Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

white matter edits
by cloud.ctrl＠me.com 23 Feb '12

23 Feb '12

According to the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, we should be looking for these holes in the white surface, but when I looked at my processed data using tkmedit SUBJECT brainmask.mgz -aux wm.mgz -surfs, I saw many such holes. They seem to be ubiquitous throughout all 20 of the brains I have processed. Some might be true mistakes in the white matter surface, but I thought maybe some might just be holes that appear because of the shape of sulci moving through 3D space. Or perhaps my Talairach is off? Is there any material that instructs how to tell the difference between holes which need to be fixed and those that don't? Thank you, Vincent

2 1

Fixing talairach registration
by cloud.ctrl＠me.com 23 Feb '12

23 Feb '12

After reading the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, I understand that I should be using "tkregister2 --mgz --s SUBJECT --fstal --surf orig" when editing my talairach transform. I have been somewhat successful at this, but I was wondering if there might be another way to adjust talairach registration, perhaps by specifying anterior/posterior commissure alignment, etc?

2 1

SupraTentorial calculation
by Michael Harms 23 Feb '12

23 Feb '12

Hi Doug or Nick, I was wondering if you could clarify once exactly how the SupraTentorial volume in the aseg.stats is calculated from an algorithmic perspective. In particular, it isn't simply the sum of CortexVol + CorticalWhiteMatterVol + SubCortGrayVol, as implied by the Wiki. thanks! -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

2 3

Contrasts
by Allie Rosen 23 Feb '12

23 Feb '12

Hi, I am trying to figure out the contrasts to use for a study. I am comparing age matched patients and controls (all female). The FSGD file has 4 columns, but I'm not sure how to make an appropriate contrast matrix. Any guidance would be appreciated. I can't seem to find an applicable example on the wiki. Thanks, Allison

1 0

overlay problem
by LAOUCHEDI MAKHLOUF 23 Feb '12

23 Feb '12

hi all i have still a problem to load an activation map on a pial surface (colin27). here are the steps followed to this end : first i run bbregister : bbregister --s colin27 --mov /home/mlaouche/bashr/V8.nii.gz --init-fsl --reg /home/mlaouche/bashr/regester1.dat --bold --surf pial then i used tksurfer to see the result which seems good: tkregister2 --mov /home/mlaouche/bashr/V8.nii.gz --reg /home/mlaouche/bashr/regester1.dat --surf i used mri_vol2surf this way : mri_vol2surf --src /home/mlaouche/bashr/V8.nii.gz --out /home/mlaouche/makh_free/v80.mgz --srcreg /home/mlaouche/bashr/regester1.dat --hemi lh i used again tksurfer to load first colin27 : tksurfer -colin27 lh pial then file/load overlay to load v80.mgz no overlay was mapped

1 0

total gray matter volume
by Yolanda Vives 23 Feb '12

23 Feb '12

Dear Freesurfer experts, In Freesurfer v5.1, aseg.stats files give the value of total gray matter volume. Is this label in the annotation file? How can I know which voxels from the brain are considered as gray matter? Thank you in advance, Yolanda

2 1

Re: [Freesurfer] Freesurfer and MATLAB
by Martijn Steenwijk 23 Feb '12

23 Feb '12

?h.aparc.stats gives an average in the different labels. You could also export the labels, then it should give - on average - the same results. Best, Martijn On Wed, Feb 22, 2012 at 9:51 PM, Antonella Kis <atorok9(a)yahoo.com> wrote: > Dear Marijn, > > Thanks again for your help. I tried to do the conversion but I am not sure > if I chooses the right files because I am not getting the same values like > the one from my lh.aparc.stats stats file. I need to get as output the > NumVert and ThickAvg as a table or ascii file. > > Thank you for helping again. > Antonella > > ------------------------------ > *From:* Martijn Steenwijk <martijnsteenwijk(a)gmail.com> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Sent:* Wednesday, February 22, 2012 2:34 PM > > *Subject:* Re: [Freesurfer] Freesurfer and MATLAB > > For the number of vertices, you could use mris_convert and convert the > surface files (overlapped with thicknesses) to ascii. > > Best, > Martijn > > On Wed, Feb 22, 2012 at 8:16 PM, Antonella Kis <atorok9(a)yahoo.com> wrote: > > Hi Martijn, > > Thank you very much for your prompt response. I knew about this option but > it doesn't let me get the no. of vertices just the thickenss which I want > but I need the no. of vertices too. Can you please help? > > MAny thanks. > AK > > ------------------------------ > *From:* Martijn Steenwijk <martijnsteenwijk(a)gmail.com> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, February 22, 2012 1:11 PM > *Subject:* Re: [Freesurfer] Freesurfer and MATLAB > > You could store them as a table (aparcstats2table), you can open the > resulting text file with matlab. > > Best, > Martijn > > > On Wed, Feb 22, 2012 at 6:59 PM, Antonella Kis <atorok9(a)yahoo.com> wrote: > > Dear All, > > > Is there a way that I can open my rh.aparc.stats files (saved in stats > after recon-all) in MATLAB as a matrix? I would like to concatenate all the > rh.aparc.stats files from all my subjects. > > Many thanks, > Antonella > > _______________________________________________ > 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. > > > > > > > >

1 0

Catching uncorrected results sig.mgh
by Antonella Kis 23 Feb '12

23 Feb '12

Dear All, I would like to know what is the best way in catching the uncorrected clusters results from the sig.mgh for a structural study: Should I use the: mri_glmfit-sim \ --glmdir lh.GroupAnalysis_Thickness_15.glmdir \ --cache 2 pos \ --cwpvalthresh .99 \ --overwrite But in this case I am not getting all the clusters regarding their significance after correction by multiple comparison? I don't want the clusters from multiple comparisons just the uncorrected one. Many thanks. AK

1 0

ICV
by Dusan Hirjak 23 Feb '12

23 Feb '12

Dear Freesurfer experts, I am a beginner in using Freesurfer. I was wondering if ICV should be treated as a potential confounder (such as age, education, chlorpromazine equivalents and duration of illness) in the statistical analysis of volumetric data/cortical thickness? Thanks in advance! Dusan

4 6

problems with dti data in magnetom skyra 3T
by John Fredy 22 Feb '12

22 Feb '12

Hello all, I am trying to use a set of dti data from a Magnetom Skyra 3T. I use the dt_recon process with data from another siemens of 1.5T without problems. With the Skyra 3T I have the following error in the log file: MRIresample(): error inverting matrix; determinant is nan, matrix is: Can someone help me with this problem? Thanks in advance John Ochoa Universidad de Antioquia

2 2

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