Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

Re: [Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain
by Douglas N Greve 04 Apr '11

04 Apr '11

Hi Scott, no there is not another space I would recommend. The cortical surfaces across subjects don't line up at all with a 12DOF transform. If you look at your activation in the volume along with surface lines, you may see that your surfaces intersect some of the activation but not others. I guess if the surface is showing your important activation, then it's probably ok. I've seen people do this before. doug Scott Burns wrote: > Doug -- > > >> After you've gone into MNI space with all of your subjects, then >> visualizing the results on the surface are of questionable value. >> > > All of our first-level and second-level statistical maps in MNI space and we wish to overlay them onto fsaverage, is there another space I could map these spmT images into that when overlayed would be more reliable/publication worthy? If this wouldn't work, what would you suggest? > > Scott > > > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

3 2

Converting an FSL label to Freesurfer space
by mmoayedi 04 Apr '11

04 Apr '11

Hi, I'm trying to convert the individual FS parcelations to individual space in FSL. I'm not sure how to proceed. I've made a label from the individual subject's parcelation, and have saved it. How would I then convert the label to use it as a mask in the subject's structural space in FSL? Would mri_label2vol suffice? What would be my --reg? Thanks, Massih

2 1

Questions about GLM, Random and Fixed Effects Analysis in FsFast
by Gabriel A. Tobon 04 Apr '11

04 Apr '11

Hello Freesurfers I would like to run a specialized group GLM analysis on the volume using estimates from the individual subject analysis in Freesurfer as summary statistics. I would like to learn a little more about how this estimation is done before doing so. I have looked at the documentation for "mri_glmfit" and the following tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial I also have your 1999/2003 manuscripts on "Signal Processing and Statistical Analysis for Event-Related fMRI" and "fMRI Analysis 101 - Univariate Analysis," but I am not sure if the method has been updated since then. * I noticed there is a weight matrix (W) described for "mri_glmfit" command. How is this derived and used? I can't find more information about it in the documentation/mailing list. * How are the nuisance regressors organized in the B matrix? I assume the conditions are first? What are the following regressors? * Do you have a similar manuscript that describes just how group analysis is implemented in FsFast? Thank you for your time and help! Gabriel

2 2

mri_ca_register error
by T. Hagen 04 Apr '11

04 Apr '11

Hello all, I got this error message while running one of my subjects (freesurfer version 5.0.0): gcamFindOptimalTimeStep: Complete in 23335.062 ms 0388: dt=0.000000, rms=0.657 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Mon Apr 4 07:57:30 EDT 2011 /home/virtualuser/apps/freesurfer/subjects/flo/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s flo exited with ERRORS at Mon Apr 4 07:57:30 EDT 2011 The recon-all.log indicates that mri_ca_register couldn’t write the talairach.m3z file. The brainmask.mgz file is skull-stripped and the cerebellum is attached. There is enough disc space. Does anyone know what this could possibly mean and how to avoid it? Thanks in advance for your advice. Thomas Hagen

2 1

Pial surface correction failure after adding control points
by Min Liu 04 Apr '11

04 Apr '11

Dear Freesurfer users, My first run of recon1&2 left some white and grey matter at temporal pole region excluded. So I edited the wm.mgz by adding a bunch of control points intending to get more white matter and expand the pial surface (please see the coronal slice in the attachment where the control points were placed). Then I ran the command 'recon-all -autorecon2-cp -subjid XX' WITHOUT '-autorecon3'. From my understanding, Freesurfer would recalculate the wm.mgz as well as the white matter and pial surfaces in temporal pole according to the control points. However, I got wm.mgz corrected and pial surface wrong (as the attached graph indicated). Did I do something wrong? Why wm.mgz got fixed while pial surface not? Thanks for help in advanced! Veronica

2 3

crop a volume
by Yang Liu 04 Apr '11

04 Apr '11

Hi surfers, I have two volumes, one is 96*96*50*272, and the other is 84*96*50*272. I want to do motion correction between the two. But I have to make their spatial size to be identical. Is there a command in Freesurfer that can crop the size 96 to 84? Thanks. Yang

1 0

Re: [Freesurfer] incorrect GM/WM surfaces
by Mayuresh K 03 Apr '11

03 Apr '11

Hi Dan and Bruce, Thanks for your getting back on the problem. My concern is more about the dura being incorrectly labeled - It appears to me that the grey-CSF boundary has been incorrectly labeled as the GM-WM boundary across the entire image. Any ideas what may have gone wrong? Thanks, Mayuresh On Sat, Apr 2, 2011 at 3:28 AM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: incorrect GM/WM surfaces (Daniel G Wakeman) > 2. problems with loading a pial surface (Iris Steinmann) > 3. Re: incorrect GM/WM surfaces (Bruce Fischl) > 4. Re: problems with loading a pial surface (Bruce Fischl) > 5. preproc-sess OSX bug fix getrunlist (Juli Dolzhenko) > 6. MRI analyst position (Keith Schneider) > 7. Distance between two points along cortical (caoaize) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2011 05:53:20 +0100 > From: Daniel G Wakeman <Daniel.Wakeman(a)mrc-cbu.cam.ac.uk> > Subject: Re: [Freesurfer] incorrect GM/WM surfaces > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <471C0967-FE19-409E-8174-31FBB56CDE1E(a)mrc-cbu.cam.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Hi Mayuresh, > > I assume you are talking about the area in the posterior midline, where the > pial surface seems to go 'squiggly'. You also seem to have a problem with > the right hemisphere (left visually: I hate radiology ;)), where some dura > seems incorrectly labeled as pial surface (although the grey matter is very > difficult to see on this sequence/ at this setting). > > To fix these I recommend this wiki page: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits > > Good Luck! > Dan > > On 2011 Apr 1, at 05:08 , <freesurfer-request(a)nmr.mgh.harvard.edu> < > freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > > > Send Freesurfer mailing list submissions to > > freesurfer(a)nmr.mgh.harvard.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > or, via email, send a message with subject or body 'help' to > > freesurfer-request(a)nmr.mgh.harvard.edu > > > > You can reach the person managing the list at > > freesurfer-owner(a)nmr.mgh.harvard.edu > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Freesurfer digest..." > > > > > > Today's Topics: > > > > 1. incorrect GM/WM surfaces (Mayuresh K) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 1 Apr 2011 15:21:18 +1100 > > From: Mayuresh K <mayureshk.82(a)gmail.com> > > Subject: [Freesurfer] incorrect GM/WM surfaces > > To: freesurfer(a)nmr.mgh.harvard.edu > > Message-ID: > > <AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello freesurfer experts, > > > > I have successfully finished running the recon-all analysis without any > > errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM > > surfaces however look incorrect and I am not sure what may have gone > wrong. > > See attached screenshot from tkmedit. > > Any suggestions how to fix this would be helpful. > > > > I have processed other datasets collected from the same scanner using the > > same sequence which seem to have correctly identified the pial and > > grey-white boundaries. I am using > > freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. > > > > Thanks, > > Mayuresh > >

2 3

creating labels in tksurfer
by Ilana Hairston 02 Apr '11

02 Apr '11

Hi there, I'm having difficulty creating labels in tksurfer (v4.5). I followed the "Creating Labels" instructions on the Wiki, however clicking Fill on the closed path didn't seem to do anything. I used save label anyway, and tried to load this new label again, and even though it says "7681 nonzero vertices found", again i see nothing. Not quite sure what i'm doing wrong. Also - which LUT file is the correct one to go with aparc.annot? i get the most bizarre labeling with FreeSurferColorLUT Thanks ilana -- ******************************* peligro! flaca pero mala! ******************************

2 3

Vertex-by-vertex analyses within ROIS?
by Dalwani, Manish 01 Apr '11

01 Apr '11

Hello Freesurfers, I am happy to find out that it is possible to carry out vertex-by-vertex analyses for specific ROIs. Can someone help me understand, 1. How to run such a vertex-by-vertex analyses for certain ROI or ROIs? 2. Can we apply cluster-wise correction or FDR to the ROI to correct for multiple comparison? Regards, Manish Dalwani

1 0

add subject to group but cannot find brain for 049
by Knut J Bjuland 01 Apr '11

01 Apr '11

I have added a subject to the to the groups of subject that was available for the qdec tutorials. with this in mind I have used make_average_subject and I have now 41 subject. But when I run this command there is always a subject for which it can not find brain. I am positive that the necessary files are available. The subject that I have add is anonymous mri picture that i have imported into freesurf, and the subject is 20 years old female. Knut J

3 6

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 April 2011