[Brains-users] insular cortex measurements

[Eugene Zeien]

Alright.  Since you're prepared, measuring cortical grey is
definitely the correct method.  As I recall, Benedicto's method
focused on how the ROI line cuts through the cortical grey ribbon,
while the interior and exterior components of the ROI receive far
less attention.

gene

PS:  I noticed that 'b2 help measureCorticalGreyVolumeList' gave
very minimal information, so I'm including the programmer's notes
from /opt/brains2/bin/scripts/iplTclScripts/b2IPLutils.tcl
# Procedure:  measureCorticalGreyVolumeList
# Developer:  Vincent A. Magnotta
#
# Synopsis:  This routine reads a file which contains a number of filenames.
#    These filenames can be ROIs or masks depending on the mode. The
#    results of the cortical ribbon grey matter volume measurements are put in
#    the file specified by outputFilename as well as
#    b2_saved_class_volumes.
#
# Prototype:   proc measureCorticalGreyVolumeList { inputFilename outputFilename mode }
#
#    inputFilename  - List of files to be measured
#    outputFilename  - FIle to save results as well as b2_saved_volumes
#    mode    - optional - roi or mask
#    Format for INPUT FILE
#    ---------------------
#      N
#      pathname-for-image-file-1 path-for-brain-mask-1 pathname-for-left-surface-file-1 pathname-for-right-surface-file-1 pathname-for-file-1a ...
#      .
#      .
#      .
#      pathname-for-image-file-N path-for-brain-mask-N pathname-for-left-surface-file-N pathname-for-right-surface-file-N pathname-for-file-Na ...
#
#    Where N is the total number of files to measure.

'pathname-for-file-1a ...' refers to the ROIs or masks to be measured on that brain.
Don't forget to include the 'N' at the top of your input file :-)

roberto wrote:
> Dear Eugene,
> 
> We have done a tissue classification of the brain image. We have 
> generated a brain surface as well. We  have followed Benedicto Crespo 
> Facorro /et al. /2000 tracing guidelines  for the insular  cortex  and  
> Jae-Jin Kim /et al./ 1999  tracing guidelines  for the temporal pole. 
> Both methods need a  brain surface so we have generated it. I have 
> realised that measurements using  "Measure/Class-Volume ROI" are 
> different from measurements using the "measureCorticalGreyVolumeList" 
> function . So I was wondering which method should we use?. Looking at 
> the tracing guidelines it seems that using the "Measure/Class-Volume 
> ROI" option is going to give us problems to obtain a good reliability.
> Thanks a lot and  hugs from Bene (he is my boss)
> Roberto
> 
> 
> 
> Eugene Zeien wrote:
> 
>> Assuming that you have done a tissue classification of the brain image,
>> and traced the regions of interest, you will only be able to use
>> "Measure/Class-Volume ROI".  "measureCorticalGreyVolumeList" function
>> requires additional work, you would need to generate a brain "surface".
>> The "cortical" measure would restrict the region measured to some range
>> near the surface of the brain.
>>
>> gene
>>
>> PS:  At least this is my understanding of the "cortical" measures...
>>
>> roberto wrote:
>>
>>> Hello everyone
>>>
>>> We want to obtain the gray matter volume of the insular cortex and the
>>> temporal pole. Should we use the Brains2 Toolbar and go to the
>>> "Measure/Class-Volume ROI" option or it is better to do it using the
>>> "measureCorticalGreyVolumeList" function through the command line?
>>>
>>> Thanks a lot
>>> Roberto Roiz Santiañez
>>> University Hospital Marques de Valdecilla
>>
> 
> 
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