morphologist -> morphometry -> brain volumes error with data imported from freesurfer

Questions about BrainVisa usage and installation

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guillaume
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morphologist -> morphometry -> brain volumes error with data imported from freesurfer

Postby guillaume » Tue Jan 16, 2018 11:45 am

Hi,

I would like to compute brain volumes on data that were imported from freesurfer.
I get the following error, meaning that the voronoi volume is locked, which is systematically the case when importing data from freesurfer.
----------------------------------------------
in CSF Classif 1 The file:/bv_database/FS5.3.0_import/OAS1_0061/t1mri/default_acquisition/default_analysis/segmentation/voronoi_OAS1_0061.nii is locked. It cannot be opened for writing. You can unlock it if necessary using the contextual menu of the parameter split_mask
--------------------------------------------

First, I notice that the voronoi volume is used but is not an input of the process, which is strange.

Then I am wondering why would the voronoi (and maybe split_brain or grey_white) volumes would be opened for writing in a process supposed to only read these files for computing the volume...

Finally, do you recommend to unlock these files to be able to run the process and compute the volumes or another way is possible?

Many thanks!
gui

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riviere
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Re: morphologist -> morphometry -> brain volumes error with data imported from freesurfer

Postby riviere » Wed Jan 24, 2018 4:00 pm

Hi,
Whew, you're completely right: this process tries to overwrite the hemispheres spit file (voronoi) for a reason that I have not investigated yet, and appears to do it using a very old, obsolete process which is not the one used now in morphologist...
So I would certainly not recommend just unlocking the file right now.
The brainvolume process is 15 years old, and several people have touched it through the years so I have to dig into it to fix it. I'll keep yo in touch.
Denis

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riviere
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Re: morphologist -> morphometry -> brain volumes error with data imported from freesurfer

Postby riviere » Fri Jan 26, 2018 10:23 am

After checking it seems that this is just a stupid bug in an old process, which declares a parameter as an output where it is an input. So the voronoi is not overwritten as I feared.
There is a patched version of the faulty process here:
ftp://ftp.cea.fr/pub/dsv/anatomist/upda ... Classif.py
You can replace the one in your brainvisa installation (at the same location) with this one.
Denis


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