External Email - Use Caution Dear Freesurfer subjects,
After saving my control.dat file into the tmp folder and running the command line recon-all -autorecon2-cp -autorecon3 -s.... It does not seem to parse the control.dat file correctly and find the control points. This is what I get (in recon-all.log): #@# Intensity Normalization2 Fri 5 May 08:01:43 CEST 2023 /home/rosalia/Desktop/CAN_RUTI/sub-041_ses-FU1/mri mri_normalize -seed 1234 -f /home/rosalia/Desktop/CAN_RUTI/sub-041_ses-FU1/tmp/control.dat -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz /bin/tcsh: /home/rosalia/software/fsl/fslpython/lib/libtinfo.so.6: no version information available (required by /bin/tcsh) setting seed for random number genererator to 1234 using control points from file /home/rosalia/Desktop/CAN_RUTI/sub-041_ses-FU1/tmp/control.dat... assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... Reading 0 control points... Doing gentle normalization with control points/label error: No such file or directory error: MRI3dGentleNormalize: mean = 0.0, nctrl = 0, norm failed Interestingly, when I saved the control points, freeview offered saving it as control.json, and the content of control.dat is, indeed, follows the JSON format. I renamed the file to control.dat (as in the tutorial). Is it possible that I should have kept it as control.json? P.S.: There is also a typo in the log. "random number genererator" should be "random number generator". :) Kind regards, Rosalia
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