Comments (7)
constructor-s
commented on August 12, 2024
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.
m-reuter
commented on August 12, 2024
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.
constructor-s
commented on August 12, 2024
I am having the same issue in
recon-surf.logusing the140_orig.mgzin 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 --parallelSorry 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
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expat 2.6.2 hebf3989_0 conda-forge
fftw 3.3.10 nompi_h6637ab6_110 conda-forge
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pyasn1 0.6.0 pyhd8ed1ab_0 conda-forge
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pybind11-abi 4 hd8ed1ab_3 conda-forge
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pycparser 2.21 pyhd8ed1ab_0 conda-forge
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python 3.10.12 h01493a6_0_cpython conda-forge
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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
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tornado 6.4 py310hd125d64_0 conda-forge
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tzdata 2023c h71feb2d_0 conda-forge
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xz 5.2.6 h57fd34a_0 conda-forge
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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.
constructor-s
commented on August 12, 2024
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.
m-reuter
commented on August 12, 2024
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.
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bradmoffat
commented on August 12, 2024
Many thanks to both. Apologies I did not get back and post the pip freeze
myself.
Otherwise I can report back it seems to work very well on my 7T data
…On Mon, Jun 17, 2024 at 5:39 AM Martin Reuter ***@***.***> wrote:
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.
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m-reuter
commented on August 12, 2024
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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