Hi
I am reaching out to ask some questions about segmenting PET data. I am working with an
open access dataset
(ADNIDOD Updated ADNIDOD Datasets Now Available | ADNI) to analyze neurobiological differences in veterans with a history of TBI. I am hoping to use the PET data (there are the raw dicoms and preprocessed PET data) to segment the choroid plexus using a specific segmentation
software (GitHub - EhsanTadayon/choroid-plexus-segmentation: Segmentation of Choroid Plexus using Gaussian Mixture Model) I have already done the segmentation on the T1 images, but am hoping to apply
the masks to the preprocessed PET images. I was looking at using the
“mri_gtmpvc” with freesurfer or fslstats with fsl command to segment the choroid plexus using the mask I already created but was hoping for some guidance. There are also several options of preprocessed PET data I can chose from, including “co-registered averaged standardized image and voxel” including
“co-registered averaged standardized image and voxel with uniform resolution”
and “co-registered averaged” or “co-registered dynamic”. When using fslstats i get a message saying my mask and image are different sizes.
MASK:
fslinfo lh_choroid_gmmb_mask_susan.nii.gz
data_type FLOAT64
dim1 256
dim2 256
dim3 256
dim4 1
datatype 64
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 1.000000
cal_max 0.000000
cal_min 0.000000
file_type NIFTI-1+
PET image
fslinfo I433008_AV45_Coreg,_Avg,_Standardized_Image_and_Voxel_Size_20140604160707_3.nii
data_type FLOAT32
dim1 160
dim2 160
dim3 96
dim4 1
datatype 16
pixdim1 1.500000
pixdim2 1.500000
pixdim3 1.500000
pixdim4 0.000000
cal_max 0.000000
cal_min 0.000000
file_type NIFTI-1+
If anyone are willing to help or can connect me to someone how might have time
to reply or quickly chat, that would be great. I appreciate the support.