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. Any ideas on how to
fix this? Thanks in advance
[https://secure-web.cisco.com/1-tPaSq4iZ9Q-F34RzLl4jzze_sEBHj_wzcNlV8b6z-2ieM18NeYRmFHAkP0trwr_vIVBaFlff1ocymwzbP5pdy1Ano283A41Lgdz0sFunLmtyx1lR1TQCfan02BACgz72rG8QN0a9QU-4HWnPT6lJM3XPyWX2Se9JBHVlhBDOuwF9doue0LruRcpvZfMt7nFtHTXVKaT-A2MEoO9wMhPan3sV-ypmcCXlpj16fXCbxqaCm1KMqoSqv4HyeGH-PeXQIUSSkhsHiE1VgjAzs4ehTd_5iur_WVL9oZgajrUmyhdzRGrtXq3OBS5jphDooZG/https%3A%2F%2Fwww.unifg.it%2Fsites%2Fdefault%2Ffiles%2F2021-11%2Fbanner%2520hr.jpg]
SamsegLongitudinal.py
Description: SamsegLongitudinal.py
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
