protected]] Sent: Thursday, April 16, 2015 12:20 PM To: Book, Gregory; [email protected]<mailto:[email protected]> 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 <[email protected]<mailto:[email protected]>> Date: Thursday, April 16, 2015 at 9:30 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> 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. 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