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Thank you so much yujing, it worked.
Il giorno lun 10 mar 2025 alle 14:24 Huang, Yujing YHUANG43@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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. Any ideas on how to fix this? Thanks in advance
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