Radiological/neurological convention and usage of aimsrc configuration

Radiological/neurological convention and usage of aimsrc configuration
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Warning

This part of the tutorial is related to display problems that can occur when using Analyze format. It is highly recommended to use Nifti format instead of Analyze format. Indeed, Analyze format used to lack information about convention, which leads to ambiguities in the way of displaying images.

KEYWORDS: .aimsrc file, minf file.

Before beginning, please note the difference between the Anatomist display, how data are stored and how data are read:

What does "the Anatomist display" mean: the display is independant of storing and reading data on your disk. You can display data in neurological convention even if they are stored and read like radiological data. It depends on settings (Settings -> Preferences -> Windows).
How data is stored: this corresponds to the file organization. By using our tools (Aims Library), data is considered in radiological convention.
How data is read: attributes contained in .aimsrc and .minf file can give additional information. For instance, the spm_radio_convention indicates that the data is in radiological convention if value is 1 otherwise SPM data will read in neurological convention.

So, in our tools two files can give information about reading data: .minf and the .aimsrc file. The .minf file have priority. To summarize, volumes are considered in radiological convention, then information from .minf and/or .aimsrc file are read and data is displayed according to Anatomist settings.

Here we have many examples of configuration. Tests are run with an analyze data set with or without the .minf file. If you want to try them, then you must create the .minf file (<name_data>.img.minf) and the .aimsrc (if your user account doesn't have it) with a text file editor. In order to try the configurations, you can use the following demonstration data, which can be found in the data_for_anatomist/right_and_left directory. A correct display will be checked by visualizing a lesion located in the right hemisphere. Note that the data is stored in radiological convention and normalized with SPM2. In other words, normalized data is in radiological convention, but WARNING the output convention after normalisation depends on your SPM configuration. In our case, we considere that the input and output convention after SPM2 normalization are the same.

Table 4.1. minf/aimsrc files

Configuration

Normalized data and display with radiological convention

No_Normalized data and display with radiological convention

.minf file: none

.aimsrc file

attributes = {
                  '__syntax__' : 'aims_settings',
                  'spm_input_radio_convention' : 1,
                  'spm_input_spm2_normalization' : 0,
                  'spm_output_radio_convention' : 1,
                  'spm_output_spm2_normalization' : 0,
                  }

The display is not correct. Why: data is normalized with SPM2 and the settings indicate the SPM99 mode use with spm_input_spm2_normalization = 0 (thus a flip on x axis is done).

The display is correct.

.minf file: none

.aimsrc file

attributes = {
                  '__syntax__' : 'aims_settings',
                  'spm_input_radio_convention' : 1,
                  'spm_input_spm2_normalization' : 1,
                  'spm_output_radio_convention' : 1,
                  'spm_output_spm2_normalization' : 1,
                  }

The display is correct.

.minf file (for each volume)

attributes = {
                  'spm_spm2_normalization': 1
                  }

.aimsrc file

attributes = {
                  '__syntax__' : 'aims_settings',
                  'spm_input_radio_convention' : 1,
                  'spm_input_spm2_normalization' : 0,
                  'spm_output_radio_convention' : 1,
                  'spm_output_spm2_normalization' : 0,
                  }

The display is correct. But: information between the .minf and the .aimsrc are different. The correct information is contained in the .minf file, which is read in priority.

The display is correct. But: information contained in the .minf file is not adapted to the volume.

.minf file (for each volume)

attributes = {
                  'spm_spm2_normalization': 0
                  }

.aimsrc file

attributes = {
                  '__syntax__' : 'aims_settings',
                  'spm_input_radio_convention' : 1,
                  'spm_input_spm2_normalization' : 1,
                  'spm_output_radio_convention' : 1,
                  'spm_output_spm2_normalization' : 1,
                  }

The display is not correct. Why: data is normalized with SPM2 and the settings indicate the SPM99 mode use with spm_spm2_normalization = 0 (thus a flip on x axis is done).

The display is correct. But: information contained in the .minf file is not adapted to the volume.

.minf file (for each volume)

attributes = {
                  'spm_radio_convention' : 1
                  }

.aimsrc file

attributes = {
                  '__syntax__' : 'aims_settings',
                  'spm_input_radio_convention' : 1,
                  'spm_input_spm2_normalization' : 0,
                  'spm_output_radio_convention' : 1,
                  'spm_output_spm2_normalization' : 0,
                  }

The display is correct. But: information contained in the .minf file is not adapted to the volume.

The display is correct.

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