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MIC-DKFZ / HD-BET

MRI brain extraction tool
Apache License 2.0
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pip3 NOT pip! #8

Open drswgw opened 4 years ago

drswgw commented 4 years ago

Ubuntu18 and Mate19 have python 2.7 and python 3.7 running, but python 2.7 is the default.

the install directions need to include (for Ubuntu18 & Mate19)

sudo apt-get install python3-pip cd ~/HD-BET pip3 install -e .

the directions as written use pip (which defaults to python 2.7 in ubuntu and generates a "there is no python3.5 or greater" error when trying to install HD-BET)

which then prompts one to one either try and alias out the python2.7 in ubuntu, which works poorly...or uninstall python 2.7, and for ubuntu, that leads to a truly epic fail/disaster.

existing install directions are TOO GENERAL...need to be more specific as stated above if the install is to work smoothlyfor Ubuntu18 or MATE19

FabianIsensee commented 4 years ago

Hi, I will add a notification that users should also try pip3 if they run into problems. This should however not be the default recommendation, because what pip points to depends on your system. For me and many others, pip is python3 as it should be (Python2 is end of life). Best, Fabian

drswgw commented 4 years ago

Hi Fabian, I am actually trying different OS flavors... MATE 19 is so far, a bust....a lot/too many path problems on install. Ubuntu16 is a work in progress...no path problems...but more pip problems...now the egg won't install...and it complains about pip3 being version 8 instead of version 20....

In short...version control for HD-BET is lacking...so far....no install...or more precisely...install leads to a non-operating tool...command won't fly...no hd-bet command....

Is there another way to install other than pip...so far pip is a disaster....

Scott Gordon, Ph.D.

Advanced Imaging Center at

Dartmouth Hitchcock Medical Center

& Thayer School of Engineering

Dartmouth College

802-355-3225

From: Fabian Isensee notifications@github.com Sent: Tuesday, March 24, 2020 6:05 AM To: MIC-DKFZ/HD-BET HD-BET@noreply.github.com Cc: Scott W. Gordon Scott.W.Gordon@dartmouth.edu; Author author@noreply.github.com Subject: Re: [MIC-DKFZ/HD-BET] pip3 NOT pip! (#8)

Hi, I will add a notification that users should also try pip3 if they run into problems. This should however not be the default recommendation, because what pip points to depends on your system. For me and many others, pip is python3 as it should be (Python2 is end of life). Best, Fabian

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMIC-DKFZ%2FHD-BET%2Fissues%2F8%23issuecomment-603145394&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Cab924d9853914ac8e5cc08d7cfdadbed%7C995b093648d640e5a31ebf689ec9446f%7C0%7C1%7C637206411213959257&sdata=FwsuCpCHkVtcdo5aTa%2B5jnYfqIXCdQVutob60ETx3vY%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO5OB77GDEMI253ISVLXNHDRJCAV5ANCNFSM4LSJKX6A&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Cab924d9853914ac8e5cc08d7cfdadbed%7C995b093648d640e5a31ebf689ec9446f%7C0%7C1%7C637206411213969251&sdata=jFqfmcN7%2BnHKlnkPRFEfHKX%2BDMy6aibR7t9gdVafpzk%3D&reserved=0.

FabianIsensee commented 4 years ago

Hi Scott, pip is really the best and easiest tool to install anything in python. I am surprised that you have so many problems. My recommendation is to create a virtual environment. On Ubuntu this is really easy:

virtualenv -p python3 my_venv # creates a folder my_venv with the virtual environment files
source my_venv/bin/activate # activates the virtual environment. You nee to do this every time you intend to run hd-bet
pip install --upgrade pip # this will update pip and it won't complain anymore. And yes it's pip, not pip3. The virtual environment will make it point to the correct one
# now proceed to install hd-bet from here

Best, Fabian

drswgw commented 4 years ago

Hi Fabian, Loving the virtual environment! And the pip version thing...outside venv...no pip...inside venv...pip 20. Installed from the same files...no install errors! Guessing you might be able to run a venv on MATE19 too.... Anyway, will keep you posted once I upload some brain files to play with... my fingers and ventricles are most definitely crossed!

Scott Gordon, Ph.D.

Advanced Imaging Center at

Dartmouth Hitchcock Medical Center

& Thayer School of Engineering

Dartmouth College

802-355-3225

From: Fabian Isensee notifications@github.com Sent: Tuesday, March 24, 2020 8:09 AM To: MIC-DKFZ/HD-BET HD-BET@noreply.github.com Cc: Scott W. Gordon Scott.W.Gordon@dartmouth.edu; Author author@noreply.github.com Subject: Re: [MIC-DKFZ/HD-BET] pip3 NOT pip! (#8)

Hi Scott, pip is really the best and most easy tool to do anything in pyhton. I am surprised that you have to many problems. My recommendation is to create a virtual environment. On Ubuntu this is really easy:

virtualenv -p python3 my_venv # creates a folder my_venv with the virtual environment files source my_venv/bin/activate # activates the virtual environment. You nee to do this every time you intend to run hd-bet pip install --upgrade pip # this will update pip and it won't complain anymore. And yes it's pip, not pip3. The virtual environment will make it point to the correct one

now proceed to install hd-bet from here

Best, Fabian

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMIC-DKFZ%2FHD-BET%2Fissues%2F8%23issuecomment-603201917&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Ce1957d8498164d8bffd108d7cfec2957%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206485524443051&sdata=19bQcHzirbT5nky%2FeRPFjq8qcaV3dKQ8EshN6v4xFDE%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO5OB7YIIFCCYJLYO6LBUK3RJCPGNANCNFSM4LSJKX6A&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Ce1957d8498164d8bffd108d7cfec2957%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206485524443051&sdata=ZEbubRUQqImIq2yHjf0ldLcMxA73r%2FgxXwpyPueXF24%3D&reserved=0.

drswgw commented 4 years ago

Hi Fabian, Using the python venv, got HD-BET to run...somewhat....on a test file made using dcm2nii on raw Siemens multi-slice 3D data to make... myfile.nii.gz

ran hd-bet - i infolderpath -o outfolderpath (there is no outfolder yet...but hoping it will create one with output...)

it downloaded from xenodo.org OK, filled up the bet-params folder with that...

then went into traceback mode...and came up with...

Assertion Error: Found no nvidia driver on your system, please check that you have an nvidia gpu....

yep...no nvidia...it's a core i5 vPro computer (a thinkpad 430) that uses INTEL video and which gets implemented using MESA and openGL 3 in ubuntu 16 in this case.

Don't have a fancy computer to burn for a linux box...this one is nice...but nothing fancy...time to run is not an issue..the computer is dedicated and can run for days...literally...

Scott Gordon, Ph.D.

Advanced Imaging Center at

Dartmouth Hitchcock Medical Center

& Thayer School of Engineering

Dartmouth College

802-355-3225

From: Fabian Isensee notifications@github.com Sent: Tuesday, March 24, 2020 8:09 AM To: MIC-DKFZ/HD-BET HD-BET@noreply.github.com Cc: Scott W. Gordon Scott.W.Gordon@dartmouth.edu; Author author@noreply.github.com Subject: Re: [MIC-DKFZ/HD-BET] pip3 NOT pip! (#8)

Hi Scott, pip is really the best and most easy tool to do anything in pyhton. I am surprised that you have to many problems. My recommendation is to create a virtual environment. On Ubuntu this is really easy:

virtualenv -p python3 my_venv # creates a folder my_venv with the virtual environment files source my_venv/bin/activate # activates the virtual environment. You nee to do this every time you intend to run hd-bet pip install --upgrade pip # this will update pip and it won't complain anymore. And yes it's pip, not pip3. The virtual environment will make it point to the correct one

now proceed to install hd-bet from here

Best, Fabian

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMIC-DKFZ%2FHD-BET%2Fissues%2F8%23issuecomment-603201917&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Ce1957d8498164d8bffd108d7cfec2957%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206485524443051&sdata=19bQcHzirbT5nky%2FeRPFjq8qcaV3dKQ8EshN6v4xFDE%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO5OB7YIIFCCYJLYO6LBUK3RJCPGNANCNFSM4LSJKX6A&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Ce1957d8498164d8bffd108d7cfec2957%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206485524443051&sdata=ZEbubRUQqImIq2yHjf0ldLcMxA73r%2FgxXwpyPueXF24%3D&reserved=0.

FabianIsensee commented 4 years ago

Hi Scott, have you tried running hd-bet with -device cpu -mode fast -tta 0 Best, Fabian

drswgw commented 4 years ago

Hi Fabian, As an option to the hd-bet command? meaning hd-bet -i foldin -o foldout -device etc.

can that be called as a separate hd-bet command i.e. before setting folders and so on?

I will mess around...and keep you posted....

Scott Gordon, Ph.D.

Advanced Imaging Center at

Dartmouth Hitchcock Medical Center

& Thayer School of Engineering

Dartmouth College

802-355-3225

From: Fabian Isensee notifications@github.com Sent: Tuesday, March 24, 2020 1:51 PM To: MIC-DKFZ/HD-BET HD-BET@noreply.github.com Cc: Scott W. Gordon Scott.W.Gordon@dartmouth.edu; Author author@noreply.github.com Subject: Re: [MIC-DKFZ/HD-BET] pip3 NOT pip! (#8)

Hi Scott, have you tried running hd-bet with -device cpu -mode fast -tta 0 Best, Fabian

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMIC-DKFZ%2FHD-BET%2Fissues%2F8%23issuecomment-603405579&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Cbf0ee8f8f1e34cdeeb5208d7d01bec0c%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206690660043479&sdata=sDYurhvK%2F2S5gCLLmnmViHQmdYkbItMbRfqeopCHFR0%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO5OB7424BMXPYWVVV6H5ETRJDXIPANCNFSM4LSJKX6A&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Cbf0ee8f8f1e34cdeeb5208d7d01bec0c%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206690660043479&sdata=pAkVwthRdedkcfxIEfEUDbs03kI%2FSrKWqpblLlMH5Lo%3D&reserved=0.

drswgw commented 4 years ago

Hi Fabian, Getting REALLY close now....

RuntimeError: [enforce fail at CPUAllocator.cpp:64] . DefaultCPUAllocator: can't allocate memory: you tried to allocate 5350883328 bytes. Error code 12 (Cannot allocate memory)

(my_venv) scott@earthmars:~/HD-BET$ cd (my_venv) scott@earthmars:~$ free -g total used free shared buff/cache available Mem: 5 0 3 0 1 4 Swap: 0 0 0

Scott Gordon, Ph.D.

Advanced Imaging Center at

Dartmouth Hitchcock Medical Center

& Thayer School of Engineering

Dartmouth College

802-355-3225

From: Fabian Isensee notifications@github.com Sent: Tuesday, March 24, 2020 1:51 PM To: MIC-DKFZ/HD-BET HD-BET@noreply.github.com Cc: Scott W. Gordon Scott.W.Gordon@dartmouth.edu; Author author@noreply.github.com Subject: Re: [MIC-DKFZ/HD-BET] pip3 NOT pip! (#8)

Hi Scott, have you tried running hd-bet with -device cpu -mode fast -tta 0 Best, Fabian

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMIC-DKFZ%2FHD-BET%2Fissues%2F8%23issuecomment-603405579&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Cbf0ee8f8f1e34cdeeb5208d7d01bec0c%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206690660043479&sdata=sDYurhvK%2F2S5gCLLmnmViHQmdYkbItMbRfqeopCHFR0%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO5OB7424BMXPYWVVV6H5ETRJDXIPANCNFSM4LSJKX6A&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Cbf0ee8f8f1e34cdeeb5208d7d01bec0c%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206690660043479&sdata=pAkVwthRdedkcfxIEfEUDbs03kI%2FSrKWqpblLlMH5Lo%3D&reserved=0.

drswgw commented 4 years ago

Hi Fabian, Added an internal swapfile, think it's running...but in virtual memory..so slow...if I could set the memory to 4 GB, I'm guessing it will run faster...will keep you posted...as to the results....

Scott Gordon, Ph.D.

Advanced Imaging Center at

Dartmouth Hitchcock Medical Center

& Thayer School of Engineering

Dartmouth College

802-355-3225

From: Fabian Isensee notifications@github.com Sent: Tuesday, March 24, 2020 1:51 PM To: MIC-DKFZ/HD-BET HD-BET@noreply.github.com Cc: Scott W. Gordon Scott.W.Gordon@dartmouth.edu; Author author@noreply.github.com Subject: Re: [MIC-DKFZ/HD-BET] pip3 NOT pip! (#8)

Hi Scott, have you tried running hd-bet with -device cpu -mode fast -tta 0 Best, Fabian

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMIC-DKFZ%2FHD-BET%2Fissues%2F8%23issuecomment-603405579&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Cbf0ee8f8f1e34cdeeb5208d7d01bec0c%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206690660043479&sdata=sDYurhvK%2F2S5gCLLmnmViHQmdYkbItMbRfqeopCHFR0%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO5OB7424BMXPYWVVV6H5ETRJDXIPANCNFSM4LSJKX6A&data=02%7C01%7Cscott.w.gordon%40dartmouth.edu%7Cbf0ee8f8f1e34cdeeb5208d7d01bec0c%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637206690660043479&sdata=pAkVwthRdedkcfxIEfEUDbs03kI%2FSrKWqpblLlMH5Lo%3D&reserved=0.

drswgw commented 4 years ago

Nope...gobbling up the swap memory too...

RuntimeError: [enforce fail at CPUAllocator.cpp:64] . DefaultCPUAllocator: can't allocate memory: you tried to allocate 10701766656 bytes. Error code 12 (Cannot allocate memory)

(my_venv) scott@earthmars:~/HD-BET$ free -g total used free shared buff/cache available Mem: 5 0 4 0 0 4 Swap: 4 0 4

Scott Gordon, Ph.D.

Advanced Imaging Center at

Dartmouth Hitchcock Medical Center

& Thayer School of Engineering

Dartmouth College

802-355-3225

From: Fabian Isensee notifications@github.com Sent: Tuesday, March 24, 2020 1:51 PM To: MIC-DKFZ/HD-BET HD-BET@noreply.github.com Cc: Scott W. Gordon Scott.W.Gordon@dartmouth.edu; Author author@noreply.github.com Subject: Re: [MIC-DKFZ/HD-BET] pip3 NOT pip! (#8)

Hi Scott, have you tried running hd-bet with -device cpu -mode fast -tta 0 Best, Fabian

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drswgw commented 4 years ago

File: sgAxT2.nii preprocessing... image shape after preprocessing: (34, 137, 124) prediction (CNN id)... 0 Traceback (most recent call last): File "/home/scott/my_venv/bin/hd-bet", line 7, in exec(compile(f.read(), file, 'exec')) File "/home/scott/HD-BET/HD_BET/hd-bet", line 119, in run_hd_bet(input_files, output_files, mode, config_file, device, pp, tta, save_mask, overwrite_existing) File "/home/scott/HD-BET/HD_BET/run.py", line 101, in run_hd_bet cf.val_min_size, device, cf.da_mirror_axes) File "/home/scott/HD-BET/HD_BET/predict_case.py", line 100, in predict_case_3D_net p = net(a) # np.copy is necessary because ::-1 creates just a view i think File "/home/scott/my_venv/lib/python3.5/site-packages/torch/nn/modules/module.py", line 532, in call result = self.forward(*input, kwargs) File "/home/scott/HD-BET/HD_BET/network_architecture.py", line 200, in forward x = self.up4(x) File "/home/scott/my_venv/lib/python3.5/site-packages/torch/nn/modules/module.py", line 532, in call result = self.forward(*input, *kwargs) File "/home/scott/HD-BET/HD_BET/network_architecture.py", line 79, in forward x = F.leaky_relu(self.bn(self.upsample_conv(self.upsample(x))), negative_slope=self.leakiness, File "/home/scott/my_venv/lib/python3.5/site-packages/torch/nn/modules/module.py", line 532, in call result = self.forward(input, kwargs) File "/home/scott/my_venv/lib/python3.5/site-packages/torch/nn/modules/conv.py", line 480, in forward self.padding, self.dilation, self.groups) RuntimeError: [enforce fail at CPUAllocator.cpp:64] . DefaultCPUAllocator: can't allocate memory: you tried to allocate 10701766656 bytes. Error code 12 (Cannot allocate memory)

Scott Gordon, Ph.D.

Advanced Imaging Center at

Dartmouth Hitchcock Medical Center

& Thayer School of Engineering

Dartmouth College

802-355-3225

From: Fabian Isensee notifications@github.com Sent: Tuesday, March 24, 2020 1:51 PM To: MIC-DKFZ/HD-BET HD-BET@noreply.github.com Cc: Scott W. Gordon Scott.W.Gordon@dartmouth.edu; Author author@noreply.github.com Subject: Re: [MIC-DKFZ/HD-BET] pip3 NOT pip! (#8)

Hi Scott, have you tried running hd-bet with -device cpu -mode fast -tta 0 Best, Fabian

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FabianIsensee commented 2 years ago

Have you been able to run hd-bet in the meantime?