test run

[golansapir]

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!

[ashgillman]

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

[golansapir]

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::wrapexceptboost::program_options::unknown_option'
what(): unrecognised option '-b'
./test.sh: line 3: 353194 Aborted (core dumped) /home/sapir/Mirorr-master/build/bin/mirorr -m Sample_Male_Pelvis_CT.nii.gz -f Sample_Male_Pelvis_MR.nii.gz -b 3 -c 3 -t rigid -l output/CT_to_MR-rigid.tfm --save-moving output/CT_in_MR-rigid.nii.gz --fresh

real 0m0.221s
user 0m0.054s
sys 0m0.016s
terminate called after throwing an instance of 'boost::wrapexceptboost::program_options::unknown_option'
what(): unrecognised option '-b'
./test.sh: line 4: 353196 Aborted (core dumped) /home/sapir/Mirorr-master/build/bin/mirorr -m Sample_Male_Pelvis_CT.nii.gz -f Sample_Male_Pelvis_MR.nii.gz -b 3 -c 3 -t affine -l output/CT_to_MR-affine.tfm --save-moving output/CT_in_MR-affine.nii.gz --fresh

real 0m0.120s
user 0m0.025s
sys 0m0.000s

*I deleted the -b from test.sh and ran I again with success.

[ashgillman]

Ah, looks like you've found a bug there, -b was removed in this commit: 7c2260a

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.

[ashgillman]

Whoops, didn't mean to close this - let me know if it works.

[golansapir]

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

[ashgillman]

You should be able to get very good alignment - are you able to share the parameters you used? Was the MNI contrast MR?

[golansapir]

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

[ashgillman]

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.

[ashgillman]

You may also get better results if you can include a mask (--moving-mask or --fixed-mask)

[golansapir]

Thank you I'll take a look at these options today and will update

[golansapir]

Hey,
I was unable to find the full list of parameters you can use.
mirorr --help
did not execute.
Can you please assist?

[ashgillman]

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?

[golansapir]

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.

[ashgillman]

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