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MIndboggle (latest) crashing on processing freesurfer 6 data #196
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Hi @cecs1, thank you very much for posting this problem. Before we go any further: are you using Could you maybe also post an example of how you run Best, Peer |
Thanks Peer.
I run the docker container version
docker run --rm -ti -v $HOST:$DOCK -p 5000:5000 nipy/mindboggle
Then, I set variables:
export HOST=/home/csteward
export DOCK=/home/jovyan/work
export ID=0315
export FREESURFER_OUT=$DOCK/freesurfer_subjects
export FREESURFER_SUBJECT=$FREESURFER_OUT/$ID
export OUT=$DOCK/mindboggled
Then I run Mindboggle on the freesurfer 6 output (which was run separately outside the docker container)
mindboggle $FREESURFER_SUBJECT --out $OUT
I can tell you if I run everything in the docker container ie freesurfer and mindboggle, there are no problems.
I can also tell you that the output from running freesurfer 6 separately compared to the freesurfer 6 output that mindboggle generates are different ie at least in terms of number of files generated eg the surf directory has 80 folders using mindboggle freesurfer, but 96 using external freesurfer. I run freesurfer with recon-all and no special options - I assume mindboggle is doing the same?
regards,
Chris
**************************************************
Dr Chris Steward
Dept of Medicine and Radiology,
Imaging Manager, MBC@RMH
University of Melbourne/Royal Melbourne Hospital
Grattan St, Parkville, 3050
Tel: (03) 903 56508
E-mail: [email protected]
****************************************************
…________________________________
From: Peer Herholz <[email protected]>
Sent: 04 December 2019 01:25
To: nipy/mindboggle <[email protected]>
Cc: Chris Steward <[email protected]>; Mention <[email protected]>
Subject: Re: [nipy/mindboggle] MIndboggle (latest) crashing on processing freesurfer 6 data (#196)
Hi @cecs1<https://github.com/cecs1>,
thank you very much for posting this problem.
Before we go any further: are you using Mindboggle within a container (docker/singularity) or through the bare-metal installation?
That function wasn't changed in a while I think, hence I'm wondering where this is coming from...
Could you maybe also post an example of how you run freesurfer and mindboggle?
Best, Peer
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Hi @cecs1, thank you very much for the additional information. Hm, interesting. I never saw that/heard of it before. How about you @binarybottle, @satra? @cecs1 did you already try an older version of the |
I am afraid I haven't run into this problem before. |
The inside vs. outside container FS data thingy indeed seems weird... @cecs1 could you maybe try the following for both, the
where |
@PeerHerholz you can inspect the contents of https://dl.dropbox.com/s/nnzcfttc41qvt31/recon-all-freesurfer6-3.min.tgz. it was made using the instructions in freesurfer/freesurfer#70 (comment). the binaries are exactly the same as in freesurfer version 6.0.0, there are just fewer of them (the package was trimmed to only include things necessary for recon-all). |
Hello,
I'm trying to process some data through mindboggle on data that was ran successfully through Freesurfer 6. It doesn't matter which scan I use, the same error occurs.
I'm getting errors below (there are many after this of similar nature) - they appear to relate to the Surface_to_vtk routine.
Any advice appreciated.
Thanks,
Chris
191202-20:16:59,146 nipype.workflow INFO:
Workflow Mindboggle settings: ['check', 'execution', 'logging', 'monitoring']
191202-20:16:59,197 nipype.workflow INFO:
Running serially.
191202-20:16:59,198 nipype.workflow INFO:
[Node] Setting-up "Mindboggle.Freesurfer_annot" in "/home/jovyan/work/mindboggled/working/0315/Mindboggle/_hemi_rh/Free
surfer_annot".
191202-20:16:59,201 nipype.workflow INFO:
[Node] Running "Freesurfer_annot" ("nipype.interfaces.io.DataGrabber")
191202-20:16:59,205 nipype.workflow INFO:
[Node] Finished "Mindboggle.Freesurfer_annot".
191202-20:16:59,206 nipype.workflow INFO:
[Node] Setting-up "Mindboggle.Surfaces" in "/home/jovyan/work/mindboggled/working/0315/Mindboggle/_hemi_rh/Surfaces".
191202-20:16:59,209 nipype.workflow INFO:
[Node] Running "Surfaces" ("nipype.interfaces.io.DataGrabber")
191202-20:16:59,211 nipype.workflow INFO:
[Node] Finished "Mindboggle.Surfaces".
191202-20:16:59,212 nipype.workflow INFO:
[Node] Setting-up "Mindboggle.Surface_to_vtk" in "/home/jovyan/work/mindboggled/working/0315/Mindboggle/_hemi_rh/Surfac
e_to_vtk".
191202-20:16:59,274 nipype.workflow INFO:
[Node] Running "Surface_to_vtk" ("nipype.interfaces.utility.wrappers.Function")
191202-20:16:59,656 nipype.workflow WARNING:
Storing result file without outputs
191202-20:16:59,656 nipype.workflow WARNING:
[Node] Error on "Mindboggle.Surface_to_vtk" (/home/jovyan/work/mindboggled/working/0315/Mindboggle/hemi_rh/Surface_to
vtk)
191202-20:16:59,659 nipype.workflow ERROR:
Node Surface_to_vtk.a1 failed to run on host a460efb46421.
191202-20:16:59,660 nipype.workflow ERROR:
Saving crash info to /root/crash-20191202-201659-root-Surface_to_vtk.a1-12bb0046-09dc-4661-bf46-c45e734ce5aa.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 479, in run
result = self._run_interface(execute=True)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 569, in _run_interface
return self._run_command(execute)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 662, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 382, in run
runtime = self._run_interface(runtime)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/interfaces/utility/wrappers.py", line 144, in _run_inte
rface
out = function_handle(**args)
File "", line 54, in freesurfer_surface_to_vtk
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nibabel/freesurfer/io.py", line 179, in read_geometry
coords = np.fromfile(fobj, ">f4", vnum * 3).reshape(vnum, 3)
ValueError: cannot reshape array of size 1287294 into shape (389005987,3)
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