Where to edit tkregister2 code to run with Freesurfer v6 on Mac Big Sur OS?

[akelkar26]

Hi,

I am trying to run easy_lasuanne on Freesurfer v6. I have installed it on Python 2.7.18.
When the command runs it gives a bad CPU executable error as tkregister2 is deprecated in Freesurfer in Mac OS Big Sur .

Here is the error:
DEBUG : 2021-09-14 15:23:32,323 : runCmd : Running: tkregister2 --regheader --mov /Users/neurouser1/Documents/TNI/qsiprep_out/freesurfer/sub-TNI002/mri/rawavg.mgz --targ /Users/neurouser1/Documents/TNI/qsiprep_out/freesurfer/sub-TNI002/mri/orig.mgz --regheader --reg /Users/neurouser1/Documents/TNI/lausanneoutput/T1-TO-orig.dat --fslregout /Users/neurouser1/Documents/TNI/lausanneoutput/T1-TO-orig.mat --noedit INFO : 2021-09-14 15:23:32,832 : main : /Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable. CRITICAL : 2021-09-14 15:23:32,832 : runCmd : Return Value: 1 DEBUG : 2021-09-14 15:23:32,837 : runCmd : Running: convert_xfm -omat /Users/neurouser1/Documents/TNI/lausanneoutput/T1-TO-b0.mat -concat /Users/neurouser1/Documents/TNI/lausanneoutput/orig-TO-b0.mat /Users/neurouser1/Documents/TNI/lausanneoutput/T1-TO-orig.mat INFO : 2021-09-14 15:23:33,346 : main : Could not open matrix file /Users/neurouser1/Documents/TNI/lausanneoutput/T1-TO-orig.mat INFO : 2021-09-14 15:23:33,346 : main : Cannot read input-matrix CRITICAL : 2021-09-14 15:23:33,346 : runCmd : Return Value: 254 ERROR : 2021-09-14 15:23:33,346 : main : An error occurred. Linear transformation file /Users/neurouser1/Documents/TNI/lausanneoutput/T1-TO-b0.mat not generated. Traceback (most recent call last): File "/Users/neurouser1/opt/anaconda3/envs/py2/bin/easy_lausanne", line 4, in <module> __import__('pkg_resources').run_script('Easy-Lausanne==0.5', 'easy_lausanne') File "/Users/neurouser1/opt/anaconda3/envs/py2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/Users/neurouser1/opt/anaconda3/envs/py2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1469, in run_script exec(script_code, namespace, namespace) File "/Users/neurouser1/opt/anaconda3/envs/py2/lib/python2.7/site-packages/Easy_Lausanne-0.5-py2.7.egg/EGG-INFO/scripts/easy_lausanne", line 79, in <module>

I edited the registration.py script to have it read in tkregisterfv but the error still persists. I also tried tkregister2_cmdl but the error persists. Both solutions were given in this freesurfer thread.
https://www.mail-archive.com/[email protected]/msg64576.html

tkregisterfv_command = 'tkregisterfv --regheader --mov %s --targ %s --regheader --reg %s --fslregout %s --noedit' % ( op.join(FS_DIR, 'mri', 'rawavg.mgz'), op.join(FS_DIR, 'mri', 'orig.mgz'), op.join(output_directory, 'T1-TO-orig.dat'), op.join(output_directory, 'T1-TO-orig.mat'), ) runCmd(tkregisterfv_command, log)

Could you please advise if there is anywhere else I need to make changes in the code to get it to work?
Thanks in advance.
Best,
Apoorva