Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Validation
by Weisinger, Brian (NIH/OD) [E] 09 Oct '09

09 Oct '09

Hello, I am going to present some of my findings that I obtained with freesurfer at an upcoming meeting and was wondering if someone could tell me of a published paper that discusses the validity/reliability of sub cortical structure volumes (thalamus) that I could cite in my presentation. Thank you, Brian Weisinger

2 1

skull stripped image with the original resolution
by Jose Luis Cantero Lorente 09 Oct '09

09 Oct '09

Hi there, would it be feasible to save to .nii the skull stripped image obtained with Freesurfer but keeping the original image resolution? As it is, Freesurfer allows you this operation, but the resultant .nii image comes with a poor resolution (8-bits) which is useless for my purpose. Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

3 2

Hemispheric orientation
by Dankner, Nathan (NIH/NIMH) [F] 09 Oct '09

09 Oct '09

Hello all, This is a rather basic question, but I've run into some problems answering it due to the fact that is seems so simple. Much of the data that I have been processing seems to have volumetric asymmetries the opposite of which would be expected, so I was curious as to how freesurfer determines which hemisphere is right and which is left. Does the orientation of the brain matter, or are there labels affixed to each hemisphere in header files? I am using afni .BRIK and .HEAD files. Any help would be appreciated. Thanks, Nathan

2 1

Re: [Freesurfer] skull stripped image with the original resolution
by Jose Luis Cantero Lorente 09 Oct '09

09 Oct '09

Thanks, Nick. In which coordinates system are these skull stripped imaged? Is it possible to save to .nii these skull stripped images transformed to MNI coordinates? Thanks again. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/ ----- Mensaje original ----- De: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> Fecha: Viernes, Octubre 9, 2009 6:26 pm Asunto: Re: [Freesurfer] skull stripped image with the original resolution > add -odt int to the mri_convert flag: > > mri_convert -odt int brainmask.mgz brainmask.nii > > which saves the output file in 'integer' data format. > > On Fri, 2009-10-09 at 18:16 +0200, Jose Luis Cantero Lorente wrote: > > Hi there, > > > > would it be feasible to save to .nii the skull stripped image > obtained with Freesurfer but keeping the original image > resolution? As it is, Freesurfer allows you this operation, but > the resultant .nii image comes with a poor resolution (8-bits) > which is useless for my purpose. > > > > Thanks in advance. > > > > Best, > > Jose > > --- > > Jose Luis Cantero, Ph.D. > > Laboratory of Functional Neuroscience > > Department of Physiology, Anatomy, and Cell Biology > > University Pablo de Olavide > > Ctra. de Utrera, Km.1 > > 41013 - Sevilla > > - Spain - > > > > Phone: +34 954 977433 > > Fax: +34 954 349151 > > Email: jlcanlor(a)upo.es > > http://www.upo.es/neuroaging/es/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

2 1

Re: [Freesurfer] skull stripped image with the original resolution
by Jose Luis Cantero Lorente 09 Oct '09

09 Oct '09

MNI152 --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/ ----- Mensaje original ----- De: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Fecha: Viernes, Octubre 9, 2009 6:46 pm Asunto: Re: [Freesurfer] skull stripped image with the original resolution > which MNI? > > Jose Luis Cantero Lorente wrote: > > Thanks, Nick. > > > > In which coordinates system are these skull stripped imaged? Is > it possible to save to .nii these skull stripped images > transformed to MNI coordinates? > > > > Thanks again. > > > > Best, > > Jose > > > > --- > > Jose Luis Cantero, Ph.D. > > Laboratory of Functional Neuroscience > > Department of Physiology, Anatomy, and Cell Biology > > University Pablo de Olavide > > Ctra. de Utrera, Km.1 > > 41013 - Sevilla > > - Spain - > > > > Phone: +34 954 977433 > > Fax: +34 954 349151 > > Email: jlcanlor(a)upo.es > > http://www.upo.es/neuroaging/es/ > > > > ----- Mensaje original ----- > > De: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > > Fecha: Viernes, Octubre 9, 2009 6:26 pm > > Asunto: Re: [Freesurfer] skull stripped image with the original > resolution> > > > >> add -odt int to the mri_convert flag: > >> > >> mri_convert -odt int brainmask.mgz brainmask.nii > >> > >> which saves the output file in 'integer' data format. > >> > >> On Fri, 2009-10-09 at 18:16 +0200, Jose Luis Cantero Lorente wrote: > >> > >>> Hi there, > >>> > >>> would it be feasible to save to .nii the skull stripped image > >>> > >> obtained with Freesurfer but keeping the original image > >> resolution? As it is, Freesurfer allows you this operation, but > >> the resultant .nii image comes with a poor resolution (8-bits) > >> which is useless for my purpose. > >> > >>> Thanks in advance. > >>> > >>> Best, > >>> Jose > >>> --- > >>> Jose Luis Cantero, Ph.D. > >>> Laboratory of Functional Neuroscience > >>> Department of Physiology, Anatomy, and Cell Biology > >>> University Pablo de Olavide > >>> Ctra. de Utrera, Km.1 > >>> 41013 - Sevilla > >>> - Spain - > >>> > >>> Phone: +34 954 977433 > >>> Fax: +34 954 349151 > >>> Email: jlcanlor(a)upo.es > >>> http://www.upo.es/neuroaging/es/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > > > > _______________________________________________ > > 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 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >

1 0

spatial smoothing and retinotopic analyses
by Aspell Jane 09 Oct '09

09 Oct '09

Hi I spatially smoothed my data (Gaussian kernel of FWHM 5mm) prior to running retinotopy analyses. Is this a bad thing - would it have blurred the boundaries between visual areas significantly? What is the usual recommendation for spatial smoothing and retinotopic analyses? Many thanks, Jane Aspell

2 1

Monte Carlo simulations: documentation
by c.k.tamnes＠psykologi.uio.no 09 Oct '09

09 Oct '09

Dear Freesurfer users We have run some analyses on cortical thickness using Monte Carlo simulations (mri_glmfit-sim --sim mc-z) in FS 4.50. Can anyone advice me on documentation where this procedure is described? A paper where it has been used would also be very helpfull. Best Regards Christian -- Christian K. Tamnes Center for the Study of Human Cognition Department of Psychology, University of Oslo PB 1094 Blindern, 0317 Oslo, Norway Cell ph: (+47) 97572410

3 2

Qdec problem
by Dankner, Nathan (NIH/NIMH) [F] 08 Oct '09

08 Oct '09

Hello, Recently when trying to create difference maps in qdec I've been receiving this error: Error in Analyze: command failed: mri_glmfit -y [path]/.mgh --fsgd [path]qdec.fsgd dods --glmdir [path] --surf fsaverage rh --C [path]/contrasts/rh-Avg-Intercept-thickness.mat --C [path]/contrasts/rh-Diff-Group1-Group2-Intercept-thickness.mat The reason his is strange is because I have executed these exact commands in qdec dozens of times with no problem. Any help would be appreciated. Thanks, Nathan

2 1

mri_nu_correct.mni intensity correction problem
by Jeff Sadino 07 Oct '09

07 Oct '09

Hello, I asked this question a couple days ago, but never got an answer. Please excuse the double posting. I am running FS 3 and am having problems with auto-recon1, in particular the mri_nu_correct.mni step. My orig volume has intensities around 150-250, but my nu.mgz image has intensities all below 20. I am having errors further down the line, but I think they are all due to this step. Can anyone help me get my intensity values to work out right? Thank you! Jeff Sadino

2 1

Smaller
by Jeff Sadino 07 Oct '09

07 Oct '09

Hello Surfers, I have a number of subjects that are displaying a large number of small holes in the superior region of their white matter. I believe the medical term for them is virchow-robin spaces. We would like to try to quantify the volume that these holes occupy. Is there any way to break down the Right-Cerebral-White-Matter and Left-Cerebral-White-Matter segmentation labels in aseg.mgz into finer regions so that we can quantify the volume of these holes? Or would it simply be easier to go through the volumes and manually label the holes as a label that is not being used? Thank you, Jeff Sadino

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer