[Freesurfer] Poor automatic segmentation of the cerebellum
Dear list, I'm interested in measuring cerebellar volumes using freesurfer. However, the automatic segmentation (aseg) seems to be doing a poor job of capturing the whole structure for many subjects. Specifically, it is chopping off the bottom of the cerebellum. Here is an example: https://drive.google.com/open?id=0B68CY3v4cg7tS0hSNkVVMWNiZV8xYWR2eTJQQlhFeVM0Q2Jn The issue seems to be when the cerebellum is very close to the bottom of the image, as is the case in many of our scans. Has anyone encountered similar issues with cerebellum segmentation, and if so, have any advice about how to improve it? Many thanks, -- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06511 http://www.srmathias.com ___ 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 using LGI script despite making suggested changes to Matlab script.
Dear all, I'm running into the following error when running "recon-all -s -lgi" using the latest version of FreeSurfer and Matlab R2016a: ERROR: make_roi_paths did not complete successfully! It seems like this is a common issue when using more recent versions of Matlab, so I editted the script as documented here: http://freesurfer.net/fswiki/ReleaseNotes?highlight=%28%28LGI%29%29 However, this did not fix my problem and I get the exact same error message. Any ideas? -- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06511 http://www.srmathias.com ___ 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] QCACHE always produces zeros for some vertices in the left hemisphere
Dear list,
I'm trying to extract vertex-level measures of thickness, area, etc, for
all of my subjects. I ran recon-all -all on all subjects as normal, then
ran:
recon-all -s {subject} -qcache
where {subject} is the subject ID. This was followed by `mris_convert` to
make the values human-readable:
mris_convert -c {subj_dir}/surf/{hem}.{meas}.fwhm25.fsaverage.mgh
{fsavg_dir}/surf/lh.sphere {subj_dir}/surf/{hem}.{meas}.fwhm25.fsaverage.asc
I did this for each subject, hemisphere, and measure (thickness, area,
sulc). Many of the vertices in the left hemisphere always produce values of
0, for every subject, and for every measure. The first offending vertex is
#9. So if I head a randomly chosen file, I get:
[sm2286@grace0 surf]$ head lh.area.fwhm25.fsaverage.asc
000 0.0 0.0 100.0 0.43150
001 27.64000 -85.07000 44.72000 0.39083
002 89.44000 0.0 44.72000 0.33804
003 27.64000 85.07000 44.72000 0.81910
004 -72.36000 52.57000 44.72000 0.41731
005 -72.36000 -52.57000 44.72000 0.37795
006 -27.64000 -85.07000 -44.72000 0.77490
007 72.36000 -52.57000 -44.72000 0.49643
008 72.36000 52.57000 -44.72000 0.0 <--- this value
This is a different subject:
[sm2286@grace0 surf]$ head lh.sulc.fwhm25.fsaverage.asc
000 0.0 0.0 100.0 0.00692
001 27.64000 -85.07000 44.72000 -0.45451
002 89.44000 0.0 44.72000 0.38711
003 27.64000 85.07000 44.72000 0.17178
004 -72.36000 52.57000 44.72000 -0.54163
005 -72.36000 -52.57000 44.72000 -0.01465
006 -27.64000 -85.07000 -44.72000 -0.07269
007 72.36000 -52.57000 -44.72000 0.46408
008 72.36000 52.57000 -44.72000 0.0 <--- this value
Bizarrely this also happens when I switch the target of qcache to
fsaverage5. The right hemisphere is never affected. Does anyone have any
clue what's going one here?
--
Samuel R. Mathias, Ph.D.
Associate Research Scientist (ARS)
Neurocognition, Neurocomputation and Neurogenetics (n3) Division
Yale University School of Medicine
40 Temple Street, Room 694
New Haven CT 06511
http://www.srmathias.com
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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.
Re: [Freesurfer] QCACHE always produces zeros for some vertices in the left hemisphere
Just a correction from my previous message; this issue actually affects both hemispheres, but different vertices in each one. -- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06511 http://www.srmathias.com ___ 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.
