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Hi,
I have scans for ~60 participants, and for some reason the scans are of visibly poor quality when I convert them to .mgz (blurry, very low contrast). The white boundary also seems to exclude considerable white matter in the occipital in about half of the scans. Because of the extremely low contrast, I am unable to manually add control points as I cannot visibly tell the difference between wm and gm. I am attaching orig.mgz for one participant here.
Acquisition parameters for these scans were: High-resolution T1-weighted anatomical images (1 × 1 × 1 mm3) were acquired with an MPRAGE pulse sequence (TI=900 ms, sagittal slices, 256 × 256 matrix) using a Siemens Allegra 3T head-only scanner.
I tried running more iterations of during the nu_correct (as suggested here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-November/008985....) using the following command:
mc2835% recon-all -autorecon1 -nuintensitycor -nuiterations 10 -subjid 30026_FS
but got the following error:
ERROR: Flag -nuiterations unrecognized.
-autorecon1 -nuiterations 10 -subjid 30026_FS
Darwin Ifats-Mac-Pro.med.yale.internal 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Tue Jun 19 14:56:04 EDT 2018
For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Is there any way to salvage this data for analysis?
Any help will be really appreciated.
Thank you!
Megha