error on PostFreeSurferPipeline

[Xin Niu]

Dear experts,

I am running the PostFreeSurferPipeline on the example data (non GDC). The parameters are set the same as the PreFreeSurfer and FreeSurfer scripts. But I got the following error:

Thu Aug 11 16:30:55 EDT 2022:PostFreeSurferPipeline.sh: ERROR: --processing-mode=HCPStyleData was requested, but the following settings are not compliant:
Thu Aug 11 16:30:55 EDT 2022:PostFreeSurferPipeline.sh: ERROR:  T2w image not present
Thu Aug 11 16:30:55 EDT 2022:PostFreeSurferPipeline.sh: ERROR: Fix these settings or consider requesting 'LegacyStyleData' mode instead.

Shall I change the parameter processing-mode to something else? But I cannot find this parameter in the script.

Thank you!

Best,

Xin

[Glasser, Matt]

How did you call the pipeline?  It looks like you didn’t include the T2w data.

Matt.

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[Xin Niu]

Hi Matt,

Thanks for your quick response. I just called the pipeline without any inputs as I did for the previous script. Shall I add the directory for the T2w data?

Currently, I am running on the example data. We plan to run the pipeline on the ADNI data set which might not have the T2w data.

Best,

Xin

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[Coalson, Timothy Scott (S&T-Student)]

The Examples/Scripts/<whatever>Batch.sh are not the pipelines, they are example launch scripts.  They generally loop through the subjects, based on how you edit them, and then call an actual pipeline script on each subject (in this case, $HCPPIPDEDIR/PostFreeSurfer/PostFreeSurferPipeline.sh).

Did you actually run the PreFreeSurfer and FreeSurfer HCP pipelines first?  You should not manually run recon-all if you want to use the HCP pipelines, but rather start with our PreFreeSurfer pipeline.  PostFreeSurfer should not be run without running those 2 first, and it just so happens that the check for a T2w image is basically the first thing in PostFreeSurfer that can throw an error (before something else can complain about not finding any of the outputs of the FreeSurfer HCP pipeline).

Tim

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From: Xin Niu <michael...@gmail.com>
Sent: Thursday, August 11, 2022 6:58 PM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] error on PostFreeSurferPipeline

 

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[Xin Niu]

Hi Tim,

Thanks for your reply. I run the PreFreeSurferPipelineBatch.sh and PostFreeSurferPipelineBatch.sh on the example data and got the following results in the subjects directory:

MNINonLinear  release-notes  T1w  T2w  unprocessed

I think MNINonLinear, T1w, and T2w are generated by the first 2 scripts. Is that correct?

I am also wondering what if I just have T1w and functional images in my own data. Can I edit the script to skip T2w images?

thank you!

Best,

Xin

[Glasser, Matt]

--processing-mode=LegacyStyleData needs to be specified if you aren’t using a T2w image.

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[Xin Niu]

Hi,

Thanks for your reply.

I just added ' --processing-mode="legacyStyleData" ' to the command in the script PostFreeSurferPipelineBatch.sh and got the following error: 

Error submitting job - /home/xin/Downloads/BrainImaging_HCPpipeline/HCPpipelines-4.3.0/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 160: mri_info: command not found

Is this because freesurfer is not correctly installed? I can run freeview in the command line.

Thank you!

Best,

Xin

[Xin Niu]

One more question: shall I use ' --processing-mode="legacyStyleData" '  to run PostFreeSurferPipelineBatch.sh and FreeSurferPipelineBatch.sh If I don't have t2w images?

Currently, I run the 2 scripts with t2w images and get the error that t2w images are not present.

Sorry for having so many questions...

Best,

Xin

[Coalson, Timothy Scott (S&T-Student)]

freeview is basically a separate piece of software.  If mri_info isn't found, then freesurfer itself isn't properly installed.  Check that your FREESURFER_HOME environment variable is correct, and then do 'source "$FREESURFER_HOME/SetUpFreeSurfer.sh" ', and then run the PostFreeSurfer launch script.  Usually, the SetUpFreeSurfer.sh command is put into .bashrc or similar, to do this automatically in all of your terminals.

Tim

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From: Xin Niu <michael...@gmail.com>
Sent: Monday, August 15, 2022 1:50 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: glas...@wustl.edu <glas...@wustl.edu>; Coalson, Timothy Scott (S&T-Student) <tsc...@mst.edu>

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[Coalson, Timothy Scott (S&T-Student)]

What you need to start with is PreFreeSurfer, which has a t2 argument.  This also requires --processing-mode=LegacyStyleData if you want to run without a t2w image.

Tim

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From: Xin Niu <michael...@gmail.com>
Sent: Monday, August 15, 2022 1:59 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Xin Niu <michael...@gmail.com>; glas...@wustl.edu <glas...@wustl.edu>; Coalson, Timothy Scott (S&T-Student) <tsc...@mst.edu>