error in import T1 with brainvisa3.2

[faillenot]

I've installed the last brainvisa version on a XP machine.
I wanted to import a T1 image I already used with he 3.1 version without problem. I met an error :

BVerrT1MRIimport.tiff (35.36 KiB) Viewed 10908 times

I've updated the database, declared my database, and the file 'subject.referential' exists in the good path !

please help me !

[Yann Cointepas]

I suppose that you did not use the red database icon to select output file name. BrainVISA have a problem with the output file name. To find in which database to store the file, BrainVISA compares databases directory name with the begining of the output file name. If no matching database directory is found, you get the error message you have sent. If I where you I would check that the output file name is in a BrainVISA database directory and that this database is selected (in preferences). Hint, the directory name comparison is case sensitive. For instance a directory "C:\MyDirectory" is not considered to be the same as "C:\mydirectory" (I know this is not correct on most Windows and Mac file systems).

[faillenot]

I used the red database icon to select the output.
The data base is selected in preferences.
Here is my data base where the importation process have created the 'protocole', subject' and 'acquisition' directories...

BVerrT1MRIimport2.tiff (15.57 KiB) Viewed 10875 times

BVerrT1MRIimport.tiff (24.76 KiB) Viewed 10882 times

[Yann Cointepas]

In the error message from the process, the output file name is in "G:\laure\..." whereas the database directory you showed is in "G:\isabelle\...". This can explain the error message. But what I cannot understand, is how BrainVISA had been able to create a file name starting with "G:\laure" if this directory is not in its databases. Have you done something like moving the database directory and reopened a previously saved process ?

[faillenot]

As I changed in the previous post, in fact I tried to import the T1 under 2 different users and I made a mistake in copying the error message in the forum. Sorry.
It isn't the problem

[riviere]

Hi Isabelle,

In your first post, the database was in "laure" whereas in the second it is in "isabelle". I guess you have two databases and have the same problem on both, but just to be sure...
Then the data seems to have actually been written, but not inserted in the database. Can you chech in the preferences that you don't have two redundant databases (with the same path) ?
In the meantime, you can also perform an "update database" to see if the imported data are recognized afterwards. It's not a definitive solution but it may allow you to work until we find our which was the problem. However even if the update works, you may possibly get the same error at each database insertion (during processing, segmentation etc) so it will maybe not help at all.

Oh I just notice that in your database browser snapshot, the image appears with a "?" icon, meaning that the data is not at a recognized location in a database (so actually a DB update will probably not work). But it seems to be a valid location for the brainvisa-3.1 ontology (with protocol=SII, subject=arsac8, acquisition=sens). So maybe you could check if your database is defined with the correct ontology or not: in the preferences, database section, select the corresponding database and click "edit", then open the "expert settings" and check that the ontology is really "brainvisa-3.1.0". If not, that's the problem.

Denis

[faillenot]

Dear Denis and Yann,

I have the same error when I tried to import an image from G/laure/... to G/laure/BASEbrainvisa/... (when I am logged as Laure user) or from G/laure/... to G/isabelle/BASEbrainvisa/... (when I am logged as Isabelle user).
I check in the preferences that there is only one database
I have done an "update database" many time.
I check that my database is defined with the "brainvisa-3.1.0" ontology.
I even deleted the old database and install the cartopak3.2 again.

and it worked perfectly with that image with the 3.1 version.

same error...

[Yann Cointepas]

Ok, I found it. A Windows specific bug had been introduced in 3.2.0 version. This is due to a wrong usage of system directory separator ("/" on Linux and MacOS but "\" on Windows) when reading database ontology (only "/" must be used here). Hopefully, we are going to release 3.2.1 soon (at the end of this month unless we find another unexpected bug) and the problem will be corrected.

[faillenot]

Bravo Yann !

Is there a easy mean to go further ? or I wait untill the new version...
thanks anyway

Isabelle

PS : may I have answers from my posts in 'fMRI & Hrf' area ???

[Yann Cointepas]

To solve the problem, you can replace two Python files in your BrainVISA directory with the ones attached to this message. Then restart BrainVISA and update your databases (including the shared database) even if BrainVISA does not ask for it.

I will remind the fMRI/HRF developers that there are question for them on the forum.

[faillenot]

it works !
even if there are / and \ in the output filename...

BVerrT1MRIimport.tiff (18.5 KiB) Viewed 10797 times

thanks a lot
Isabelle

[faillenot]

I found a new error of the same type (well, I think) when I was running the Parallel recognition process (Morphology).

BVerrT1MRIimport2.tiff (56.52 KiB) Viewed 10788 times

[Yann Cointepas]

After your previous message I also fixed the mixing of "/" and "\" in file names. There are only "\" now on Windows. I attached the modified file (located in python/brainvisa/data directory) if you want to try it.

[faillenot]

Nice, it fixes it !

thank you

[Dominique Geffroy]

Hi,

The new version 3.2.1 of Brainvisa is now available. This problem is fixed in this update.

Dominique