Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Building FreeSurfer with OpenMP enabled
by Akio Yamamoto 14 Jun '12

14 Jun '12

Hi all, I'm attempting to build FreeSurfer with OpenMP enabled. After checking out a copy of the main dev trunk from the CVS repository, I did the configuration with "--enable-openmp" option and run 'make'. Compilation successfully finished and all of 'make check' tests passed. Now I have two questions. (1) Although 'recon-all' finished without error, the results are slightly different from those obtained by the binary distribution (stable v5.1.0). I also find that the message format in a log file (recon-all.log) is not the same as that of the stable version, so I wonder if the source code in the main dev trunk is modified/updated from the stable version... Is it okay to ignore the slight difference of the results? (2) Despite the openmp option being enabled, it looks like the program runs as a single-thread mode. I actually find the message "NUMBER OF OPENMP THREADS = 1" in a log file. Do I need to specify some option when running 'recon-all' script? Any suggestion and/or help would be appreciated. Best, Akio Yamamoto

3 4

suggestions for bandpass filters?
by Caspar M. Schwiedrzik 14 Jun '12

14 Jun '12

Dear all, I would like to apply a bandpass filter both to my fMRI data as well as to regressors in my GLM. I was wondering whether anyone has suggestions for particular filter types and filter orders? I find this seldomly reported in fMRI papers. I was thinking in using Matlab's filtfilt. Any suggestions would be appreciated. Thanks, Caspar

1 0

Mris_anatomical_stats: smoothing does not work with surface area maps
by Jürgen Hänggi 14 Jun '12

14 Jun '12

Dear FS experts I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted. When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far. However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option. It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps. Is there any solution to also smooth surface area maps with mris_anatomical_stats? I use the Mac FS 5.1.0 version Thanks in advance Best regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

4 7

creating surface intermediate between white and pial: mri_surf2surf and mri_surf2vol
by Jeff Eriksen 13 Jun '12

13 Jun '12

I am hoping to create a new surface that is half-way between the white and pial surfaces, then project it back to the volume. I have seen some examples of creating normals this way, but I am unclear as to how to just create the surface itself. The Wiki page is not too helpful, as it does not list the -sval switch in the following example: mri_surf2surf --s subject --hemi lh --sval-nxyz pial --tval ./pial_nrml_srf_lh.mgz mri_surf2vol --surfvalpial_nrml_lh.mgz --hemi lh --outvol pial_nrml_vol_lh.mgz --identity subject --template T1.mgz --projfac 0.5 Is there another version of the mri_surf2surf documentation that discusses the —sval switch? For mri_surf2vol, I do not understand the –projfac implementation and cannot find a complete description of it. I would like to use it do do a smooth interpolation between the pial and white surfaces (with normals as well), but it is not apparent to me that this is possible. Thanks, -Jeff

2 1

Export Functional Data Overlayed Onto Sphere
by Luis R. Piloto 13 Jun '12

13 Jun '12

Hello, I've specifically adopted Freesurfer for its ability to map a brain into a sphere. I've ran a subject's structural data through the recon-all pipeline using the -all option. With this reconstruction completed, I'd like to overlay functional data on the sphere. More specifically, I'd like the ability to programmatically query a point on the sphere and get the corresponding activation. Is there a reasonable way to do this within the Freesurfer pipeline? I already have the ability to programmatically query my initial functional data, so it would suffice to get a transformation matrix from my structural data to the spherical coordinates. Any thoughts/suggestions would be appreciated. Regards, Luis Piloto

2 2

vertex-by-vertex thickness
by Shantanu Ghosh 13 Jun '12

13 Jun '12

Hi FS experts, Sorry if this is a newbie question. I want to display how an individual patient's crtical thickness varies from the normal group average, vertex-by-vertex. What is the commandline to do that? I want to display the overlay on MNI152 instead of fsaverage. Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for Biomedical Imaging Harvard-MIT Program in Health Sciences & Technology

2 4

(no subject)
by mdkruepke＠uwalumni.com 13 Jun '12

13 Jun '12

Freesurfers A real real general question here: if i am running a glm_fit for cortical thickness with a fsgd with 2 groups (G1, G2) and 3 continues variables and have a matrix of 1 -1 0 0 0, red/yellow areas mean that G1 is thicker in this area than G2, correct? Best- Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

2 1

aseg inaccuracy in cortex
by Nicole Senecal 13 Jun '12

13 Jun '12

Hi all, I'm noticing that when pulling up a brainmask volume with surfs and aseg on, the pial and white surfaces are (thankfully) very often correct, but the aseg in cortex is a bit off - often including parts of the skull/dura as gray matter - even though the pial surface does follow this boundary correctly. As long as the surfaces are correct, and my primary interest will be cortical thickness, do I need to worry about these inaccuracies in the aseg? Is checking the aseg primarily done for ensuring accuracy in subcortical structures rather than in cortex? thanks, Nicole -- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371

2 1

Correction for Multiple Comparisons
by mdkruepke＠uwalumni.com 13 Jun '12

13 Jun '12

Freesurfers- When correcting for multiple comparisons using: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.4\ --overwrite What does the sign mean (ie - the neg, pos, abs). Also for the mc-z simulation type do we no longer need to include the smoothness of our data (FWMH)? Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

2 2

cortical thickness with a continuous variable
by mdkruepke＠uwalumni.com 13 Jun '12

13 Jun '12

Freesurfers- I am looking to investigate the whether cortical thickness varies in regards to a continues variable, while controlling for other continues variables. I am having a little trouble wrapping my head around this as i am unsure how to compare thickness in regards to a continues variable, how the contrast would look, ect. Looking at this example FSGD ( http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V) GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variables Age Input subject1 Group1 30 Input subject2 Group2 40 I am thinking i may need to randomly define two groups, and then use a contrast similar to 0 0 0.5 0.5 (contrast 4 on the same page). Which asks: Null Hypothesis: does mean of group age slope differ from 0? Is there an average affect of age regressing out the effect of group? Am i correct in thinking that if i use this contrast i would be able to determine whether there is a difference in cortical thickness based on any continuous variable (like age, IQ)? Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

2 3

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