Freesurfer March 2011

freesurfer@nmr.mgh.harvard.edu

111 participants
170 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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retinotopy manual?
by Michelle Umali 05 Apr '11

05 Apr '11

Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer. Thanks. Michelle

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Re: [Freesurfer] Interpreting results from Qdec
by Nick Schmansky 05 Apr '11

05 Apr '11

Courtney, if i understand your question, i think one way to do that is to use qdec to draw a label on the blob of interest, and the run 'map label to subjects', which creates a label file in each subjects label dir, then you can run stats on that with mris_anatomical_stats. (btw, i'm putting this answer on the list, as others may have better ideas.) n. On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote: > Hi Nick > > Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer. > > A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. > Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance? > > Thanks in advance! > Courtney > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Thursday, December 30, 2010 2:44 PM > To: Gallen, Courtney (NIH/NIDA) [F] > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Interpreting results from Qdec > > ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a > plot of the data at that surface vertex will appear. the group will be > apparent from that (say, demented group is thinner than non-demented > group). this data is significance data (log p, so '2' is 0.01), so mean > and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data > of all subjects in the analysis, so you could extract mean and stdev > from that. > > ans. 2. - slide the 'annotation' opacity slider to show the annotation > data (cortical parcellation). the ctrl left click will also put the > region info for that vertex on the lower left of the display. > > see also: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis > > n. > > On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] > wrote: > > Hi, > > > > > > > > I’m currently running analyses in Qdec and have identified areas that > > show significant effects in my contrasts. I have two questions related > > to interpreting these results. > > > > > > > > 1. How can you interpret the effect in each “blob?” (i.e., which > > group has a greater cortical surface area, etc.). Right now, all I > > know is that there is an effect in certain areas. Can you export this > > data to get means and standard errors? > > > > 2. Is there a way to localize where these effects are? E.g., a > > tool that tells you this effect is located in __ area of the brain? > > > > > > > > Thanks in advance > > > > Courtney > > > > > > > > Courtney Gallen > > > > Post-baccalaureate IRTA > > > > Neuroimaging Research Branch > > > > National Institute on Drug Abuse (IRP) > > > > 251 Bayview Blvd > > > > Suite 200 > > > > Baltimore, MD 21224 > > > > Tel: (443) 740-2631 > > > > > > _______________________________________________ > > 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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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

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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

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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

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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

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Where can I find long_mris_slopes
by lan lin 01 Apr '11

01 Apr '11

I installed freesurfer 5.0 and want to use long_mris_slopes to prepare the longitudinal data but couldn't find the command. Where can I find it? thanks Lan

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Visualizing SPM Results on Template FreeSurfer Brain
by Andrew Jahn 31 Mar '11

31 Mar '11

Hello, I have second-level results in .img/.hdr format that I have just run through SPM. I was wondering whether there is a way to visualize these results onto a template FreeSurfer surface model in MNI space. Is this possible, or can you only visualize second-levels which have been processed through FreeSurfer? Thanks, -Andrew

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A question about make_average_subject
by soft.join Huang 31 Mar '11

31 Mar '11

Hi all: Recently, I have a question about some details of the function make_average_subject, which creates some average surfaces and volumes based on the specified subjects' files. And I'm wondering how it make an average one. In my opinion, every specified subject's volume and surface register to a existed template( something like fsaverage) and we can acquire a transform matrix or something like it. According to the transformation, we can register them roughly. And then we can average them to a mean one. I don't know whether my thought right or not. Can anyone give me some tips? :) Thanks in advance Lijie Huang

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Freesurfer March 2011