open-discussion > Create objectmap from surfaces using mask function
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May 4, 2018  09:05 AM | jenny
Create objectmap from surfaces using mask function
Hi there,

I am new to the Bioimage Suite.

Is there a way to create objectmap from surfaces using mask function, and then do VOI Volume/stats computation from the command line?

Thanks a lot,

Jenny
May 5, 2018  09:05 AM | Xenophon Papademetris
Create objectmapfrom surfaces using mask function
Short answer is yes – are you physically at Yale? There is a tool (I will check Monday once I have the source code in front of me) that can do roi analysis on the command line.
May 7, 2018  06:05 AM | jenny
RE: Create objectmapfrom surfaces using mask function
Thanks a lot, but I am at Washington U in St. Louis. Would you please email the code to me, if it is possible?
May 7, 2018  12:05 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)
May 7, 2018  12:05 PM | jenny
RE: Createobjectmapfrom surfaces using mask function
Thanks a lot for your reply. I think I need to do the "Mask" function first, which I will use as my objectmap in the ROI. It will be great I could have a command line for that.

Thanks again,

Jenny
May 7, 2018  12:05 PM | Xenophon Papademetris
RE:Createobjectmapfrom surfaces using mask function
Try bis_maskimage (bis_maskimage -h for help)
May 9, 2018  10:05 AM | jenny
RE:Createobjectmapfrom surfaces using mask function
Thanks. I tried to load the functional image and spline stack file to create the MASK. I wonder if bis_maskimage is the right command to use. :(