Cannot analyze BIDS dataset

[wanderine]

Using this command

docker run -i --rm -v /Users/andek/Research_projects/BIDSSPM/test/ds003:/bids_dataset -v /Users/andek/Research_projects/BIDSSPM/test/results:/outputs bids/spm /bids_dataset /outputs participant --participant_label 01

For this BIDS dataset

https://drive.google.com/open?id=0B2JWN60ZLkgkSEtlSl8wd0xhbzQ

I got this error

SPM12: BIDS PARTICIPANT sub-01 13:08:04 - 27/02/2017

Execution failed: /opt/spm12/pipeline_participant.m Execution failed: /opt/spm12/spm_BIDS_App.m Reference to non-existent field 'filename'. Error in spm (line 1202) Error in spm (line 1202) Error in spm_standalone (line 47)

[gllmflndn]

Not sure what is going on as I don't get the same message:

docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v /home/gflandin/data/anders/ds003:/bids_dataset -v /home/gflandin/data/bids_tmp:/outputs bids/spm /bids_dataset /outputs participant --participant_label 01
SPM12 (6906): /opt/spm12/spm12_mcr/spm12
 ___  ____  __  __                                            
/ __)(  _ \(  \/  )                                           
\__ \ )___/ )    (   Statistical Parametric Mapping           
(___/(__)  (_/\/\_)  SPM12 - http://www.fil.ion.ucl.ac.uk/spm/

SPM12: BIDS PARTICIPANT sub-01                     14:00:29 - 27/02/2017
========================================================================

------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Realign: Estimate & Reslice'

SPM12: spm_realign (v6070)                         14:00:30 - 27/02/2017
========================================================================
Completed                               :          14:00:48 - 27/02/2017

Have you built the container yourself or is it the one from Docker Hub (in case there is a mismatch or if I am myself using a different cached one)?

I also just pushed a few changes I made earlier and will trigger a new build.

Also note that in its current form, the SPM BIDS-App expects the user to provide a configuration file describing the pipeline to execute:

docker run ... --config /bids_dataset/pipeline.m

If none is provided, a default one pipeline_participant.m or pipeline_group.m is used but is just for illustration on how to write one.

[wanderine]

With the bids/spm pre-built container the realign works but then I get this error

Running 'Coregister: Estimate'

Failed 'Coregister: Estimate'

Error using read_hdr (line 32)

Error reading header file "/outputs/sub-01/anat/sub-01_T1w.nii/sub-01_inplaneT2.nii".

In file "/opt/spm12/spm12_mcr/spm12/@nifti/private/read_hdr.m" (???), function "read_hdr" at line 32.

In file "/opt/spm12/spm12_mcr/spm12/@nifti/nifti.m" (???), function "nifti" at line 26.

In file "/opt/spm12/spm12_mcr/spm12/spm_select.m" (???), function "spm_select_get_nbframes" at line 268.

In file "/opt/spm12/spm12_mcr/spm12/spm_select.m" (???), function "spm_select_expand" at line 254.

In file "/opt/spm12/spm12_mcr/spm12/spm_select.m" (???), function "spm_select" at line 130.

In file "/opt/spm12/spm12_mcr/spm12/config/spm_run_coreg.m" (???), function "spm_run_coreg" at line 17.

2017-02-27 15:29 GMT+01:00 Guillaume notifications@github.com:

Not sure what is going on as I don't get the same message:

docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v /home/gflandin/data/anders/ds003:/bids_dataset -v /home/gflandin/data/bids_tmp:/outputs bids/spm /bids_dataset /outputs participant --participant_label 01 SPM12 (6906): /opt/spm12/spm12_mcr/spm12

---

/ )( ( \/ ) _ \ )_/ ) ( Statistical Parametric Mapping (/() (/\/_) SPM12 - http://www.fil.ion.ucl.ac.uk/spm/

SPM12: BIDS PARTICIPANT sub-01 14:00:29 - 27/02/2017

---

Running job #1

Running 'Realign: Estimate & Reslice'

SPM12: spm_realign (v6070) 14:00:30 - 27/02/2017

Completed : 14:00:48 - 27/02/2017

Have you built the container yourself or is it the one from Docker Hub (in case there is a mismatch or if I am myself using a different cached one)?

I also just pushed a few changes I made earlier and will trigger a new build.

Also note that in its current form, the SPM BIDS-App expects the user to provide a configuration file describing the pipeline to execute:

docker run ... --config /bids_dataset/pipeline.m

If none is provided, a default one pipeline_participant.m or pipeline_group.m is used but is just for illustration on how to write one.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/SPM/issues/6#issuecomment-282735511, or mute the thread https://github.com/notifications/unsubscribe-auth/AEGryJXsssmwZbMEzV6uzq2PEsuUkjAZks5rgt3MgaJpZM4MNGQU .

-- Anders Eklund, PhD

[gllmflndn]

Yes, the default within-subject pipeline expects a single anatomy file per subject. Commit b93a8e82 should fix this. I'll tag this version to trigger a new Docker Hub build.

Or you can copy and modify pipeline_participant.m to fit your needs and use it through the --config flag, without having to rebuild the container.

[wanderine]

The preprocessing now works, but no statistical analysis is performed.

2017-02-27 17:04 GMT+01:00 Guillaume notifications@github.com:

Yes, the default within-subject pipeline expects a single anatomy file per subject. Commit b93a8e8 https://github.com/BIDS-Apps/SPM/commit/b93a8e82459ba89d0baa06e9edbc0985121203d0 should fix this. I'll tag this version to trigger a new Docker Hub build.

Or you can copy and modify pipeline_participant.m to fit your needs and use it through the --config flag, without having to rebuild the container.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/SPM/issues/6#issuecomment-282763674, or mute the thread https://github.com/notifications/unsubscribe-auth/AEGryK5FiTPgL1oFKAB3FfYgIhRinkLmks5rgvQpgaJpZM4MNGQU .

-- Anders Eklund, PhD

[gllmflndn]

Without the BIDS extension on model and hypothesis specification I cannot see how you can perform any statistical analysis automatically, apart from something anecdotal.

Once again, the way this App works is that the user provides the MATLAB script detailing the analysis to perform, with the help of the BIDS structure. The default scripts are just here to illustrate how to write your own one.