What was the format of your original image? This generally means that the direction cosines were incorrect in it. Don’t worry about the resampling artifacts – that is because it is interpolating the 001.mgz into the voxel space of the orig.mgz.
If you load the 001.mgz without the orig it will look fine. Are you sure that the 001.mgz looks fine in all views (like are inferior/superior correct)?
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Krystal Xiwing Yau
Sent: Monday, June 19, 2023 3:51 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [FreeSurfer] Talairach Failure Detection
External Email - Use Caution
Dear Freesurfer experts,
I would like to seek for help regarding talairach error. I have browsed through the forum about it but still not solving my problem...
The following steps are the solutions I have tried:
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Re-run recon-all with -notal-check
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Re-run recon-all with -notalairach
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The above flags gave the same error message as follow:
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WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108
after smoothing, mri peak at 0, scaling input intensities by inf
error: Numerical result out of range
error: GCAhistoScaleImageIntensities: could not find wm peak
Command exited with non-zero status 252
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Ran the command to fix the registration: tkregisterfv --s Sub-108 --fstal --no-surfs
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The view for this subject is weird because it shows the
axial view when the coronal view is selected
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The correct view showed up when the coronal view is selected
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When I viewed 001.mgz in Freeview, there was no such problem. However, some artifact (i.e. the weird lines) occurred in certain slices, as circled in pink:
I am not sure how to fix it with tkregisterfv and what are the standards for it.
It would be so much appreciated if someone could help out with this issue.
Regards,
Krystal
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