No bin folder under mantis/ITKStuff/Build.${ARCH}/MANTiS-build

[lekai-crystal]

Hi, I have a question. After the installation of mantis, I found no "bin" folder under the "mantis/ITKStuff/Build.${ARCH}/MANTiS-build" directory. I use macos Ventura 13.2.1 with apple M2 chip, matlab2023b. Could you tell me how to solve the problem? Thanks a lot.

[lekai-crystal]

Though there is no "bin" folder, I can open the mantis GUI through spm GUI. Does it matter?

[lekai-crystal]

I tired the mantis found it didn't work.

I have read the previously raised issues and found the same question (No bin folder in MANTiS-build #13). I tired the solution:"Try deleting the cloned folder. Reclone, then do cd mantis git checkout BumpITKVersion" but I failed. The command showed:"error: pathspec 'BumpITKVersion' did not match any file(s) known to git" I have installed git cmake and xcode.

Could you tell me how to solve the problem.

Thank you in advance.

Regards, Lekai Luo

[richardbeare]

First up - I haven't tested on an M2 mac, hopefully we'll be able to do something.

The bin directory won't exist until you've run a cmake configuration step and build (which should take some time).

I can't see why the git checkout command didn't work. Are you sure you've run these commands:

git clone https://github.com/DevelopmentalImagingMCRI/mantis.git
cd mantis
git submodule init
git submodule update

before running

git checkout BumpITKVersion

[lekai-crystal]

Hi， Thank you so much for your response. I deleted the mantis folder and reinstalled it as the way you suggested. But it didn't work. There is still an error with "git checkout BumpITKVersion"

I would really appreciate it if you could help me with this problem.

[lekai-crystal]

Then I tried the following steps:

cd ITKStuff
export ARCH=MACA64
mkdir Build.${ARCH} 
cd Build.${ARCH}
cmake ../SuperBuild

When running "cmake ../SuperBuild", there might be something wrong. I saw some steps failed as reported in the terminal window.

There is no "bin" folder under the "MANTiS-build" directory. I'm looking forward to your reply.

Sincerely, Lekai Luo

[richardbeare]

Ah - you need to run "make" after cmake. cmake is the configuration step, make does the building.

I think the BumpITKVersion branch must have been integrated into the main, then deleted.

[lekai-crystal]

Dear Richard, Thanks for your advice. After running "make" after "cmake", the bin folder under "MANTiS-build" is made.

But there is still an error with "git checkout BumpITKVersion". As before, the terminal command window showed "error: pathspec 'BumpITKVersion' did not match any file(s) known to git".

Then I tried to use mantis through spm on matlab. The matlab command window showed:

SPM: spm_mantis (1) 22:46:34 - 14/05/2024

Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item tools: No field(s) named mantis Item file_move: Dependency 'Mantis: Phase 1 tissue classification: Seg Params' could not be added. Item file_move: Dependency 'Folders for phases - image files get placed here: Phase1 single subfolder' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: c1 Images' could not be added. Item file_move: Dependency 'Folders for phases - image files get placed here: Phase1 single subfolder' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: c3 Images' could not be added. Item file_move: Dependency 'Folders for phases - image files get placed here: Phase1 single subfolder' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: c2 Images' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: c4 Images' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: c5 Images' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: c6 Images' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: c7 Images' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: c8 Images' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: c9 Images' could not be added. Item file_move: Dependency 'Folders for phases - image files get placed here: Phase1 single subfolder' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: Forward Deformations' could not be added. Item file_move: Dependency 'Folders for phases - image files get placed here: Phase1 single subfolder' could not be added. Item file_move: Dependency 'Mantis: Phase 1 tissue classification: Inverse Deformations' could not be added. Item file_move: Dependency 'Folders for phases - image files get placed here: Phase1 single subfolder' could not be added.

I'm sorry to bother you again. But how to solve the problem?

Sincerely, Lekai Luo

[richardbeare]

At what point did those errors appear? Had you restarted matlab and spm after the mantis install process was complete?

I might need screenshots to solve this

[lekai-crystal]

Dear Richard, When I open mantis and click on mantis/mantis segmentation pipeline, the matlab command window will show the error.

I'm using the development version of spm, which support the macbook with apple silicon (https://github.com/spm/spm/). The common spm12 doesn't work on my macbook.
So what is the problem? 

Sincerely, Lekai

[richardbeare]

I'm afraid I have no insight into this. I'll do some tests on my M1 mac, but can't promise anything. It will take some time, I'm afraid.

[richardbeare]

I think we may be over the first hurdle - there is at least something for you to test.

go to your mantis folder and run

git pull
git checkout DevSPMSupport

Then test again - no need to rebuild etc.

The problem I have found was caused by a change in a core spm function about 3 years ago, leading to a structure element being returned as a function handle instead of the results of a function call.

I've only tested that this fixes the first problem, which it seems to. There are likely to be others as you work your way through.

[lekai-crystal]

Dear Richard, Now I can successfully open the mantis segmentation pipeline. I'm so happy. Thanks a lot. I'm trying the other steps. ^_^

Best wishes, Lekai