External Email - Use Caution
Hi experts,
While running recon-all on subjects with 3T T1 scans, I ran into an error with one subject during skullstripping stage. Recon-all was running with 3T flag.
The error message is the following:
register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 56, 29) --> (216, 255, 255) using (103, 122, 142) as brain centroid... mean wm in atlas = 108, using box (82,97,114) --> (123, 146,169) to find MRI wm before smoothing, mri peak at 73 robust fit to distribution - 72 +- 7.4 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf Numerical result out of range
I tried the following suggestion in https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12605.html but to no avail.
It's just strange because only one subject has this issue and the subject's scan looks fine- no part of the brain seems cutoff.
Any suggestions would be helpful. Best, Julia Shin
Hi Julia
Can you check the output of the skull stripping and see if it failed?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Hye Min Shin Sent: Tuesday, October 20, 2020 1:13 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error during skullstripping: numerical result out of range
External Email - Use Caution Hi experts,
While running recon-all on subjects with 3T T1 scans, I ran into an error with one subject during skullstripping stage. Recon-all was running with 3T flag.
The error message is the following:
register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 56, 29) --> (216, 255, 255) using (103, 122, 142) as brain centroid... mean wm in atlas = 108, using box (82,97,114) --> (123, 146,169) to find MRI wm before smoothing, mri peak at 73 robust fit to distribution - 72 +- 7.4 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf Numerical result out of range
I tried the following suggestion in https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12605.html but to no avail.
It's just strange because only one subject has this issue and the subject's scan looks fine- no part of the brain seems cutoff.
Any suggestions would be helpful. Best, Julia Shin
freesurfer@nmr.mgh.harvard.edu
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Fischl, Bruce -
Hye Min Shin