BrainVISA

Sorry but I do not understand your question. Did you change the label in the graph ?
In that case you have to save the graph afterwards.
Olivier

Hello, the error you get means that the remeshing process did not produce what is expected. For instance if you give the wrong label, it won't find anything to remesh in the graph. This is probably what hapenned : for the label_value you wrote 'S.F.sup_left' and you should have written 'S.F.sup._lef...

I think your problem comes from the fact that you do not define your sulcus well, and the process cannot find it, which usually leads to the error you have. You have to check in the graph how your sulcus is called. For instance, if you need to get the left central sulcus and your graph has been labe...

Hello, it turns out your log file is from Brainvisa 3.0.2, and because of critical changes it cannot be read by more recent versions of Brainvisa. My advice would be first to install the latest Brainvisa version and try to process your sulci with it. There have been major changes since BV 3.0.2, inc...

Hello, Is RIC process related to Sulcus parameterization?? ( cortical Surface ->referentials -> tools-> Sulcus parameteriation) As far as I know, it is. I think you need to first run the Sulcus parameterization process and then run the sulcal depth tool. The parmaterization provides the inter-subjec...

the rar archive is corrupted, i cannot extract it properly. Would you please recreate it and send it again ?

I just posted an answer but I don't see it appearing in the thread. So here it is again, apologies if you already got this.
It seems that the previous problem is solved. Now I need the brainvisa log file to help you with this new message. Could you send it to me ?

Olivier

Could you try the following and let me know if it works ? In the ParameterizeSulcus.py, could you comment the following lines by adding the '#' character at the beginning of each lines : moving = [ 'mv', sulcusMname, self.sulcus_mesh.fullPath()] movingminf = [ 'mv', sulcusMname + '.minf', self.sulcu...

OK,
I am not very familiar with Window system commands. let me investigate that and I will come back to you later on.

olivier

Hello, I guess you are working on a different system than Linux. It must be windows... I foergot about that when I wrote the process. You have to edit the file that defines the process and change 'mv' for 'rename' at lines 138 and 139. The file is <brainvisa_install_dir>\brainvisa\toolboxes\cortical...

Hi Jeff,
I haven't really worked on the baboons for some time. This scan was to help Roberto who's playing with the same dataset and was having trouble. I will try to go a bit further.

Did he give you the details of the steps he performed with freesurfer?

No.
I'll come back on that topic.

olivier

Hi Jeff,
indeed the other version of the Histo Analysis works. But then, I also have to use the new version of the bran mask extraction to get a good result.
It's not so bad in the end considering the really poor quality of the image.
Thank you.

olivier

Hello, I am trying to process a baboon t1 image through the T1 segmentation pipeline. The quality of the image is quite poor but the bias correction works fairly well. My problem is that the histogram analysis get stuck without returning anything. The log for this particular step is : Reading volume...

Hello,
which parcellation are you talking about ? Arnaud Cachia's or Cédric Clouchoux's ? The latter is available in the cortical surface toolbox. The other one is probably available as well, but I am not sure where.

Olivier

Hello,
I would not use option 1, there are many areas where the distance computation is corrupted at least because the grey/LCR mesh does not have a sphericaml topology... THis process was not intended to be used by anybody else, we were mostly playing around with it...

olivier