Search found 310 matches
- Mon Oct 12, 2009 4:54 pm
- Forum: BrainVISA
- Topic: Converting a database to the new 3.1 format
- Replies: 1
- Views: 2858
Re: Converting a database to the new 3.1 format
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...
- Sun Sep 27, 2009 1:21 pm
- Forum: BrainVISA
- Topic: Query for DiskItem query in brainvisa databases
- Replies: 2
- Views: 3491
Re: Query for DiskItem query in brainvisa databases
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...
- Mon Jun 29, 2009 2:26 pm
- Forum: BrainVISA
- Topic: DTI echo-planar distortion correction
- Replies: 3
- Views: 4580
Re: DTI echo-planar distortion correction
Hi Muriel,
Could you send us your data so that we see if we have the same error ?
Yann
Could you send us your data so that we see if we have the same error ?
Yann
- Wed Mar 11, 2009 10:05 pm
- Forum: Anatomist
- Topic: cropping an image + referentials correspondance
- Replies: 3
- Views: 5780
Re: cropping an image + referentials correspondance
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 ...
- Mon Mar 02, 2009 10:46 am
- Forum: BrainVISA
- Topic: How to handle lots of data in batch mode?
- Replies: 24
- Views: 26265
Re: How to handle lots of data in batch mode?
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...
- Thu Feb 12, 2009 10:52 pm
- Forum: BrainVISA
- Topic: DTI Scalar feature
- Replies: 1
- Views: 2891
Re: DTI Scalar feature
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...
- Tue Feb 03, 2009 1:32 pm
- Forum: BrainVISA
- Topic: Anisotropic voxels
- Replies: 14
- Views: 9596
Re: Anisotropic voxels
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...
- Thu Jan 22, 2009 12:01 am
- Forum: BrainVISA
- Topic: importing a mnc file: is there a database format?
- Replies: 12
- Views: 10160
Re: importing a mnc file: is there a database format?
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...
- Tue Jan 06, 2009 1:55 pm
- Forum: BrainVISA
- Topic: How to handle lots of data in batch mode?
- Replies: 24
- Views: 26265
Re: How to handle lots of data in batch mode?
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...
- Fri Dec 19, 2008 1:58 pm
- Forum: BrainVISA
- Topic: Brainvisa Installation
- Replies: 7
- Views: 6857
Re: Brainvisa Installation
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 ...
- Wed Dec 17, 2008 10:35 am
- Forum: Anatomist
- Topic: Automatic segmentation into Brodmann Areas
- Replies: 10
- Views: 14824
Re: Automatic segmentation into Brodmann Areas
Hi Arno,
I sent an email to Marie with a link to your message.
Best regards,
Yann Cointepas
I sent an email to Marie with a link to your message.
Best regards,
Yann Cointepas
- Tue Dec 16, 2008 10:58 pm
- Forum: BrainVISA
- Topic: Centos OS 4.5 or Ubuntu
- Replies: 7
- Views: 6887
Re: Centos OS 4.5 or Ubuntu
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...
- Sun Nov 02, 2008 10:00 pm
- Forum: BrainVISA
- Topic: linux session reopening issue
- Replies: 1
- Views: 2828
Re: linux session reopening issue
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". ...
- Fri Oct 24, 2008 9:32 am
- Forum: BrainVISA
- Topic: Save process issue for ListOf(ReadDiskItem)
- Replies: 2
- Views: 3436
Re: Save process issue for ListOf(ReadDiskItem)
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.
- Thu Oct 23, 2008 8:22 am
- Forum: BrainVISA
- Topic: Iteration of importation process
- Replies: 2
- Views: 3593
Re: Iteration of importation process
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" ...