HI, FSL experts,
I am trying to calculate total intracranial calculations using SIENAX, according to the steps below (based on previous posts of this forum). My aim is to calculate a total intracranial volume for each subject; and then to use this to normalise brain volumes that were calculated with FAST. For the total brain volumes I have used CSF+GM+WM from the FAST segmentation. However in some subjects the total intracranial volume calculated via the method below returned values which were less than the total brain volume calculated with FAST. This does not make sense. Perhaps there is something wrong with my procedure with SIENAX as outlined below.
I would be very grateful for any help.
Gilberto Sousa Alves
Wolfgang Goethe Universität
Frankfurt am Main - Germany
1) fslroi input output xmin xsize ymin ysize zmin zsize
2) Review image using the fslview
3) Run the command sienax image_cropped.nii.gz -o image_sienax -B "-f 0.3 -R"
4) See the report.html file and confirm if the segment is good
5) Open the report.sienax file
6) Obtain the ICV value, after multiplying Brain times VSCALING
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