[Freesurfer] create surface mesh from arbitrary volume?
External Email - Use Caution
hello, i would like to create a mesh, such as the one in surf/lh.pial, using an
arbitrary binary volume.
i'm aware that freesurfer can convert the subcortical volume ROIs to surfaces,
does anyone know if this can be applied to an arbitrary binary volume?
i would like to replicate the script by Anderson Winkler (see below) but
instead of on subcortical aseg, on an arbitrary volume that i supply. is this
possible? thanks,
# Pre-tessellate
echo "==> Pre-tessellating: ${s}, ${lab0}"
${FREESURFER_HOME}/bin/mri_pretess \
${SUBJECTS_DIR}/${s}/mri/aseg.mgz ${lab} \
${SUBJECTS_DIR}/${s}/mri/norm.mgz \
${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz
# Tessellate
echo "==> Tessellating: ${s}, ${lab0}"
${FREESURFER_HOME}/bin/mri_tessellate \
${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz \
${lab} ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth
# Smooth
echo "==> Smoothing: ${s}, ${lab0}"
${FREESURFER_HOME}/bin/mris_smooth -nw \
${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth \
${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}
# Convert to ASCII
echo "==> Converting to ASCII: ${s}, ${lab0}"
${FREESURFER_HOME}/bin/mris_convert \
${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} \
${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc
mv ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc \
${SUBJECTS_DIR}/${s}/ascii/aseg_${lab0}.srf
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] error during volume_stats
External Email - Use Caution i receive this error when i try to run recon-all from my home directory on neurodebian: anyone know what is causing this? thanks, Iteration 1 Fri Jul 27 09:24:33 EDT 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.2638/nu0.mnc ./tmp.mri_nu_correct.mni.2638/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2638/0/ -iterations 1000 -distance 50 [brain@neurodebian:/home/brain/fstest/test1/mri/] [2018-07-27 09:24:33] running: /opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2638/0/ ./tmp.mri_nu_correct.mni.2638/nu0.mnc ./tmp.mri_nu_correct.mni.2638/nu1.imp /opt/minc/1.9.16/bin/volume_stats: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /opt/minc/1.9.16/bin/volume_stats) nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux recon-all -s test1 exited with ERRORS at Fri Jul 27 09:24:33 EDT 2018 For more details, see the log file /home/brain/fstest/test1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] how to estimate skull/scalp thickness
hello, i was wondering if it is possible to estimate skull/scalp thickness using freesurfer? if so does anyone know how this can be accomplished? thanks, Russell Butler ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] how to get intrinsic/gaussian curvature in custom FMRI ROI?
Hi, i would like to use an FMRI ROI as a label from which to extract some curvature metrics in single subjects. all my FMRI ROIs are in nifti volume format, in the same space as my freesurfer segmentations. i've tried this tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness? and it works for cortical thickness, but don't know how to use it to get the other metrics like curvature. thanks, Russell? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
