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Pial surface generation fails
Hi and thank you for this really interesting project!
I succesfully ran the software in the native environment but unfortunately when I set the --pial option it fails at the last step: Surface optimization failed (while if I remove it, it works)
In pipeline.py I saw this:
https://github.com/IndiLab/FastCSR/blob/f1f95d964babb77dfa6976847b0ad5130e06dea3/pipeline.py#L281-L290
As far as I know there is not a -white option in the recon-all command (or maybe I missed something)
Surface generation failed.
HI author, I try to run the project with docker, but the render failed.
It did not show what had happed in the error.
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py Please cite the following paper when using FastCSR:
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/orig.mgz file already exists, skip this step.
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py -----------------------Generate mri/filled.mgz file-------------------------------
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/filled.mgz file already exists, skip this step.
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py --------------------Generate mri/aseg.presurf.mgz file----------------------------
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/aseg.presurf.mgz file already exists, skip this step.
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py ---------------------Generate mri/brainmask.mgz file------------------------------
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/brainmask.mgz file already exists, skip this step.
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py -------------------------Generate mri/wm.mgz file---------------------------------
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/wm.mgz file already exists, skip this step.
[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py -------------------Generate mri/?h_levelset.nii.gz file---------------------------
[INFO] 2023-08-12 03:40:50 PID: 1 pipeline.py Levelset model regression inference completed.
[INFO] 2023-08-12 03:40:50 PID: 1 pipeline.py -------------------Generate mri/brain.finalsurfs.mgz file-------------------------
[INFO] 2023-08-12 03:40:50 PID: 1 pipeline.py The mri/brain.finalsurfs.mgz file already exists, skip this step.
[INFO] 2023-08-12 03:40:50 PID: 1 pipeline.py -----------------------------Generate surface-------------------------------------
[ERROR] 2023-08-12 03:41:07 PID: 1 pipeline.py Surface generation failed.
About hardware and memory consumption
Hello, first of all, thank you for your kind words. I am currently trying to reproduce this work, but my GPU has only 4GB of memory. I'm not sure if it meets the requirements. Could you please provide me with information about the memory consumption of the model in your experiments?
Levelset regression model inference failed.
I tried to run the tool on the test data provided and get this error:
python3 pipeline.py --sd ../data --sid sub-001 --t1 ../data/sub-001.nii.gz
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py Please cite the following paper when using FastCSR:
****************************************
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py ------------------------Generate mri/orig.mgz file--------------------------------
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py The mri/orig.mgz file already exists, skip this step.
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py -----------------------Generate mri/filled.mgz file-------------------------------
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py The mri/filled.mgz file already exists, skip this step.
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py --------------------Generate mri/aseg.presurf.mgz file----------------------------
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py The mri/aseg.presurf.mgz file already exists, skip this step.
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py ---------------------Generate mri/brainmask.mgz file------------------------------
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py The mri/brainmask.mgz file already exists, skip this step.
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py -------------------------Generate mri/wm.mgz file---------------------------------
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py The mri/wm.mgz file already exists, skip this step.
[INFO] 2023-12-08 07:10:30 PID: 15 pipeline.py -------------------Generate mri/?h_levelset.nii.gz file---------------------------
[ERROR] 2023-12-08 07:10:47 PID: 15 pipeline.py Levelset regression model inference failed.
this is the list of python packages installed and their versions:
Package Version
------------------- --------------------
antspyx 0.4.2
batchgenerators 0.25
certifi 2019.11.28
chardet 3.0.4
chart-studio 1.1.0
contourpy 1.1.1
cycler 0.12.1
dbus-python 1.2.16
dicom2nifti 2.4.9
distro-info 0.23+ubuntu1.1
fonttools 4.46.0
future 0.18.3
idna 2.8
imageio 2.33.0
importlib-resources 6.1.1
joblib 1.3.2
kiwisolver 1.4.5
lazy-loader 0.3
linecache2 1.0.0
matplotlib 3.7.4
MedPy 0.4.0
networkx 3.1
nibabel 5.1.0
nighres 1.2.0
nnunet 1.7.0
numpy 1.24.4
packaging 23.2
pandas 2.0.3
patsy 0.5.4
Pillow 10.1.0
pip 20.0.2
plotly 5.18.0
psutil 5.9.6
pydicom 2.4.3
PyGObject 3.36.0
pyparsing 3.1.1
python-apt 2.0.1+ubuntu0.20.4.1
python-dateutil 2.8.2
python-gdcm 3.0.22
pytz 2023.3.post1
PyWavelets 1.4.1
PyYAML 6.0.1
requests 2.22.0
requests-unixsocket 0.2.0
retrying 1.3.4
scikit-image 0.21.0
scikit-learn 1.3.2
scipy 1.10.1
setuptools 45.2.0
sh 2.0.6
SimpleITK 2.3.1
six 1.14.0
sklearn 0.0.post12
statsmodels 0.14.0
tenacity 8.2.3
threadpoolctl 3.2.0
tifffile 2023.7.10
torch 1.9.1+cpu
torchaudio 0.9.1
torchvision 0.10.1+cpu
tqdm 4.66.1
traceback2 1.4.0
typing-extensions 4.8.0
tzdata 2023.3
unattended-upgrades 0.1
unittest2 1.1.0
urllib3 1.25.8
webcolors 1.13
wheel 0.34.2
zipp 3.17.0
how to train on my own data
Thank you for your open sorce job,but there are only inference code,can you tell me how to train the model on my own data ,Or can you provide the training code,thank you
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