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30135 discussions

including missing gray matter voxels
by Kendrick Kay 04 Dec '15

04 Dec '15

I am trying to figure out how to manually expand the pial surface boundary (generated via automatic segmentation with recon-all) to include additional gray matter voxels which have been erroneously labeled as skull or CBF. i found extensive documentation on how to delete voxels (for example from white matter mask), but i can't seem to find relevant information advising how to manually include some missing gray matter voxels (on either ends of the cortex - i.e. white matter/gray matter boundary or gray matter/pial surface boundary). Any help would be appreciated. -- Kendrick Kay, PhD Assistant Professor Center for Magnetic Resonance Research University of Minnesota, Twin Cities Web: http://cvnlab.net <http://cvnlab.net/> E-mail: kay(a)umn.edu <mailto:kay@umn.edu> Cell: 510-206-1059 Skype: kendrickkay

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How to divide the lateral and medial vertex index of fsaverage4?
by Meiling Li 04 Dec '15

04 Dec '15

Dear Freesurfer Now I have two ROIs on the fsaverage4, one on the lateral and the other is the on the medial, how can i separate apart the two rois? Acutally, how can i divide the vertex index of the lateral and medial on fsaverage4 or fsaverage5? Thanks in advance! Meiling

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bring volumes to fsaverage space
by Shani Ben Amitay 04 Dec '15

04 Dec '15

Dear freesurfers, I would like to know what will be the best way to bring volumes in the individual subject's space to the fsaverage space. Thanks, Shani

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Path Problem
by LIEWALD David 04 Dec '15

04 Dec '15

Environment : Opensuse 13.2 Freesurver Version 6 (Beta) Hi I hope you can help with this problem I'm using the version 6 Beta due to problems with license authentication. Freesurfer runs but bails out with a file not found error : Iteration 1 Fri Dec 4 09:38:57 GMT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc ./tmp.mri_nu_correct.mni.24767/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist! Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 (ec183cc) x86_64 x86_64 x86_64 GNU/Linux on examination of the file structure a directory named "tmp.mri_nu_correct.mni.24767" has been created under the "mri"directory and nothing has been created under the "tmp" directory in the subject root. I am guessing that this is the cause of the error. any advice on correcting this would be extremely useful Dave Liewald The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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g-w.pct vs. g-w. ratio
by Andrews, Derek 04 Dec '15

04 Dec '15

>Dear FreeSurfer Support team, > >Thank you for your quick response. > >Is it fair to present both g-w.pct (100*(w-g)/((w+g)/2)) and g-w.ratio >(g/w) as GWR? I have seen the pct calculation presented as GWR in an >abstract that cited Salat (2009) in its introduction text. >Also, is it fair to say that decreases in in g-w.pct indicate less >definition between >the g/w matter boundary as a decrease in g-w.ratio would indicate? If I >want to make a statement about reduced definition between the g/w matter >boundary, what calculation would you suggest? > >Thank you very much for your clarifications on this. > >Best, Derek > > > > >________________________________________ >Derek Sayre Andrews, MSc >PhD Candidate > >The Sackler Institute for Translational Neurodevelopment >Department of Forensic and Neurodevelopmental Sciences >Institute of Psychiatry, Psychology & Neuroscience, King's College London > >Telephone: +44 (0)20 7848 5701 >Email: Derek.Andrews(a)kcl.ac.uk > > > > > >On 03/12/2015 17:26, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > >>g-w.pct is computed as >> >>pct = 100*(w-g)/((w+g)/2) >> >>in the pctsurfcon script >> >> >>On 12/03/2015 12:18 PM, Andrews, Derek wrote: >>> Dear FreeSurfer Support team and Community >>> >>> I am wondering if someone can give me an explanation of the difference >>> between g-w.pct and g:w ratio (as calculated by; fscalc lh.gm.mgh div >>> lh.wm.mgh -o lh.ratio.mgh) >>> Will both these measures essentially measure the relationship between >>> grey and white matter signal intensity but in a different way? >>> >>> >>> Best, Derek >>> >>> >>> >>>------------------------------------------------------------------------ >>> >>> *Derek Sayre Andrews, MSc* >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> >>> Department of Forensic and Neurodevelopmental Sciences >>> >>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: Derek.Andrews(a)kcl.ac.uk >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>-- >>Douglas N. Greve, Ph.D. >>MGH-NMR Center >>greve(a)nmr.mgh.harvard.edu >>Phone Number: 617-724-2358 >>Fax: 617-726-7422 >> >>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)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. >> >

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brainstemSsLabels.v10.mgz sub-labels (e.g., brainstem, pons, etc.) not included in mri_convert
by Jonathan Plasencia 03 Dec '15

03 Dec '15

Hello Everyone, I've run the Freesurfer 6.0 and created the sub-brainstem structures (e.g., pons, midbrain, etc.). I would like to convert the brainstemSsLabels.v10.mgz results to a .nii file. However, unlike when I use mri_convert for aseg.mgz, I only get an image of the brainstem itself as a single intensity (or label) and not subparts (or labels for pons, midbrain, etc.). Is there a way to get the labels for all sub-brainstem parts included in the nii writeout, using mri_convert or another function in freesurfer? Best, Jon

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segmentation labels
by Lim, Lena 03 Dec '15

03 Dec '15

Dear Experts, I tried to run the following to get the segmentation volumes but encountered the errors below... How can I get the volumes of the insula and thalamus and also the inferior prefrontal cortex please? [spjwker@nanlnx2 FSL]1% asegstats2table --subjects PAC01... PAC70 --segno 9 48 19 55 --tablefile aseg.vol.table SUBJECTS_DIR : /home/spjwker_PAC/Lena/CT_SA/FSL Parsing the .stats files Building the table.. ERROR: cannot find the corresponding segmentation for the id:19 you provided in any of the .stats files parsed Many thanks, Lena

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Grey matter， white matter and CSF volumes
by Jinsong Tang 03 Dec '15

03 Dec '15

Hello, I want to calculate the Grey matter, white matter and CSF volumes. The total gray matter volume is already in the ASEG file. Then I add up following volumes for ventricular CSF: Left Lateral Ventricle + Left Inferior Lateral Ventricle + Right lateral Ventricle + Right Inf Lateral Ventricle + 3rd Ventricle + 4th Ventricle + 5th Ventricle + Right choroids plexus + left choroids plexus. also, I add up following volumes for white matter volume: CorticalWhiteMatterVol +Left-Cerebellum-White-Matter + Right-Cerebellum-White-Matter. Are these right? Thanks, Jinsong

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converting labels to MNI space
by Francesca Strappini 03 Dec '15

03 Dec '15

Dear FreeSurfer experts, I'm trying to convert some retinotopic labels I created on the surface of each individual subject to MNI305 space for FSL. I run the following commands, but the output is not registered correctly. It seems to be shifted downward. mni152reg --s LG mri_label2label --srclabel lh.V1dorsalLG.label --s LG --regmethod surface --trglabel lh.V1dorsalLG_new.label --hemi lh mri_label2vol --label lh.V1dorsalLG_new.label --reg /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_new_MNI.nii.gz Thanks for your help, Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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g-w.pct vs. g-w. ratio
by Andrews, Derek 03 Dec '15

03 Dec '15

Dear FreeSurfer Support team and Community I am wondering if someone can give me an explanation of the difference between g-w.pct and g:w ratio (as calculated by; fscalc lh.gm.mgh div lh.wm.mgh -o lh.ratio.mgh) Will both these measures essentially measure the relationship between grey and white matter signal intensity but in a different way? Best, Derek ________________________________ Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: Derek.Andrews(a)kcl.ac.uk

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