Search found 8 matches
- Wed Dec 05, 2018 8:18 am
- Forum: BrainVISA
- Topic: KeyError while running Morphologist on command line
- Replies: 9
- Views: 21837
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...
- Thu Nov 22, 2018 9:15 am
- Forum: BrainVISA
- Topic: KeyError while running Morphologist on command line
- Replies: 9
- Views: 21837
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 ...
- Wed Nov 21, 2018 2:08 pm
- Forum: BrainVISA
- Topic: KeyError while running Morphologist on command line
- Replies: 9
- Views: 21837
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
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
- Tue Nov 13, 2018 6:24 pm
- Forum: BrainVISA
- Topic: KeyError while running Morphologist on command line
- Replies: 9
- Views: 21837
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...
- Tue Nov 13, 2018 2:49 pm
- Forum: BrainVISA
- Topic: running a .bvproc from the command line?
- Replies: 4
- Views: 17308
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...
- Mon Oct 01, 2018 9:57 am
- Forum: BrainVISA
- Topic: bvproc : parameter is not readable or does not exist ERROR
- Replies: 2
- Views: 13322
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
Durai
- Mon Oct 01, 2018 9:55 am
- Forum: BrainVISA
- Topic: bvproc : parameter is not readable or does not exist ERROR
- Replies: 2
- Views: 13322
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 ...
- Thu Sep 27, 2018 8:36 am
- Forum: BrainVISA
- Topic: KeyError while running Morphologist on command line
- Replies: 9
- Views: 21837
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...