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Dear FreeSurfer experts,
I am running mri_deface for all relevant volume files of more than 700 subjects
(~3500 MGZ files in total). For roughly 10% of the files, the command fails,
i.e., it stops with non-zero exit code and does not produce a result file.
The relevant part of the mri_deface output is:
after smoothing, mri peak at 0, scaling input intensities by inf
GCAhistoScaleImageIntensities: could not find wm peak
The full command line, an example file and the full output can be found in the
footer of this email.
Is there anything I can try to fix this?
Some more information/observations:
I noticed that for the subjects with errors, there are almost *always* the same
3 files affected:
* mri/orig.mgz
* mri/rawavg.mgz
* mri/orig/001.mgz
The file mri/T1.mgz is never affected. The file mri/orig_nu.mgz is only
affected 2 times in total, and in these cases the image quality is extremely
bad, so they can be ignored.
Therefore, I suspect that the problems with the orig/rawavg/001 files are
related to intensity inhomogeneity, which may lead to issues with the
registration to the skull/face templates.
Tim
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
* Demo file: rawavg.mgz uploaded via FTP to /transfer/incoming/rawavg.mgz on
surfer.nmr.mgh.harvard.edu
* System info: FreeSurfer v6 stable, MacOS
* Full mri_deface command and output for the demo file:
$ SKULL_TEMPLATE="${FREESURFER_HOME}/average/talairach_mixed_with_skull.gca"
$ FACE_TEMPLATE="${FREESURFER_HOME}/average/face.gca"
$ mri_deface /path/to/subject/mri/rawavg.mgz "${SKULL_TEMPLATE}"
"${FACE_TEMPLATE}" ~/defaced.mgz
logging results to defaced.log
reading '/Applications/freesurfer/average/talairach_mixed_with_skull.gca'...
reading '/path/to/subject/mri/rawavg.mgz'...
changing type of input volume to 8 bits/voxel...
MRIchangeType: Building histogram
bounding unknown intensity as < 10.3 or > 1461.6
total sample mean = 111.8 (0 zeros)
spacing=8, using 2055 sample points, tol=1.00e-03...
resetting wm mean[0]: 143 --> 144
resetting gm mean[0]: 89 --> 89
input volume #1 is the most T1-like
using real data threshold=6.0
skull bounding box = (40, 39, 17) --> (213, 255, 225)
using (98, 111, 121) as brain centroid...
mean wm in atlas = 144, using box (77,84,95) --> (119, 137,146) to find MRI wm
before smoothing, mri peak at 89
robust fit to distribution - 89 +- 6.7
distribution too broad for accurate scaling - disabling
WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=109, mri_peak=141
after smoothing, mri peak at 0, scaling input intensities by inf
GCAhistoScaleImageIntensities: could not find wm peak
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