[Freesurfer] Repeated measures ANOVA with covariate

Hi freesurfer experts, Is there a way to perform a repeated measures ANOVA with a between subjects factor (two groups)? I am interested in comparing cortical thickness differences between the matched scans between the two groups i.e. measures*group interaction. How would I setup this design in fr

Re: [Freesurfer] fsaverage of freesurfer v5

yes, it is a 6th order icosahedron. Here is a list of the number of vertices with each order 3 642 42562 5 10242 6 40962 7 163842 On 5/25/11 11:08 PM, Dai Dai wr

[Freesurfer] fsaverage of freesurfer v5

hi, all does freesurfer v5 have multiple fsaverage subjects with varying number of vertices? see the following mails; where does fsaverage6 locate? Nick Schmansky nicks at nmr.mgh.harvard.edu Fri Sep 10 15:23:09 EDT 2010

Re: [Freesurfer] qdec error message

Hi Nick I run Qdec 1.2 and all cases have been processed with freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Olivier On 25/05/2011, at 21:18, Nick Schmansky wrote: > what version of freesurfer does this happen with? > > n. > On Wed, 2011-05-25 at 14:17 +1000, Olivier Piguet wrote: >> Good aft

[Freesurfer] for low resolution monitors, tksurfer dialog fix

Hi all, It's been pointed out that tksurfer's "Configure Overlay Display" dialog gets clipped for low resolution monitors where it's impossible to see and interact with the buttons. This is how it looks: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksurferclipped.jp

[Freesurfer] Export table of cluster stats from Qdec

Hi, I have 2 questions regarding Qdec: 1. We would like to save the results of 'cluster stats' (the printout on the terminal after pressing the "Find clusters and go to max" button) to a text file. Is there a way to do that? Or is it automatically saved in somewhere and where would that locat

Re: [Freesurfer] analysis interpretion question

Hi Ilana have you visually inspected the asegs? I would make sure that there are no systematic and/or biased segmentation results in which the putamen/insula are misassigned so that one is "stealing" from the other. Bruce On Wed, 25 May 2011, Ilana Hairston wrote: > Hi there, > I have two be

[Freesurfer] analysis interpretion question

Hi there, I have two behavioural variables that are inversely related to each other. One was correlated with thinning of the posterior insula (using glm_mri), while the other is positively correlated with the putamen volume (extracting aseg tables and running in SPSS). The region of the insula

Re: [Freesurfer] rtview and color bar

Can you send a picture? Michelle Umali wrote: > Hi Freesurfers! > I ran rtview, and I couldn't find a color bar/legend. I'm just > wondering how thow the colors get assigned. Is each color a position > of wedge stimulus? > > I'm trying to define V1/V2/V3 boundaries and was wondering how to g

[Freesurfer] rtview and color bar

Hi Freesurfers! I ran rtview, and I couldn't find a color bar/legend. I'm just wondering how thow the colors get assigned. Is each color a position of wedge stimulus? I'm trying to define V1/V2/V3 boundaries and was wondering how to get the horizontal and vertical meridians. Any help wo

Re: [Freesurfer] Freesurfer GLM and measurement of an interaction

Hi Chris, It is a t-test. In the case of one variate (a single row to the contrast matrix), an F-test is the same as an unsigned t-test. doug Chris Hyatt wrote: > For a two factor GLM analysis with two levels, I'm uncertain as to why > the Freesurfer GLM measurement of the interaction effect o

Re: [Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

Hi, And Mac users should wait for this instead of my suggested temporary fix earlier today. Thanks, -Krish On May 25, 2011, at 2:57 PM, Nick Schmansky wrote: > Hyunwoo (and Mac users), > > We're going to have to post a new build of v5.1 later today which > fixes > this problem. In general,

Re: [Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

Hyunwoo (and Mac users), We're going to have to post a new build of v5.1 later today which fixes this problem. In general, our goal is to have a Mac build that doesnt require special libraries, like libgfortran, but both our build and test machines had that lib for other reasons, so it slipped th

[Freesurfer] Freesurfer GLM and measurement of an interaction

For a two factor GLM analysis with two levels, I'm uncertain as to why the Freesurfer GLM measurement of the interaction effect of say, group and gender, is a t-test and not an F-test. In my case, my factors are group (healthies vs patients) and gender (male vs female). For a 2x2 two-way ANOVA a

[Freesurfer] Stats for HC and lobar volumes in template space

Hello, We are thinking about the hippocampal and lobar volumes in FS template space, do we have such stats? Thanks. Aize ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.ed

[Freesurfer] job opportunity

Beginning August 15th, a two-year position is available for a highly motivated and talented postdoctoral fellow in the Department of Psychology at the University of Arizona. The goal of this research program is to study the neural processes that support vision, perception and attention using funct

Re: [Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

Hi Hyunwoo Our build system seems to pick up the dynamic gfortran libraries for OSX. We'll post a fixed mri_robust_register ( and similar binaries which depend on that dynamic library) soon. For a temporary fix: save ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/libgfortran

Re: [Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

Hi, I am not familiar with the mac build and think Krish can probably give more details. You are missing the libgfortran dynamic library. I don't think it is installed on the mac by default. On the mac we use the veclib framework, not sure why the error shows up and what consequences it has.

[Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

Dear FreeSurfer Hello, I am currently trying the following freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 and I noticed the following. During the first step ( rec

Re: [Freesurfer] flattened patch ascii file & matlab

Actually, it goes beyond visualisation. That works fine using tksurfer; although, while we're at it: I'd like to use a different colormap (say the jet colormap) but don't seem to be able to do so... suggestions?. I'd like to resample the activation maps and do some surface based searchlight analysi

Re: [Freesurfer] flattened patch ascii file & matlab

Hi Cris, why not just visualize it in tksurfer instead? cheers Bruce On Wed, 25 May 2011, Cris Lanting wrote: > Dear all, > > I'm trying to read a flattened patch (ascii) using matlab but I'm > slightly confused: > after performing mris_flatten and > mris_convert -p rh.patch.flat rh.patch.flat.

[Freesurfer] flattened patch ascii file & matlab

Dear all, I'm trying to read a flattened patch (ascii) using matlab but I'm slightly confused: after performing mris_flatten and mris_convert -p rh.patch.flat rh.patch.flat.asc I get the following file: #!ascii version of patch ./rh.orig. The 1st index is not a vertex number 12755 25052 -46888 v

Re: [Freesurfer] Error compiling freesurfer

The lXmu libraries are installed on my system. Now the error is: Making all in mri_em_register make[2]: Entering directory `/tmp/dev/mri_em_register' /bin/sh ../libtool --tag=CC --mode=link g++ -I../include -I../include/dicom -I/usr/local/cuda/include -DFS_CUDA -L/tmp/packages/mni/current/lib

Re: [Freesurfer] temporal pole label

the easiest thing to do is to convert all the annotations to labels, then just use the temporal pole one. I don't think there is an option at the moment to only extract a single label, but Doug will correct me if I'm wrong :) cheers Bruce On Wed, 25 May 2011 k...@rice.edu wrote: > Dear Bruce,

Re: [Freesurfer] temporal pole label

Hi Kareen, I'll cc the list as others may be interested. You can use mri_annotation2label to extract the label you want. As for which to use, it depends what you want to do with it, but I would expect the individual labels are what you want since they are adjusted to account for individual va

Re: [Freesurfer] new FreeSurfer release, v5.1

glad to hear it. Let us know how it goes. Bruce On Wed, 25 May 2011, Alan Francis wrote: > Hi Nick and Bruce: > > Congratulations and thanks for releasing FS 5.1. We have a longitudinal > study of First Episode Schizophrenia that was awaiting this release. > > best, > > Alan Francis > Beth Israe

Re: [Freesurfer] new FreeSurfer release, v5.1

Hi Nick and Bruce: Congratulations and thanks for releasing FS 5.1. We have a longitudinal study of First Episode Schizophrenia that was awaiting this release. best, Alan Francis Beth Israel Deaconess Medical Center On Tue, May 24, 2011 at 4:28 PM, Nick Schmansky wrote: > FreeSurfer Users, > >

Re: [Freesurfer] Error compiling freesurfer

lacking -lXmu ? On Wed, 25 May 2011, Jordi Delgado wrote: >../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a >../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU -lGL >-L/usr/X11R6/lib -lX11 -lm ../glut/libglut.a -lz -lm -lcrypt -ldl >-lpthread -lnetcdf

Re: [Freesurfer] FS5.1 for CentOS4 works for CentOS5-like OS?

Yes. It works -- iOS 4.3 Em 25/05/2011, às 10:14, Xinian Zuo escreveu: > Dear FS team, Only see new 5.1 version for CentOS4 in the website. Thanks, XN. > > -- > Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) > ___ > Freesurfer mail

Re: [Freesurfer] temporal pole label

Hi Kareem, both the annotations we automatically compute contain temporal pole labels. Also, the average subject we provide (fsaverage) has both parcellations, so you could just use one of them cheers Bruce On Wed, 25 May 2011 k...@rice.edu wrote: > Hello, > > I have a question about the lab

[Freesurfer] FS5.1 for CentOS4 works for CentOS5-like OS?

Dear FS team, Only see new 5.1 version for CentOS4 in the website. Thanks, XN. -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

[Freesurfer] Error compiling freesurfer

Hi Freesurfers, I've downloaded FS from CVS, and I have Cent OS 5.5 (32 bits) I've done: ./configure --prefix="/tmp/freesurfer" --with-mni-dir="/tmp/packages/mni/current" --with-tcl-dir="/tmp/packages/tcltktixblt/current" --with-vtk-dir="/tmp/packages/vtk/current" --with-vxl-dir="/tmp/packages/v

[Freesurfer] temporal pole label

Hello, I have a question about the labeling in tksurfer. My goal is to take an average inflated surface of 10 controls and then make a temporal pole label out of that average. Alternatively, if FS provides a label for the TP for each patient I could average the labels together. Do you have

Re: [Freesurfer] Error from cudadetect

5.1 was released yesterday -- iOS 4.3 Em 25/05/2011, às 09:42, R Edgar escreveu: > On Wed, May 25, 2011 at 7:59 AM, Howison, Mark wrote: > >> We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute >> cluster at Brown and are seeing the following error when running >> 'cudadetect': >

Re: [Freesurfer] Error from cudadetect

On Wed, May 25, 2011 at 7:59 AM, Howison, Mark wrote: > We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute > cluster at Brown and are seeing the following error when running > 'cudadetect': > > ERROR: cuda driver does not appear to be installed! > Detecting CUDA... There are 2 devi

Re: [Freesurfer] overlay properties tksurfer window incomplete...

i had a similar problem with my macbook (i think), and was told to use spacebar in lieu of enter. On 23 May 2011, at 01:04, Gonzalo Rojas Costa wrote: > Hi: > > I have an ubuntu based computer with Freesurfer 5, and it seems that > because the font size or the screen resolution, the lowes

[Freesurfer] Error from cudadetect

Dear Freesurfer developers, We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute cluster at Brown and are seeing the following error when running 'cudadetect': ERROR: cuda driver does not appear to be installed! Detecting CUDA... There are 2 devices supporting CUDA: Device 0: "Tesla

Re: [Freesurfer] qdec error message

what version of freesurfer does this happen with? n. On Wed, 2011-05-25 at 14:17 +1000, Olivier Piguet wrote: > Good afternoon, > > When running qdec, I receive the following error message: > > Writing to > /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh > reading group av