Open golansapir opened 3 years ago
Hi there,
Would you be able to provide the details of the build? Did you follow the standard build instructions from the Readme?
Cheers, Ash
Hey, thank you for your replay!
I installed everything from the beginning and tried the test.sh again.
sapir@wslinux57549:~/Mirorr-master/test$ ./test.sh
terminate called after throwing an instance of 'boost::wrapexcept
real 0m0.221s
user 0m0.054s
sys 0m0.016s
terminate called after throwing an instance of 'boost::wrapexcept
real 0m0.120s user 0m0.025s sys 0m0.000s
*I deleted the -b from test.sh and ran I again with success.
Ah, looks like you've found a bug there, -b
was removed in this commit: https://github.com/aehrc/Mirorr/commit/7c2260a32d520621f0f72717f0e899684ad87023
Removing -b
should work though, did you remove it from both commands? It works for me.
Anyway, I will update master with the fix, let me know if it helps.
Whoops, didn't mean to close this - let me know if it works.
Hey, It ran after I removed -b from both commands. I am trying to align brain PET scans to the MNI template, as I received a recommendation from Pierrick Bourgeat. After the analysis, the PET scan is not perfectly aligned to the MNI template, but I assume it's the best outcome that can be archived. Thank you, Sapir
You should be able to get very good alignment - are you able to share the parameters you used? Was the MNI contrast MR?
Hey, yes the MNI is MR. I used the same parameters for my analysis as in the test code:
time "/home/sapir/Mirorr-master/build/bin/mirorr" -m "/home/sapir/Mirorr-master/test/"$field2"_rst1PET-1-3.nii.gz" -**f "/home/sapir/Mirorr-master/test/MNI152_T1_1mm_brain.nii.gz" -c 3 -t rigid -l "/home/sapir/Mirorr-master/test/output/"$field2"_PET-MNI-rigid.tfm" --save-moving "/home/sapir/Mirorr-master/test/output/"$field2"_PET-MNI-rigid.nii.gz" --fresh**
Hey Sapir,
Perhaps try removing the -c 3
argument. This tells the algorithm to stop after 3 levels, e.g. from the test script output:
Pyramid Schedule:
Limits Level Spacing Sampling rate Image size
1st -> 1 m[15.125 15.125 5.000] f[12.500 12.500 6.000] m[16 16 2] f[ 8 8 4] m[ 32 32 62] f[ 32 32 35]
2 m[ 7.562 7.562 5.000] f[ 6.250 6.250 6.000] m[ 8 8 2] f[ 4 4 4] m[ 64 64 62] f[ 64 64 35]
Last -> 3 m[ 3.781 3.781 5.000] f[ 3.125 3.125 6.000] m[ 4 4 2] f[ 2 2 4] m[128 128 62] f[128 128 35]
4 m[ 1.891 1.891 2.500] f[ 1.562 1.562 3.000] m[ 2 2 1] f[ 1 1 2] m[256 256 125] f[256 256 70]
5 m[ 0.945 0.945 2.500] f[ 1.562 1.562 1.500] m[ 1 1 1] f[ 1 1 1] m[512 512 125] f[256 256 140]
So the lowest resolution it goes to there is 3.8xx3.8x5 mm. You could also try using the `--blockmetric mi' argument, which would use mutual information (although I might have thought the default, normalized correlation, would be adequate.
Run mirorr --help
for a full list of parameters you can use.
You may also get better results if you can include a mask (--moving-mask
or --fixed-mask
)
Thank you I'll take a look at these options today and will update
Hey, I was unable to find the full list of parameters you can use. mirorr --help did not execute. Can you please assist?
You'll have to give some more details sorry, that should work. It look like before you were using the full path for mirorr because it wasn't on your $PATH, did you do this?
Hey, I've added the mirror master folder to my path as you suggested.
sapir@wslinux57549:~$ echo $PATH /home/sapir/bin:/home/sapir/Mirorr-master
still,
sapir@wslinux57549:~$ mirorr --help mirorr: command not found sapir@wslinux57549:~$ Mirorr --help Mirorr: command not found
the mirror isn't recognized..
I assume there is something very basic that I don't understand.
Hi Sapir, yes I think it is just that your $PATH is still not quite right.
You can either run /home/sapir/Mirorr-master/build/bin/mirorr --help
Or if you'd like to add it to your $PATH:
export PATH=$PATH:/home/sapir/Mirorr-master/build/bin
mirorr --help
Either should work, adding to your $PATH is just optional and for convenience
Hey, While trying to run the test file I've received this output- sapir@wslinux57549:~$ cd /home/sapir/aehrc-Mirorr-24cc630/test sapir@wslinux57549:~/aehrc-Mirorr-24cc630/test$ '/home/sapir/aehrc-Mirorr-24cc630/test/test.sh' /home/sapir/aehrc-Mirorr-24cc630/test/test.sh: line 3: ../build/bin/mirorr: No such file or directory
real 0m0.001s user 0m0.001s sys 0m0.001s /home/sapir/aehrc-Mirorr-24cc630/test/test.sh: line 4: ../build/bin/mirorr: No such file or directory
real 0m0.001s user 0m0.001s sys 0m0.000s
I have installed the cmake build system and its gui by
sudo apt-get install cmake cmake-curses-gui
The bin folder exists, but it's empty.Will be happy to receive your input. Thank you!