Comments (7)
I am having the same issue in recon-surf.log
using the 140_orig.mgz
in the tutorial.
I am using an M1 MacBook with 8 GB of RAM with native installation with the following command:
bash run_fastsurfer.sh --t1 ~/my_fastsurfer_analysis/140_orig.mgz --sid 140 --sd ~/my_fastsurfer_analysis --parallel
Sorry that I am new to both FreeSurfer and FastSurfer so this all looks cryptic to me.
=========== Creating surfaces rh - map input asegdkt_segfile to surf ===============
mris_sample_parc -ct /Applications/freesurfer/7.4.1/average/colortable_desikan_killiany.txt -file /Users/USERNAME/FastSurfer/recon_surf/rh.DKTatlaslookup.txt -projmm 0.6 -f 5 -surf white.preaparc 140 rh aparc.DKTatlas+aseg.orig.mgz aparc.DKTatlas.mapped.prefix.annot
embedding color table /Applications/freesurfer/7.4.1/average/colortable_desikan_killiany.txt into output annot file
using as translation fname
projecting 0.60 mm along surface normal
applying mode filter 5 times to parcellation
using white.preaparc as surface name
reading parcellation volume from /Users/USERNAME/my_fastsurfer_analysis/140/mri/aparc.DKTatlas+aseg.orig.mgz...
reading input surface /Users/USERNAME/my_fastsurfer_analysis/140/surf/rh.white.preaparc...
pass 1: 1800 segments changed
pass 2: 15 segments changed
pass 3: 11 segments changed
pass 4: 11 segments changed
pass 5: 11 segments changed
pass 6: 11 segments changed
pass 7: 11 segments changed
pass 8: 11 segments changed
pass 9: 11 segments changed
pass 10: 11 segments changed
pass 11: 11 segments changed
mode filtering sample labels...
iter 0: 2346 changed, 2678 zero
iter 1: 1763 changed, 2507 zero
iter 2: 1565 changed, 2605 zero
iter 3: 1442 changed, 2652 zero
iter 4: 1377 changed, 2674 zero
writing annotation to aparc.DKTatlas.mapped.prefix.annot...
python3.10 /Users/USERNAME/FastSurfer/recon_surf/smooth_aparc.py --insurf /Users/USERNAME/my_fastsurfer_analysis/140/surf/rh.white.preaparc --inaparc /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.aparc.DKTatlas.mapped.prefix.annot --incort /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.cortex.label --outaparc /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.aparc.DKTatlas.mapped.annot
Reading in surface: /Users/USERNAME/my_fastsurfer_analysis/140/surf/rh.white.preaparc ...
Reading in annotation: /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.aparc.DKTatlas.mapped.prefix.annot ...
Reading in cortex label: /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.cortex.label ...
Non-cortex vertices with labels: 70
Fill Round: 1
rows: 294 reduced to 189
Traceback (most recent call last):
File "/Users/USERNAME/FastSurfer/recon_surf/smooth_aparc.py", line 367, in <module>
smooth_aparc(options.insurf, options.inaparc, options.incort, options.outaparc)
File "/Users/USERNAME/FastSurfer/recon_surf/smooth_aparc.py", line 333, in smooth_aparc
labels_new = mode_filter(adjM, labels, fillonlylabel, np.array([fillonlylabel]))
File "/Users/USERNAME/FastSurfer/recon_surf/smooth_aparc.py", line 238, in mode_filter
labels_new[ids[row]] = mvals[0]
IndexError: invalid index to scalar variable.
from fastsurfer.
Thanks for reporting. @bradmoffat is your error also on a Mac (what chip)?
Also can you two post a pip freeze or conda list . I suspect an incompatibility with one of the libraries. E.g. some versions of scipy break sparse matrix behaviour.
from fastsurfer.
I am having the same issue in
recon-surf.log
using the140_orig.mgz
in the tutorial.I am using an M1 MacBook with 8 GB of RAM with native installation with the following command:
bash run_fastsurfer.sh --t1 ~/my_fastsurfer_analysis/140_orig.mgz --sid 140 --sd ~/my_fastsurfer_analysis --parallel
Sorry that I am new to both FreeSurfer and FastSurfer so this all looks cryptic to me.
=========== Creating surfaces rh - map input asegdkt_segfile to surf =============== mris_sample_parc -ct /Applications/freesurfer/7.4.1/average/colortable_desikan_killiany.txt -file /Users/USERNAME/FastSurfer/recon_surf/rh.DKTatlaslookup.txt -projmm 0.6 -f 5 -surf white.preaparc 140 rh aparc.DKTatlas+aseg.orig.mgz aparc.DKTatlas.mapped.prefix.annot embedding color table /Applications/freesurfer/7.4.1/average/colortable_desikan_killiany.txt into output annot file using as translation fname projecting 0.60 mm along surface normal applying mode filter 5 times to parcellation using white.preaparc as surface name reading parcellation volume from /Users/USERNAME/my_fastsurfer_analysis/140/mri/aparc.DKTatlas+aseg.orig.mgz... reading input surface /Users/USERNAME/my_fastsurfer_analysis/140/surf/rh.white.preaparc... pass 1: 1800 segments changed pass 2: 15 segments changed pass 3: 11 segments changed pass 4: 11 segments changed pass 5: 11 segments changed pass 6: 11 segments changed pass 7: 11 segments changed pass 8: 11 segments changed pass 9: 11 segments changed pass 10: 11 segments changed pass 11: 11 segments changed mode filtering sample labels... iter 0: 2346 changed, 2678 zero iter 1: 1763 changed, 2507 zero iter 2: 1565 changed, 2605 zero iter 3: 1442 changed, 2652 zero iter 4: 1377 changed, 2674 zero writing annotation to aparc.DKTatlas.mapped.prefix.annot... python3.10 /Users/USERNAME/FastSurfer/recon_surf/smooth_aparc.py --insurf /Users/USERNAME/my_fastsurfer_analysis/140/surf/rh.white.preaparc --inaparc /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.aparc.DKTatlas.mapped.prefix.annot --incort /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.cortex.label --outaparc /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.aparc.DKTatlas.mapped.annot Reading in surface: /Users/USERNAME/my_fastsurfer_analysis/140/surf/rh.white.preaparc ... Reading in annotation: /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.aparc.DKTatlas.mapped.prefix.annot ... Reading in cortex label: /Users/USERNAME/my_fastsurfer_analysis/140/label/rh.cortex.label ... Non-cortex vertices with labels: 70 Fill Round: 1 rows: 294 reduced to 189 Traceback (most recent call last): File "/Users/USERNAME/FastSurfer/recon_surf/smooth_aparc.py", line 367, in <module> smooth_aparc(options.insurf, options.inaparc, options.incort, options.outaparc) File "/Users/USERNAME/FastSurfer/recon_surf/smooth_aparc.py", line 333, in smooth_aparc labels_new = mode_filter(adjM, labels, fillonlylabel, np.array([fillonlylabel])) File "/Users/USERNAME/FastSurfer/recon_surf/smooth_aparc.py", line 238, in mode_filter labels_new[ids[row]] = mvals[0] IndexError: invalid index to scalar variable.
Also can you two post a pip freeze or conda list . I suspect an incompatibility with one of the libraries. E.g. some versions of scipy break sparse matrix behaviour.
It well could be. There was so many errors when I used requirements.mac.txt
so I essentially removed all the version restrictions and installed it. I also did not use a virtual environment as it seemed to be okay in my base environment.
Your requirements.mac.txt asked for scipy==1.8.0
while I have scipy 1.12.0 py310hf4b343e_2 conda-forge
. You think this could be it? Do you know which libraries are the most picky about versions? I can try to make sure those versions are installed.
Side note: if I run bash run_fastsurfer.sh --t1 ~/my_fastsurfer_analysis/140_orig.mgz --sid 140 --sd ~/my_fastsurfer_analysis --parallel --surf_only
again it says ERROR: running on top of an existing subject directory! The output directory must not contain data from a previous invocation of recon-surf.
So to debug this issue, is there a way I can quickly resume from the error or I have to start from the beginning?
FastSurfer % mamba list
# packages in environment at /opt/homebrew/Caskroom/miniforge/base:
#
# Name Version Build Channel
absl-py 2.1.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.9.5 py310hd125d64_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
aom 3.9.0 h537b5a7_0 conda-forge
appnope 0.1.4 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
blinker 1.8.2 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 hc338f07_0 conda-forge
boltons 23.0.0 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 hb547adb_0 conda-forge
brotli-bin 1.1.0 hb547adb_0 conda-forge
brotli-python 1.1.0 py310h1253130_0 conda-forge
brunsli 0.1 h9f76cd9_0 conda-forge
bzip2 1.0.8 h3422bc3_4 conda-forge
c-ares 1.28.1 h93a5062_0 conda-forge
c-blosc2 2.12.0 ha57e6be_0 conda-forge
ca-certificates 2024.6.2 hf0a4a13_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.3 pyhd8ed1ab_0 conda-forge
certifi 2024.6.2 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py310h2399d43_3 conda-forge
charls 2.4.2 h13dd4ca_0 conda-forge
charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge
chevron 0.14.0 pyhd3deb0d_1 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
conda 23.3.1 py310hbe9552e_0 conda-forge
conda-libmamba-solver 23.3.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.2.0 pyh38be061_0 conda-forge
conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge
contourpy 1.2.0 py310hd137fd4_0 conda-forge
cryptography 41.0.3 py310hdd3b5e7_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hb547adb_0 conda-forge
debugpy 1.8.1 py310h692a8b6_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.14 pyh1a96a4e_0 conda-forge
eigen 3.4.0 h1995070_0 conda-forge
et_xmlfile 1.1.0 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.6.2 hebf3989_0 conda-forge
fftw 3.3.10 nompi_h6637ab6_110 conda-forge
filelock 3.15.1 pyhd8ed1ab_0 conda-forge
fmt 9.1.0 hffc8910_0 conda-forge
fonttools 4.49.0 py310hd125d64_0 conda-forge
freetype 2.12.1 hadb7bae_2 conda-forge
frozendict 2.4.0 py310hd125d64_0 conda-forge
frozenlist 1.4.1 py310hd125d64_0 conda-forge
genanki 0.13.1 pyhd8ed1ab_0 conda-forge
giflib 5.2.2 h93a5062_0 conda-forge
gmp 6.3.0 hebf3989_1 conda-forge
gmpy2 2.1.5 py310h3bc658a_1 conda-forge
google-auth 2.30.0 pyhff2d567_0 conda-forge
google-auth-oauthlib 1.2.0 pyhd8ed1ab_0 conda-forge
gradescope-utils 0.5.0 pyhd8ed1ab_0 conda-forge
grpcio 1.62.2 py310hf7687f1_0 conda-forge
h5py 3.11.0 nompi_py310h92897fd_102 conda-forge
hdf5 1.14.3 nompi_hec07895_105 conda-forge
humanize 4.9.0 pyhd8ed1ab_0 conda-forge
icu 73.2 hc8870d7_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
imagecodecs 2023.9.18 py310hfbe61c4_0 conda-forge
imageio 2.34.1 pyh4b66e23_0 conda-forge
importlib-metadata 7.0.2 pyha770c72_0 conda-forge
importlib_metadata 7.0.2 hd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.3 pyh3cd1d5f_0 conda-forge
ipython 8.22.2 pyh707e725_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
jsonpatch 1.32 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
jupyter_client 8.6.1 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py310hbe9552e_0 conda-forge
jxrlib 1.1 h93a5062_3 conda-forge
kiwisolver 1.4.5 py310h38f39d4_1 conda-forge
krb5 1.21.2 h92f50d5_0 conda-forge
lapy 1.0.1 pyhd8ed1ab_0 conda-forge
lazy_loader 0.4 pyhd8ed1ab_0 conda-forge
lcms2 2.15 h40e5a24_2 conda-forge
lerc 4.0.0 h9a09cb3_0 conda-forge
libabseil 20240116.2 cxx17_hebf3989_0 conda-forge
libaec 1.1.3 hebf3989_0 conda-forge
libarchive 3.6.2 h82b9b87_1 conda-forge
libavif16 1.0.4 hb18d617_4 conda-forge
libblas 3.9.0 21_osxarm64_openblas conda-forge
libbrotlicommon 1.1.0 hb547adb_0 conda-forge
libbrotlidec 1.1.0 hb547adb_0 conda-forge
libbrotlienc 1.1.0 hb547adb_0 conda-forge
libcblas 3.9.0 21_osxarm64_openblas conda-forge
libcurl 8.8.0 h7b6f9a7_0 conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libdeflate 1.19 hb547adb_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h642e427_1 conda-forge
libexpat 2.6.2 hebf3989_0 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_3 conda-forge
libgfortran5 13.2.0 hf226fd6_3 conda-forge
libgrpc 1.62.2 h9c18a4f_0 conda-forge
libhwloc 2.9.3 default_h4394839_1009 conda-forge
libiconv 1.17 he4db4b2_0 conda-forge
libitk 5.3.0 h541f4bf_7 conda-forge
libjpeg-turbo 2.1.5.1 hb547adb_1 conda-forge
liblapack 3.9.0 21_osxarm64_openblas conda-forge
libmamba 1.4.2 h7d1d596_0 conda-forge
libmambapy 1.4.2 py310h34b6e76_0 conda-forge
libnghttp2 1.58.0 ha4dd798_1 conda-forge
libopenblas 0.3.26 openmp_h6c19121_0 conda-forge
libpng 1.6.43 h091b4b1_0 conda-forge
libprotobuf 4.25.3 hbfab5d5_0 conda-forge
libre2-11 2023.09.01 h7b2c953_2 conda-forge
libsodium 1.0.18 h27ca646_1 conda-forge
libsolv 0.7.24 ha614eb4_3 conda-forge
libsqlite 3.43.0 hb31c410_0 conda-forge
libssh2 1.11.0 h7a5bd25_0 conda-forge
libtiff 4.6.0 h77c4dce_1 conda-forge
libwebp-base 1.3.2 hb547adb_0 conda-forge
libxcb 1.15 hf346824_0 conda-forge
libxml2 2.11.5 h25269f3_1 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
libzopfli 1.0.3 h9f76cd9_0 conda-forge
llvm-openmp 18.1.1 hcd81f8e_0 conda-forge
lz4-c 1.9.4 hb7217d7_0 conda-forge
lzo 2.10 h642e427_1000 conda-forge
mamba 1.4.2 py310ha5d4528_0 conda-forge
markdown 3.6 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py310hd125d64_0 conda-forge
matplotlib 3.8.3 py310hb6292c7_0 conda-forge
matplotlib-base 3.8.3 py310h2439c42_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
metis 5.1.0 h13dd4ca_1007 conda-forge
mpc 1.3.1 h91ba8db_0 conda-forge
mpfr 4.2.1 h41d338b_1 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
multidict 6.0.5 py310h8e9501a_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.4 h7ea286d_0 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
networkx 3.3 pyhd8ed1ab_1 conda-forge
nibabel 5.2.1 pyha770c72_0 conda-forge
numpy 1.26.4 py310hd45542a_0 conda-forge
oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.2 h9f1df11_0 conda-forge
openpyxl 3.1.2 py310h2aa6e3c_1 conda-forge
openssl 3.3.1 hfb2fe0b_0 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.1 py310h401b61c_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.0.1 py310hadb9e77_1 conda-forge
pip 23.2.1 pyhd8ed1ab_0 conda-forge
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
plotly 5.22.0 pyhd8ed1ab_0 conda-forge
pluggy 1.3.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
protobuf 4.25.3 py310h1e88e72_0 conda-forge
psutil 5.9.8 py310hd125d64_0 conda-forge
pthread-stubs 0.4 h27ca646_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pyasn1 0.6.0 pyhd8ed1ab_0 conda-forge
pyasn1-modules 0.4.0 pyhd8ed1ab_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.4 py310h8e9501a_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyjwt 2.8.0 pyhd8ed1ab_1 conda-forge
pymupdf 1.23.8 pypi_0 pypi
pymupdfb 1.23.7 pypi_0 pypi
pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.12 h01493a6_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.10 3_cp310 conda-forge
pytorch 2.2.2 py3.10_0 pytorch
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py310h280b8fa_1 conda-forge
pyyaml 6.0.1 py310h2aa6e3c_1 conda-forge
pyzmq 25.1.2 py310hbb13138_0 conda-forge
rav1e 0.6.6 h69fbcac_2 conda-forge
re2 2023.09.01 h4cba328_2 conda-forge
readline 8.2 h92ec313_1 conda-forge
reproc 14.2.4 h1a8c8d9_0 conda-forge
reproc-cpp 14.2.4 hb7217d7_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
requests-oauthlib 2.0.0 pyhd8ed1ab_0 conda-forge
rsa 4.9 pyhd8ed1ab_0 conda-forge
ruamel.yaml 0.17.32 py310h2aa6e3c_0 conda-forge
ruamel.yaml.clib 0.2.7 py310h8e9501a_1 conda-forge
scikit-image 0.23.2 py310hd4a36ba_0 conda-forge
scikit-learn 1.4.1.post1 py310h7ef31dd_0 conda-forge
scikit-sparse 0.4.14 py310he1f27a3_0 conda-forge
scipy 1.12.0 py310hf4b343e_2 conda-forge
setuptools 68.1.2 pyhd8ed1ab_0 conda-forge
simpleitk 2.3.1 py310hd5a4765_1 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 hd04f947_1 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
suitesparse 5.10.1 h79486c6_3 conda-forge
svt-av1 2.1.0 h7bae524_0 conda-forge
sympy 1.12 pypyh9d50eac_103 conda-forge
tbb 2021.11.0 h2ffa867_1 conda-forge
tenacity 8.3.0 pyhd8ed1ab_0 conda-forge
tensorboard 2.17.0 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py310hdd3b5e7_1 conda-forge
tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.3.0 pyhc1e730c_0 conda-forge
tifffile 2024.5.22 pyhd8ed1ab_0 conda-forge
tk 8.6.12 he1e0b03_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
torchio 0.19.6 pyhd8ed1ab_1 conda-forge
torchvision 0.17.2 py310_cpu pytorch
tornado 6.4 py310hd125d64_0 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
traitlets 5.14.2 pyhd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
unicodedata2 15.1.0 py310h2aa6e3c_0 conda-forge
urllib3 2.0.4 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
werkzeug 3.0.3 pyhd8ed1ab_0 conda-forge
wheel 0.41.2 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py310hd125d64_0 conda-forge
xlsxwriter 3.1.9 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.11 hb547adb_0 conda-forge
xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yacs 0.1.8 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
yaml-cpp 0.7.0 hb7217d7_2 conda-forge
yarl 1.9.4 py310hd125d64_0 conda-forge
zeromq 4.3.5 hebf3989_1 conda-forge
zfp 1.0.1 ha8f4885_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h53f4e23_5 conda-forge
zlib-ng 2.0.7 h1a8c8d9_0 conda-forge
zstandard 0.19.0 py310h8e9501a_0 conda-forge
zstd 1.5.6 hb46c0d2_0 conda-forge
from fastsurfer.
I wonder if that is the issue.
The stable branch is:
FastSurfer/recon_surf/smooth_aparc.py
Line 234 in 818acf1
The dev branch has been changed to:
FastSurfer/recon_surf/smooth_aparc.py
Line 238 in 3622c13
Maybe I should switch to the dev branch and try.
Update: the dev branch indeed address this particular issue.
from fastsurfer.
Yes, I remember putting that into dev 5 months ago to fix compatibility with newer versions. Thanks for testing. I am closing this for now as this error is solved in dev and will be part of the next release. Feel free to re-open or post other follow-up issues separately.
from fastsurfer.
from fastsurfer.
Hi @bradmoffat , 7T is not officially supported. We had some success when running a heavy bias field correction (from SPM) beforehand (took 1h for high-res images to correct).
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Related Issues (20)
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