Search found 1348 matches

by riviere
Sun Dec 16, 2018 9:05 pm
Forum: BrainVISA
Topic: running anatomist on ubuntu 18.04
Replies: 2
Views: 3494

Re: running anatomist on ubuntu 18.04

Hi Linda, I haven't heard of you for years, how are you ? Well, I think this could be related to some 3D drivers using either a more recent libz than the one shipped with brainvisa, or a more recent libstdc++ (or both). You can try moving them away from the brainvisa distribution (in the lib/ direct...
by riviere
Sun Dec 16, 2018 9:00 pm
Forum: BrainVISA
Topic: Locked files
Replies: 2
Views: 2982

Re: Locked files

Hi Will, Yes the freesurfer conversion tools locks some files to prevent them from being re-processed and overwritten by a "regular" brainvisa run. Why is it a problem if you are not actually re-writing these files ? Anyway you're right, I don't think we have a non-GUI process to unlock fi...
by riviere
Sun Dec 16, 2018 8:54 pm
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5926

Re: KeyError while running Morphologist on command line

Hi,
You're right, there was an error in the filename of the sqlite database...
I have uploaded an updated version of the createdatabase process:
ftp://ftp.cea.fr/pub/dsv/anatomist/upda ... atabase.py

Denis
by riviere
Fri Nov 23, 2018 2:44 am
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5926

Re: KeyError while running Morphologist on command line

Oh I see, yes, it seems so familiar to me now that I forget that it is not obvious to new users, but the general principle of brainvisa is that you should create a database first (one or several), which can be done just once, and then import and process data in this database. But the operation of cr...
by riviere
Tue Nov 20, 2018 1:34 am
Forum: BrainVISA
Topic: 'SelectByNomenclature' script
Replies: 3
Views: 3556

Re: 'SelectByNomenclature' script

You can get the list of objects present in the window: w.getObjects() But let's get things clear: do you want to highlight sulci which are already visible, or display sulci which are not seen on screen ? As you have used "add_graph_nodes=True" in w.addObjects(), then all sulci should be vi...
by riviere
Wed Nov 14, 2018 6:21 pm
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5926

Re: KeyError while running Morphologist on command line

I have modified the updateDatabases process to allow running it in non-GUI mode: ftp://ftp.cea.fr/pub/dsv/anatomist/updates/4.6.1/brainvisa/toolboxes/data%20management/processes/updateDatabases.py You have to replace the older one at the same location in your brainvisa installation. Then you can run...
by riviere
Wed Nov 14, 2018 5:25 pm
Forum: BrainVISA
Topic: BrainVisa Suite installation error
Replies: 5
Views: 4308

Re: BrainVisa Suite installation error

Good. Sorry for the mistake...
Denis
by riviere
Wed Nov 14, 2018 5:24 pm
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5926

Re: KeyError while running Morphologist on command line

Hi Durai, I am surprised: step 2 should not be needed, and is especially incompatible with a batch execution if it is done using the GUI. There is probably a little bug somewhere but I think some people are using it this way here, so it sounds weird. I will try to take time to investigate. Anyway th...
by riviere
Wed Nov 14, 2018 4:36 pm
Forum: BrainVISA
Topic: running a .bvproc from the command line?
Replies: 4
Views: 5880

Re: running a .bvproc from the command line?

Hi, The completion of output file names has not worked. I see two possible reasons: - maybe the relative file name is not supported with databasing (I haven't checked), you can try using an absolute path (since the databasing and completion system needs to identify databases by the beginning of the ...
by riviere
Tue Nov 13, 2018 1:00 pm
Forum: BrainVISA
Topic: 'SelectByNomenclature' script
Replies: 3
Views: 3556

Re: 'SelectByNomenclature' script

Hi, I think I know: sulci graphs may contain 2 labels sets: one for automatic labeling (from the sulcal recognition processes) and one for manual labeling. By default, if not specified, tools in anatomist are using the auto labeling. Here I think you have manual labels. Auto labels are stored in the...
by riviere
Tue Nov 13, 2018 12:42 pm
Forum: BrainVISA
Topic: Error with process Import_FROM_FreeSurfer_TO_Morpho.py
Replies: 6
Views: 5098

Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Oh yes you're right, I have inverted the grey and white label values in the left hemisphere... Interestingly the segmentation went all right, but the left meshes were not, which caused the trouble.
I have updated the process file (same location on the ftp server)
Denis
by riviere
Fri Nov 09, 2018 6:31 pm
Forum: BrainVISA
Topic: Error with process Import_FROM_FreeSurfer_TO_Morpho.py
Replies: 6
Views: 5098

Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

OK I have tried your image, and it seems that in the ribbon.mgz image, the values are not the ones we expect. I don't know if Freesurfer 6 has changed something here, and I don't remember if we have used this version with brainvisa. Which version are you running ? Anyway the problem is that the grey...
by riviere
Sun Nov 04, 2018 2:30 am
Forum: BrainVISA
Topic: Error with process Import_FROM_FreeSurfer_TO_Morpho.py
Replies: 6
Views: 5098

Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Hi,
Does the input image look "nornal" ? Is it possible to send the example image to me so that I can try it ?
Denis
by riviere
Sun Nov 04, 2018 2:28 am
Forum: BrainVISA
Topic: Error message: htmllib.HTMLParseError: unexpected call to parse_starttag
Replies: 1
Views: 2803

Re: Error message: htmllib.HTMLParseError: unexpected call to parse_starttag

Hi, Strange. I have catched the exception in the code and print the message which causes problem in a modified version of processes.py: ftp://ftp.cea.fr/pub/dsv/anatomist/updates/4.6.1/python/brainvisa/processes.py It should at least continue the execution, and print the message in the terminal like...
by riviere
Sun Nov 04, 2018 2:24 am
Forum: BrainVISA
Topic: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database
Replies: 12
Views: 6824

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Oh I'm sorry I left again a bug in the debug info prints. Could you please replace again the file sqlFSODatabase.py and try again ?
Denis

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