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