Hi @Fikretjfm
Honestly, I have tried all possible ways to do it but my problem remains same for both platform CYGWIN and LINUX (see my last message with screenshot). If you could run the first script (mt_perp_gamma_snap or mt_prep_gamma_snap(changed) by @FeiLiu ) then you should have PATCH file and other files. Probably @AranLarra @falahfakhri @FeiLiu @annamaria @katherine or someone else could provide us a screenshot of the terminal with code how they are running the first script and also a screenshot of the folder (containing all the file) after running. Then we have to run the second script in Matlab.
If you read previous sms (or the word documnet by @falahfakhri ) then you will understand all situations and you could see that TopoPhaseRemoval has problem with Stack processing. Therefore, I am now doing everything manually as mentioned @AranLarra and only then I can let you know my status by the weekend.
Cheers
Bayzidul