Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

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

2 1

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

4 6

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

1 0

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

1 0

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

2 2

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

2 1

obtain volumetric data with qdec
by Clara Kühn 03 Dec '15

03 Dec '15

Dear FreeSurfer Experts, I'm trying to follow the steps described in the univeriate LME for longitudinal data (https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) Could you explain how you did this step: "The qdec.table.dat file was then used to collect volumetric data for all subjects within the Freesurfer's Qdec interface. This resulted in a new Qdec table which had the previous columns plus three new columns." I followed the instructions with mri_preproc and mri_surf2surf but when I then open qdec to obtain the volumetric data for (in my case) BA45 it always gives out the error "Error in Analyze: Coudln't open /path_to_subject_base/lh.thickness.fwhm0.templatename.mgz or .mgh file" I understand that it can't find that file because it isn't there. Which steps do I additionally need to perfom to be able to be able to obtain said volumetric data. Is there an extra turorial or walkthrough for that? Cheers, Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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