Dear experts,
I have an issue with mri_surf2surf (i suspect). I have resampled T1-values to the fsaverage template using mri_vol2surf and a --projfrac of 0.25 with the default white matter surface. Then I loaded these values in Matlab using MRIread, inverted them and saved them back into a file using MRIwrite. In Matlab, there were no suspicious data points (e.g. the range of R1 values excluded 0, minimum was 0.25). This was also true when loading the R1values as an overlay in Freeview. Now I wanted to smooth this image using mri_surf2surf with target and source subject being identical to fsaverage and fwhm of 10mm.
exact command was: mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage --hemi lh --sval /nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv.mgh --tval /nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv_smoothed10mm.mgh --fwhm-trg 10
But now, while it worked fine for some subjects in the 4D file for others large areas of 0 emerged in the smoothed file. Those were mostly found in inferior temporal/orbitofrontal lobe.
Does anybody have an idea what could cause this strange behaviour?
Thank you so much for your help,
Frauke
can you send your command line and terminal output?
On 04/11/2018 05:41 AM, Frauke Beyer wrote:
Dear experts,
I have an issue with mri_surf2surf (i suspect). I have resampled T1-values to the fsaverage template using mri_vol2surf and a --projfrac of 0.25 with the default white matter surface. Then I loaded these values in Matlab using MRIread, inverted them and saved them back into a file using MRIwrite. In Matlab, there were no suspicious data points (e.g. the range of R1 values excluded 0, minimum was 0.25). This was also true when loading the R1values as an overlay in Freeview. Now I wanted to smooth this image using mri_surf2surf with target and source subject being identical to fsaverage and fwhm of 10mm.
exact command was: mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage --hemi lh --sval /nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv.mgh --tval /nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv_smoothed10mm.mgh --fwhm-trg 10
But now, while it worked fine for some subjects in the 4D file for others large areas of 0 emerged in the smoothed file. Those were mostly found in inferior temporal/orbitofrontal lobe.
Does anybody have an idea what could cause this strange behaviour?
Thank you so much for your help,
Frauke
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Frauke Beyer