Search found 176 matches

by Olivier Coulon
Wed May 04, 2016 1:58 pm
Forum: BrainVISA
Topic: Manual labeling of sulci
Replies: 2
Views: 2259

Re: Manual labeling of sulci

Thanks a lot Denis, problem solved. Our process can handle both names and labels but was looking for a labeled graph. The solution was the import with specifying manual labelling.

Olivier
by Olivier Coulon
Wed May 04, 2016 10:37 am
Forum: BrainVISA
Topic: Manual labeling of sulci
Replies: 2
Views: 2259

Manual labeling of sulci

Hello, I have what looks like a simple question but don't seem to be able to find an answer. We got some brains with sulci that have been manually labeled by a collaborator. SO all the 'name' attributes are filled in the fold graphs. This has been done directly on the unlabelled graphs (L/Rsubject.a...
by Olivier Coulon
Tue Mar 15, 2016 7:33 am
Forum: BrainVISA
Topic: Manual import of external segmentations
Replies: 7
Views: 3400

Re: Manual import of external segmentations

No, unfortunately this is not the issue here. Field of view, volume dimensions, voxel size are the same, and when I check the ACPC positions with the viewer they are alright...
by Olivier Coulon
Mon Mar 14, 2016 10:39 pm
Forum: BrainVISA
Topic: Manual import of external segmentations
Replies: 7
Views: 3400

Re: Manual import of external segmentations

Indeed the difference between the original and denoised file headers is one transformation. The original file has a 'Scanner-based anatomical coordinates' referential and associated transformation, and a 'Coordinates aligned to another file or to anatomical truth' . The denoised version has twice th...
by Olivier Coulon
Mon Mar 14, 2016 10:30 pm
Forum: BrainVISA
Topic: Manual import of external segmentations
Replies: 7
Views: 3400

Re: Manual import of external segmentations

I tried to run the exact same thing with a denoised version of the image, same APC file. The behaviour is strange, I get the ridges on one side only again, but it is on the other side, see the snapshot below... https://dl.dropboxusercontent.com/u/3372764/ridges_denoised.jpg Olivier
by Olivier Coulon
Mon Mar 14, 2016 7:27 pm
Forum: BrainVISA
Topic: Manual import of external segmentations
Replies: 7
Views: 3400

Re: Manual import of external segmentations

Thanks for the answer. I have used a manual setting of AC-PC... And I'm confident I set them right. Maybe a problem with the voxel size ? At least it's a direction to work with, so I'll look into that.

Olivier
by Olivier Coulon
Mon Mar 14, 2016 4:51 pm
Forum: BrainVISA
Topic: Manual import of external segmentations
Replies: 7
Views: 3400

Manual import of external segmentations

Hi everybody. I have some unusal infant data that I would like to put in the morphologist piepeline to get surfaces and possibly sulci. I have segmentations, mask, split brain that have been made by collaborators. So basically I import an image in my database, then use a personnal script to import a...
by Olivier Coulon
Mon May 11, 2015 10:50 am
Forum: BrainVISA
Topic: Parametrization of sulci
Replies: 3
Views: 3479

Re: Parametrization of sulci

The process uses .arg files, that contain all sulci, gets the sulcus of interest based on its name or label, and then generates the appropriate mesh. So all you have to do is generate the .arg file containing all sulci (this is the las step of the morphologist pipeline), label the CS, and run the pa...
by Olivier Coulon
Thu Mar 19, 2015 10:55 am
Forum: BrainVISA
Topic: Creating my own template for split brain
Replies: 3
Views: 3327

Re: Creating my own template for split brain

Thank you for your answer. I understand why it is more complicated than I thought. For our data we specify AC-PC so the corpus callosum points in Talairach space should not be too wrong, no ? So, with respect to my orgininal question, and let apart the problems you mention, if I want to try to build...
by Olivier Coulon
Wed Mar 18, 2015 2:38 pm
Forum: BrainVISA
Topic: Creating my own template for split brain
Replies: 3
Views: 3327

Creating my own template for split brain

Hello, when processing brains that are not conventional in size or/and shape (e.g. infants, or non-human primates), one common fail is the split brain procedure. I suspect this is because the template closedvoronoi.ima does not match enough the shape of the brains we are trying to process... So I am...
by Olivier Coulon
Tue Mar 11, 2014 3:39 pm
Forum: BrainVISA
Topic: Parametrization of sulci
Replies: 3
Views: 3479

Re: Parametrization of sulci

Hello Betina, to answer your two questions: 1 - the sulcal parameterization is fully implemented in BV 4.4. It is tuned for the Central Sulcus, mostly. And in any case it will not work for sulci with several connected components and/or branches. Have a look at the following page for more help: http:...
by Olivier Coulon
Thu Jan 02, 2014 4:42 pm
Forum: BrainVISA
Topic: Importing Free Surfer thickness surface file
Replies: 1
Views: 2745

Re: Importing Free Surfer thickness surface file

Hi François,

this is a problem due to the GIFTI format and the referentials conventions (direct and undirect) in BV and FS. We have been meaning to fix it for a while but never found the time to.
Hopefully we will quite soon.

Olivier.
by Olivier Coulon
Mon Jan 28, 2013 11:07 am
Forum: BrainVISA
Topic: Exporting an entire sulci to matlab
Replies: 6
Views: 4788

Re: Exporting an entire sulci to matlab

I discover this post a little late... For the special case of the central sulcus you can use the Cortical Surface-> Referentials -> Sulcus Parameterization process. The central sulcus has ionly one component for most subject so it's easier to deal with. The process provides a parameterization of the...
by Olivier Coulon
Mon Nov 12, 2012 7:04 pm
Forum: BrainVISA
Topic: transformation to original image when flipping before Morph.
Replies: 2
Views: 2208

Re: transformation to original image when flipping before Mo

Hi Denis, can't it be written in the minf file ? I need it because there are other data in the original (non flipped) referential...

Olivier
by Olivier Coulon
Mon Nov 05, 2012 3:13 pm
Forum: BrainVISA
Topic: transformation to original image when flipping before Morph.
Replies: 2
Views: 2208

transformation to original image when flipping before Morph.

Hello, I am processing clinical images with a flipped orientation (nose down) compared to our usual standards. So I allow the flipping in the first step of Morphologist but I would like to keep the corresponding transformation to use it afterwards. For instance I would like to see the white meshes i...

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