BrainVISA

Hi Olivier, Most of the fields in the minf file are not used in BrainVISA databases, the most important thing is the full path name(s) of your data. One notable exception is "uuid" but it has no influence on parameter links. I am not sure that your problem is related to minf file. What mak...

You should not need to worry about folder in order to query database. Any single DiskItem can be reached through a database query with an appropriate set of attributes. In your case, I would do what Dominique suggests and also use values from "T1 MRI Bias Corrected" keys attributes in orde...

Hi Muriel,

Could you send us your data so that we see if we have the same error ?

Yann

You can use the following command: AimsSubVolume -i t1.ima -x 20 -y 20 -z 20 -X 150 -Y 150 -Z 150 -o /tmp/cropped.ima -motion -mdir /tmp/t1_TO_cropped.trm -minv /tmp/cropped_TO_t1.trm Then you can use one of the two output transformation matrix between t1.ima and cropped.ima in Anatomist. Note that ...

defaultContext().runProcess("ImportT1MRI", input="/home/jinju/t1_icbm.mnc", output = { 'protocol': 'a protocol', 'subject': 'a subject', 'acquisition': 'default_acquisition' } ) Or you may prefer the following syntax: defaultContext().runProcess("ImportT1MRI", input=&q...

Some features just consider a bundle as a set of 3D points. These points are projected into several images (FA, ADC, VR, etc.) and for each image a few statistical values are extracted (max, min, mean, standard deviation, etc.). For Y shape bundle, I suppose you are interessed in values extracted al...

If there is a mismatch between BrainVISA database indexation and images files, it is only visible in BrainVISA. Since, the header of your image file ( *.dim ) was modified, it means that the problem is probably elsewhere. The final voxel size read by low-level image readers used in T1 pipeline can b...

If you are lost with processes that you often use, you can create your own processes organization. 1) Start by right-clicking in the toolbox panel and choose New 2) Enter a name for the new item 3) Start drag-and-drop processes on this new "toolbox" 4) You can organize processes in the too...

Hi Jin-ju, Usually when we need to apply a process to several patients, we use the iteration BrainVISA feature that is available for most of the processes and pipelines (see http://brainvisa.info/doc/brainvisa-3.1/bv_man/en/html/ch06s03.html#N10A53 for more details). However there is a batch mode in...

Hi, It is common to install BrainVISA as root in a read-only directory and use it from other accounts, it should not cause trouble. Let's try to find out what is going on for you. There is one built-in database that is in BrainVISA package directory. It is only used for reading. For other databases ...

Hi Arno,

I sent an email to Marie with a link to your message.

Best regards,

Yann Cointepas

Hi Michel, I think there is no missing library but a syntax error in BrainVISA. BrainVISA had been tested a bit on Ubuntu 8.04 and Ubuntu 8.10. 1) You can ignore Fontconfig related messages. We provide some old system libraries (from Fedora Core 4) and old Fontconfig is not able to read newer config...

I did not checked yet but I bet that when you restart, BrainVISA is launched by KDE with wrong parameters. If KDE try to give BrainVISA a "-session" parameter, BrainVISA will interpret that as "-s ession" which means try to open a window for the process named "ession". ...

Your change is Ok Nicolas. convertStateValue could have been a static method but I do not know how to implement recursive static method that could be overloaded in a derived class. With an instance method (or a class method) we keep the possibility redefine it in a subclass.

I recently added the possibility to enter several values in attributes fields (such as protocol, subject, etc.). Just type space separated values and use double quotes if a value contains space. For instance, if you want to iterate importation on three subjects named "me", "him" ...