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Dear all,
When running the long step for a subject with 7 timepoints with FS version 7.1.0
recon-all -long SUBJECT1.1 SUBJECT1.base -all -hires
I get the following error in the mri_normalize step:
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mri_normalize -g 1 -seed 1234 -mprage -noconform nu.mgz T1.mgz
using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... reading mri_src from nu.mgz... normalizing image... talairach transform 1.21618 0.04397 -0.03619 2.40797; 0.07241 1.25030 0.38146 -0.66432; 0.05010 -0.63638 1.35133 -5.62093; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 6 Starting OpenSpline(): npoints = 6 building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed Command exited with non-zero status 253
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Oddly, it runs without problems for some timepoints but not for others, and there is nothing obviously wrong with the images for the timepoints that fail. Registrations seem fine. The error happens at least in one timepoint of several of our subjects. The image sequence is MP2RAGE and I have skull-stripped the images before running freesurfer, but the cross and base steps run normally and produce the expected results.
Do you have any hints on what may be wrong?
Best regards, Benjamin
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Benjamín Garzón, PhD Department of Neurobiology, Care Sciences and Society Aging Research Center | 171 65 Stockholm | Tomtebodavägen 18A, floor 10 benjamin.garzon@ki.se | www.ki-su-arc.se ______________________________________ Karolinska Institutet – a medical university
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