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Absorption is very high when voxel size is lower than 1mm #139
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@Edouard2laire, can you post your input file with a link (dropbox, google drive, etc) and I can take a look. |
Hello, Edouard |
of course. mcxlab script/cfg is preferred |
@Edouard2laire, sorry, I might have missed, did you send a test dataset? |
Hello, I tried to generate the json file as asked but it doesnt seems to be wroking. I added ''' mcx2json(cfg,'config_orig.json') ''' here https://github.com/Nirstorm/nirstorm/blob/master/bst_plugin/forward/process_nst_cpt_fluences.m#L321 but when loading with json2mcx i get the following error :
The output of mcx2json can be found here: https://drive.google.com/file/d/1yAyPFuyvikt96n2qQk4_Qfthrsg3P0Kr/view?usp=sharing I have put the .mat file here: https://drive.google.com/file/d/1G4PFaJMZ9HUHF6Bi31y8mSWl9PvKd_RP/view?usp=sharing
is able to reproduce the bug |
So my thought was that the error was due to some coordinate issue in Brainstorm (see brainstorm-tools/brainstorm3#543). However, it doesn't seems to be the case. One thing interesting i realized is if i divide the source position by the voxel size (here: https://github.com/Nirstorm/nirstorm/blob/master/bst_plugin/forward/process_nst_cpt_fluences.m#L309) then mcxlab(cfg,'preview'); display the source correctly on the head; however, i then run in memory issue when lunching mcxlab :
Edit: if i use a more recent GPU GeForce GTX 1080 Ti, then it run without any issue. Is that expected that lower voxel size require GPU with more memory? Just to clarify, srcpos should be the coordinate in mm or in voxel ? Also, it seems that the fluence estimation is much more smooth spatially when estimating from the 1mm resolution MRI than the 0.8mm MRI. Is that expected ? It causes issue in nirsotrm when we try to normalize the fluence by the intensity of the fluence at the entry point (eg https://github.com/Nirstorm/nirstorm/blob/master/bst_plugin/forward/process_nst_import_head_model.m#L305-L326 ) as the voxel corresponding to the source position contains 0 Edit: just saw in the example scripts that it is expected. Increased the number of photons and got good results. We can close now :) |
@Edouard2laire, sorry I did not read your updated post carefully enough - for your question regarding the unit of |
Hello @fangq
I am contacting you since I am having an issue simulating fluences with an MRI which has a 0.8mm voxel size. Fron the command output it seems that all the photons are absorbed. However, the simulation seems to run fine if i first resample the MRI and the segmentation tissue to 1mm voxel size. is that an expected behavior?
here is the output if i resample the MRI: (computation seems also lot faster)
Regards,
Edouard
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