Hi France,
two questions on orientation of T1 images in Brainvisa
About the process: "Import T1 MRI"
Why does the process automatically choose RADIOLOGICAL orientation when I input an Analyze image that I know is in NEUROLOGICAL orientation?
Then, about "Prepare subject for anatomical pipeline":
When I input the same image in Neurological orientation (and accordingly, the left hemisphere point I chose is on the left of the axial image)
The process says "image is in neurological mode
Image needs to be flipped, but you did not allow it, so it won't change. Expect problems in hemispheres separation, and sulci recognition will not work anyway."
?? Why would I need to flip the image?
Why hemisphere separation and sulci recognition would not work?
Many thanks for any enlightening answer on this...
Neurological-Radiological orientation
Neurological-Radiological orientation
Pascal Belin, PhD
Vocal Neurocognition Laboratory
Departement de Psychologie
Universite de Montreal
Vocal Neurocognition Laboratory
Departement de Psychologie
Universite de Montreal
I am not sure of my answer because I do not develop Anatomist/BrainVisa, but :
- BrainVisa processes assume the images are in radiological convention, and some of them do not work it they are not.
- You can ask Anatomist to display all images in the neurological orientation : just go to "Settings" menu in Anatomist, then "preferences", "window" tab, and you can choose the convention you want Anatomist to use.
At least it works with the development version I am using.
- BrainVisa processes assume the images are in radiological convention, and some of them do not work it they are not.
- You can ask Anatomist to display all images in the neurological orientation : just go to "Settings" menu in Anatomist, then "preferences", "window" tab, and you can choose the convention you want Anatomist to use.
At least it works with the development version I am using.
Manik Bhattacharjee
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riviere
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Our images here are acquired in radiological convention. So the default parameters consider images to be in radiological mode. But if you know your data are in neurological convention, you can just change the value of the parameter in brainvisa (there is no way to guess the orientaiton of SPM images before they go in BrainVisa/Aims). If you do so, the image will be tagged as being in neuro mode (and loaded in the correct way afterwards).
Our pipeline expects images to be INTERNALLY in radiological orientation. This doesn't exactly mean they must be in radio mode on disk (some formats can flip data at load time), but it's simpler to think they do.
Read http://brainvisa.info/doc/html/aims/en/spmformat.html and http://brainvisa.info/doc/html/aims/en/config.html for more details.
Anatomist displays images in radiological convention by default. There is an option in the preferences to change it, but be careful if you change it and remember you have changed the viewing behaviour.
BUT if images are in the wrong orientation on disk (ie in neuro orientation on disk when nothing indicates they are in this mode), they could be loaded and displayed flipped.
PrepareSubject affers the possibility to flip images that are in the wrong orientation if you enable it (it is disabled by default as you have noticed). If you have already selected the neuro mode for SPM images in the importation process, you should NOT flip it again in PrepareSubject. But this option can still be useful to deal with non-SPM images, or images acquired in sagittal or other orientation.
If you run the pipeline on an image in the wrong orientation (with left/right flipped), the segmentations will probably work, but will produce images, meshes and graphs also flipped, with the wrong orientation. You should really try to avoid it because it's a source of errors and you will probably not understand anything on your data later.
All this is a bit complex and is a source of vicious errors. We already had a number of headaches dealing with various data coming in different formats, from different scanners or different versions of SPM... We just can't detect images orientations so YOU have to indicate it the first time you process an image...
Denis
Our pipeline expects images to be INTERNALLY in radiological orientation. This doesn't exactly mean they must be in radio mode on disk (some formats can flip data at load time), but it's simpler to think they do.
Read http://brainvisa.info/doc/html/aims/en/spmformat.html and http://brainvisa.info/doc/html/aims/en/config.html for more details.
Anatomist displays images in radiological convention by default. There is an option in the preferences to change it, but be careful if you change it and remember you have changed the viewing behaviour.
BUT if images are in the wrong orientation on disk (ie in neuro orientation on disk when nothing indicates they are in this mode), they could be loaded and displayed flipped.
PrepareSubject affers the possibility to flip images that are in the wrong orientation if you enable it (it is disabled by default as you have noticed). If you have already selected the neuro mode for SPM images in the importation process, you should NOT flip it again in PrepareSubject. But this option can still be useful to deal with non-SPM images, or images acquired in sagittal or other orientation.
If you run the pipeline on an image in the wrong orientation (with left/right flipped), the segmentations will probably work, but will produce images, meshes and graphs also flipped, with the wrong orientation. You should really try to avoid it because it's a source of errors and you will probably not understand anything on your data later.
All this is a bit complex and is a source of vicious errors. We already had a number of headaches dealing with various data coming in different formats, from different scanners or different versions of SPM... We just can't detect images orientations so YOU have to indicate it the first time you process an image...
Denis