Search found 8 matches

by durai2323
Wed Dec 05, 2018 8:18 am
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5933

Re: KeyError while running Morphologist on command line

Hi Denis, Thank you for the fix. Sorry I was on vacation. I tested it and it works! But you need to update the database after creating it. That is, before you run import on it. Otherwise it throws an error. So the current way I ma runnign this on the command line is as follows - 1) create database 2...
by durai2323
Thu Nov 22, 2018 9:15 am
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5933

Re: KeyError while running Morphologist on command line

Hi Denis, python -m brainvisa.axon.runprocess --enabledb updateDatabases /path/to/a/database This works perfectly but I encountered a bug unfortunately when running the whole pipeline i.e ImportT1MRI+updateDatabase+morphologist. This time it is the ImportT1MRI process. It does not create the sqlite ...
by durai2323
Wed Nov 21, 2018 2:08 pm
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5933

Re: KeyError while running Morphologist on command line

Hi Denis,

Thank you for modifying updateDatabases.py. I checked if the command line call works and it does! I will get back to you after more testing.

Best,
Durai
by durai2323
Tue Nov 13, 2018 6:24 pm
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5933

Re: KeyError while running Morphologist on command line

Then with the given parameters, you also need to activate databasing because the normalization steps and sulci recognition steps need some additional data which are found in the internal database of brainvisa, so you wil lneed to add the "--enabledb" after "python -m brainvisa.axon.r...
by durai2323
Tue Nov 13, 2018 2:49 pm
Forum: BrainVISA
Topic: running a .bvproc from the command line?
Replies: 4
Views: 5890

Re: running a .bvproc from the command line?

Hi Denis, I tried running this command - as described by you : python -m brainvisa.axon.runprocess --enabledb morphologist ./100206_1-T1w_acpc_dc_restore_1mm.nii.gz . I get the following error - Loading toolbox cortical_surface Loading toolbox data management Loading toolbox datamind Loading toolbox...
by durai2323
Mon Oct 01, 2018 9:57 am
Forum: BrainVISA
Topic: bvproc : parameter is not readable or does not exist ERROR
Replies: 2
Views: 3071

Re: bvproc : parameter is not readable or does not exist ERROR

OK I could not attach the file, there is a "could not upload error". I am working on it..

Durai
by durai2323
Mon Oct 01, 2018 9:55 am
Forum: BrainVISA
Topic: bvproc : parameter is not readable or does not exist ERROR
Replies: 2
Views: 3071

bvproc : parameter is not readable or does not exist ERROR

Hello forum members, I am trying to run the morphologist pipeline using a bvproc form the command line using the following command - python -m brainvisa.axon.runprocess --enabledb /mnt3/bvprocs_for_singularity_c4/Morphologist_220071_1.bvproc and I get the following error. It says a parameter is not ...
by durai2323
Thu Sep 27, 2018 8:36 am
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5933

KeyError while running Morphologist on command line

Hello forum members, I am trying to run the morphologist pipeline on the command line without the bvproc(with normalizaiton enabled). It has 15 arguments. This is the command used - python -m brainvisa.axon.runprocess morphologist \ t1mri=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisiti...

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