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

Fri, 17 Apr 2015 16:16:33 -0700

We have a beta version 2.0 that works with FSL 5.0.8 in GitHub which you can test (excerpt from off list e-mail from Tim Brown to another user):

Actually the current head of the master branch (the main branch) has the code for both version 1.0 and version 2.0 of Task fMRI Analysis in it, along with a new version of the actual Pipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.shscript which does nothing but invoke TaskfMRIAnalysis.v1.0.sh if FSL v5.0.6 or older is being used and invoke TaskfMRIAnalysis.v2.0.sh if FSL v5.0.7 or newer is being used. 
 
If you want to get a copy of that code, the repository is publicly readable so you should be able to download the code from the GitHub website by using the "Download ZIP" button to the right side of the main GitHub WashU Pipelines page (https://github.com/Washington-University/Pipelines) or by using a command line git cloning command like:  git clone https://github.com/Washington-University/Pipelines.git

In terms of levels, we ended up calling level 1 single subject single run, level 2 single subject cross runs, level 3 cross subjects.  That git repo contains code for all three levels and it should still work if you only have a single run (it just passes the data on up to the next level).  

Peace,

Matt.

From: <Book>, Gregory <[email protected]>
Date: Friday, April 17, 2015 at 2:02 PM
To: Matt Glasser <[email protected]>, "[email protected]" <[email protected]>
Subject: RE: [HCP-Users] missing _Atlas.dtseries.nii

I was thinking of the FSL’s stats in terms of levels 1, 1.5, and 2. Where 1 is the run level, 1.5 is the subject, and 2 is the group. So, I was planning to the group/level 2 stats outside of the HCP.

 

However, I noticed that the problem of it not running level 1 stats was due to another error message before the level 2 error message. It says that FSL 5.0.6 is required. I just upgraded to 5.0.8. Is this version ok to use, and I can remove that check from the TaskfMRILevel1.sh script?

-G

 

From: Glasser, Matthew [mailto:[email protected]]
Sent: Friday, April 17, 2015 1:14 PM
To: Book, Gregory; [email protected]
Subject: Re: [HCP-Users] missing _Atlas.dtseries.nii

 

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 <[email protected]>
Date: Friday, April 17, 2015 at 12:09 PM
To: Matt Glasser <[email protected]>, "[email protected]" <[email protected]>
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:[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]>
Date: Friday, April 17, 2015 at 12:04 PM
To: Matt Glasser <[email protected]>, "[email protected]" <[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]
Subject: Re: [HCP-Users] missing _Atlas.dtseries.nii

 

Perhaps you should post your fMRIVolume and fMRISurface calls.

 

Peace,

 

Matt.

 

From: <Book>, Gregory <[email protected]>
Date: Thursday, April 16, 2015 at 11:47 AM
To: Matt Glasser <[email protected]>, "[email protected]" <[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]
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]>
Date: Thursday, April 16, 2015 at 9:30 AM
To: "[email protected]" <[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]

http://nidb.sourceforge.net

 


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