Does this project support running on win10 system?

[ljljlj02]

What changes would be required if the project were to run on Windows 10?

[sarthakpati]

Nothing, this should work on Windows.

[ljljlj02]

This is my first time using the git command(my system is Win10). After I download git software, I run git clone https://github.com/CBICA/BrainMaGe.git successfully。 But when I execute the XXX command git lfs pull，The following error was encountered `Error updating the git index: (0/2), 148 MB | 23 KB/s error: BrainMaGe/init.py: cannot add to the index - missing --add option? fatal: Unable to process path BrainMaGe/init.py

Errors logged to C:\Users\x\BrainMaGe.git\lfs\logs\20211105T170409.6038543.log Use git lfs logs last to view the log. batch response: Post "https://github.com/CBICA/BrainMaGe.git/info/lfs/objects/batch": read tcp 192.xxx.xxx.6:58853->20.205.243.xxx:443: wsarecv: A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond. cannot write data to tempfile "C:\Users\x\BrainMaGe\.git\lfs\incomplete\7eff7f10d541c5f2204b6e3882ea1070698c11e10a3d77918589692e36e0cf1c4123608929": LFS: read tcp 192.xxx.xxx.6:59111->185.xxx.xxx.xxx:443: i/o timeout error: failed to fetch some objects from 'https://github.com/CBICA/BrainMaGe.git/info/lfs' ` I don't know what went wrong. Any help would be greatly appreciated.

[sarthakpati]

Hey,

I am able to run the same instructions:

(base) PS C:\Users\tester> cd .\Downloads\test_brainmage\
(base) PS C:\Users\tester\Downloads\test_brainmage> git clone https://github.com/CBICA/BrainMaGe.git
Cloning into 'BrainMaGe'...
remote: Enumerating objects: 1009, done.
remote: Counting objects: 100% (291/291), done.
remote: Compressing objects: 100% (195/195), done.
remote: Total 1009 (delta 170), reused 183 (delta 96), pack-reused 718
Receiving objects: 100% (1009/1009), 241.65 KiB | 3.36 MiB/s, done.
Resolving deltas: 100% (614/614), done.
(base) PS C:\Users\tester\Downloads\test_brainmage> cd BrainMaGe
(base) PS C:\Users\tester\Downloads\test_brainmage\BrainMaGe> git lfs pull
(base) PS C:\Users\tester\Downloads\test_brainmage\BrainMaGe> conda env create -f requirements.yml
Collecting package metadata (repodata.json): done

Have you installed Git-LFS? If not, can you install and try the command once again?

[ljljlj02]

I downloaded git-lfs and executed the following command at Git Bash： `x@DESKTOP-xxx MINGW64 ~/BrainMaGe (master) $ git lfs install Updated git hooks. Git LFS initialized.

x@DESKTOP-xxx MINGW64 ~/BrainMaGe (master) $ git lfs pull Downloading LFS objects: 0% (0/1), 30 MB | 33 KB/s Downloading LFS objects: 0% (0/1), 30 MB | 33 KB/s

Downloading LFS objects: 0% (0/1), 38 MB | 14 KB/s

Error updating the git index: (0/1), 65 MB | 13 KB/s error: BrainMaGe/init.py: cannot add to the index - missing --add option? fatal: Unable to process path BrainMaGe/init.py

Errors logged to xxx\BrainMaGe.git\lfs\logs\20211106T140903.7362199.log Use git lfs logs last to view the log. batch response: Post "https://github.com/CBICA/BrainMaGe.git/info/lfs/objects/batch": dial tcp xx.xxx.x.16xx6:443: connectex: A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond. error: failed to fetch some objects from 'https://github.com/CBICA/BrainMaGe.git/info/lfs' `

I googled the error and the answer is this: https://github.com/git-lfs/git-lfs/issues/3457 It is a pity that I am not able to solve it. I think the operation mode of your project is similar to PyRadiommics, but it is difficult for me as a novice to operate Git, so I may have to find other ways to remove the skull.

[sarthakpati]

You could try using wget directly:

cd BrainMaGe
wget https://github.com/CBICA/BrainMaGe/raw/master/BrainMaGe/weights/resunet_ma.pt ./BrainMaGe/weights
wget https://github.com/CBICA/BrainMaGe/raw/master/BrainMaGe/weights/resunet_multi_4.pt ./BrainMaGe/weights

Example:

(base) user@cbica-bakas-pc06:/mnt/c/Users/user/Downloads$ wget https://github.com/CBICA/BrainMaGe/raw/master/BrainMaGe/weights/resunet_ma.pt .
--2021-11-06 09:57:24--  https://github.com/CBICA/BrainMaGe/raw/master/BrainMaGe/weights/resunet_ma.pt
Resolving github.com (github.com)... 140.82.112.4
Connecting to github.com (github.com)|140.82.112.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://media.githubusercontent.com/media/CBICA/BrainMaGe/master/BrainMaGe/weights/resunet_ma.pt [following]
--2021-11-06 09:57:24--  https://media.githubusercontent.com/media/CBICA/BrainMaGe/master/BrainMaGe/weights/resunet_ma.pt
Resolving media.githubusercontent.com (media.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.108.133, ...
Connecting to media.githubusercontent.com (media.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 33215195 (32M) [application/octet-stream]
Saving to: ‘resunet_ma.pt’

resunet_ma.pt                    100%[==========================================================>]  31.68M  13.3MB/s    in 2.4s

2021-11-06 09:57:27 (13.3 MB/s) - ‘resunet_ma.pt’ saved [33215195/33215195]

--2021-11-06 09:57:27--  http://./
Resolving . (.)... failed: No address associated with hostname.
wget: unable to resolve host address ‘.’
FINISHED --2021-11-06 09:57:29--
Total wall clock time: 5.0s
Downloaded: 1 files, 32M in 2.4s (13.3 MB/s)

This should give you the model weights without using LFS.