External Email - Use Caution Thank you so much yujing, it worked.
Il giorno lun 10 mar 2025 alle 14:24 Huang, Yujing <yhuan...@mgh.harvard.edu> ha scritto: > I have attached SamsegLongitudinal.py to fix the python error. Copy it to > /Applications/freesurfer/8.0.0/python/packages/gems/SamsegLongitudinal.py > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Paola Di Filippo > *Sent:* Sunday, March 9, 2025 8:28 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Longitudinal samseg not working - TypeError: > transform() got an unexpected keyword argument 'affine' > > > > * External Email - Use Caution * > > Hi everyone, I am trying to launch longitudinal samseg with the lesion > flag for an MS subject, in Freesurfer 8.0. I followed instructions, cross > sectional samseg for the same subject at T0 worked fine, but now I am > having troubles, described as follows: > > > > MBP-di-Paola:~ paoladifilippo$ export FS_LICENSE=$HOME/license.txt > > MBP-di-Paola:~ paoladifilippo$ export > FREESURFER_HOME=/Applications/freesurfer/8.0.0 > > MBP-di-Paola:~ paoladifilippo$ source $FREESURFER_HOME/SetUpFreeSurfer.sh > > -------- freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /Applications/freesurfer/8.0.0 > > FSFAST_HOME /Applications/freesurfer/8.0.0/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /Applications/freesurfer/8.0.0/subjects > > MNI_DIR /Applications/freesurfer/8.0.0/mni > > MBP-di-Paola:~ paoladifilippo$ export > LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/runtime/maci64:$FREESURFER_HOME/MCRv97/bin/maci64:$FREESURFER_HOME/MCRv97/sys/os/maci64:$FREESURFER_HOME/MCRv97/extern/bin/maci64 > > MBP-di-Paola:~ paoladifilippo$ cd > /Users/paoladifilippo/RM.OCT.NFL/A.C/LONGITUDINAL.SAMSEG > > MBP-di-Paola:LONGITUDINAL.SAMSEG paoladifilippo$ run_samseg_long > --timepoint A.C.2.4.91.MRI.12.9.22_t1_reg.mgz > A.C.2.4.91.MRI.12.9.22_flair_reg.mgz --timepoint > A.C.2.4.91.MRI.13.2.23_t1_reg.mgz A.C.2.4.91.MRI.13.2.23_flair_reg.mgz > --timepoint A.C.2.4.91.MRI.20.09.23_t1_reg.mgz > A.C.2.4.91.MRI.20.09.23_flair_reg.mgz --pallidum-separate --lesion > --lesion-mask-pattern 0 1 --output > /Users/paoladifilippo/RM.OCT.NFL/A.C/LONG.SAMSEG.OUTPUT/ > > Assuming an identity transformation between base and each time point > > WARNING:tensorflow:From > /Applications/freesurfer/8.0.0/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/tensorflow/python/compat/v2_compat.py:107: > disable_resource_variables (from tensorflow.python.ops.variable_scope) is > deprecated and will be removed in a future version. > > Instructions for updating: > > non-resource variables are not supported in the long term > > Traceback (most recent call last): > > File "/Applications/freesurfer/8.0.0/python/scripts/run_samseg_long", > line 209, in <module> > > samsegLongitudinal.segment(saveWarp=args.save_warp, > initTransformFile=args.init_reg) > > File > "/Applications/freesurfer/8.0.0/python/packages/gems/SamsegLongitudinal.py", > line 181, in segment > > self.constructAndRegisterSubjectSpecificTemplate(initTransformFile) > > File > "/Applications/freesurfer/8.0.0/python/packages/gems/SamsegLongitudinal.py", > line 200, in constructAndRegisterSubjectSpecificTemplate > > self.sstFileNames = self.generateSubjectSpecificTemplate() > > File > "/Applications/freesurfer/8.0.0/python/packages/gems/SamsegLongitudinal.py", > line 835, in generateSubjectSpecificTemplate > > imageBuffer = image0.transform(affine=self.tpToBaseTransforms[0]) > > TypeError: transform() got an unexpected keyword argument 'affine' > > > > > > I am working on Apple M4 Pro with 48 GB RAM, MacOS 15.2. 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