open-discussion
open-discussion > RE: Createobjectmapfrom surfaces using mask function
May 7, 2018 07:05 PM | Xenophon Papademetris
RE: Createobjectmapfrom surfaces using mask function
You need to run the tool bis_roimean.
Depending on what platform you are on and where BioImage Suite was installed you will need to source the appropriate setpaths file (e.g. on a Mac source /usr/local/bioimagesuite3/setpaths.sh or something like that)
Then run bis_roimean as
bis_roimean --inp bisweb/src/web/images/MNI_T1_2mm_stripped_ras.nii.gz --inp2 bisweb/src/web/images/yale_broadmann_2mm_ras.nii.gz --filename2 pos.txt --filename voi.txt
The first input -inp is the anatomical image
The second input -inp2 is the objectmap
The first output --filename specifies the filename to store the average intensity for each region
The second output -filename2 specifies the filename to store the centroid of each region (if you need it)
Depending on what platform you are on and where BioImage Suite was installed you will need to source the appropriate setpaths file (e.g. on a Mac source /usr/local/bioimagesuite3/setpaths.sh or something like that)
Then run bis_roimean as
bis_roimean --inp bisweb/src/web/images/MNI_T1_2mm_stripped_ras.nii.gz --inp2 bisweb/src/web/images/yale_broadmann_2mm_ras.nii.gz --filename2 pos.txt --filename voi.txt
The first input -inp is the anatomical image
The second input -inp2 is the objectmap
The first output --filename specifies the filename to store the average intensity for each region
The second output -filename2 specifies the filename to store the centroid of each region (if you need it)
Threaded View
Title | Author | Date |
---|---|---|
jenny | May 4, 2018 | |
Xenophon Papademetris | May 5, 2018 | |
jenny | May 7, 2018 | |
Xenophon Papademetris | May 7, 2018 | |
jenny | May 7, 2018 | |
Xenophon Papademetris | May 7, 2018 | |
jenny | May 9, 2018 | |