GeneralImport image flipped

Questions about BrainVisa usage and installation

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atsui
Posts: 13
Joined: Fri Jan 13, 2012 9:23 pm
Location: Davis, CA USA

GeneralImport image flipped

Post by atsui »

Hi again,

I'm using Data Management > T1 MRI > GeneralImport to import my own Left Grey White Mask for use in mesh generation in the Morphologist 2012 pipeline, but it seems like the mask is flipped with respect to left and right. Maybe it has something to do with the input_spm_orientation setting being set to Neurological? When I set the data_type to "Left Grey White Mask", the input_spm_orientation switches automatically to "Neurological". I will manually switch it to "Radiological", but when I press Run, the log suggests that the input_spm_orientation is still set to Neurological - see attached screenshot. In the window on the right, the mask is overlayed on the right hemisphere (side with the pill) when it should be on the left. I've verified that the input image is on the left side. Is this a bug or did I mess up?

--Alex
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riviere
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Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Re: GeneralImport image flipped

Post by riviere »

Hi Alex,
Oh, you're right, the General import process didn't pass the 'input_spm_orientation" parameter to specific import sub-processes. Moreover the way it was used was completely obsolete (we haven't used Analyze images for a while here). I have fixed a pair of processes (GeneralImport and ImportData). You can download them and place them in the same directory in your brainvisa install (<brainvisa_dir>/brainvisa/toolboxes/data management/import):
ftp://ftp.cea.fr/pub/dsv/anatomist/upda ... nt/import/
Denis
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