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

[Glasser, Matthew]

Is that because you don’t have the HCP script to do them yet?  There is a branch in GitHub with a new version of the tfMRI Analysis scripts including one for what we call level 3 (or group) analyses.   You can simply comment out the call to the second level code, but I’m not sure that’s what you want either, as you’ll lose some of the stuff at the end that is intended to make the data more easily viewable in Connectome Workbench (I.e. organize all the contrasts into a file and name them).  If you just call the pipeline with a single run, the level 2 won’t actually do anything to the level one maps (essentially it will just pass things up to level 3/group analysis unchanged).   Peace, Matt. From: <Book>, Gregory <gregory.b...@hhchealth.org> Date: Friday, April 17, 2015 at 12:09 PM To: Matt Glasser <glass...@wusm.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: RE: [HCP-Users] missing _Atlas.dtseries.nii 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:glass...@wusm.wustl.edu] Sent: Friday, April 17, 2015 1:06 PM To: Book, Gregory; hcp-users@humanconnectome.org 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 <gregory.b...@hhchealth.org> Date: Friday, April 17, 2015 at 12:04 PM To: Matt Glasser <glass...@wusm.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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:glass...@wusm.wustl.edu] Sent: Thursday, April 16, 2015 12:56 PM To: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] missing _Atlas.dtseries.nii   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. 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