[Freesurfer] mri_surf2surf

Dear Doug and All, I want to register the individual subject surface into the fsaverage surface. I used mdi_surf2surf command. But one error occurred. Could you please help me with this. Here are the scripts: — [root@localhost sub001]# mr

[Freesurfer] LME Matlab toolbox

Greetings, The aim of this mail is about some problems that I am facing using the standalone copy (that is becouse I am using v5.1) of the LNE Matlab Tool provided on the FreeSurfer Wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels). Currently, I am carrying out a longitud

[Freesurfer] white matter surface (tkmedit -surfs) vs wm.mgz

Dear all I am segmenting data of 2 year olds and as freesurfer fails on segmneting inferior parts of the temporal lobe, I try to edit this manually using tkmedit (protocol from fswiki: WhiteMatterEdits_tktools, PialEdits_tktools, ControlPoints_tktools). I first add control points, with successf

Re: [Freesurfer] Coomand not found

Sure, thanks! tcsh shalim-ubunut:/media/Shared_Data/freesurfer> setenv FREESURFER_HOME /media/Shared_Data/freesurfer shalim-ubunut:/media/Shared_Data/freesurfer> source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment

Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

Dear Bruce & Matt, thank you for your help. @Bruce: I would be happy to send you the data, just let me know by e-mail which files you would need. @Matt: Could you please specify the commands for the flags -nsigma_above and -nsigma_below and how you would rerun the pipeline? Also what values woul

Re: [Freesurfer] EM registration: brain centroid

Hi Mark if you upload a subject that failed and the gca I'll take a look Bruce On Mon, 12 May 2014, Mark Plantz wrote: Yes, I created my own atlas for use with 1-2 year olds. It seems to be happening for all of the subjects. I am wondering if changing the recon-all code to load the manual t

Re: [Freesurfer] Measuring cortical thickness at a specific location

I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate - that wouldn't be a problem. You just don't want to measure it that way cheers Bruce On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > H

Re: [Freesurfer] mri_surf2surf

Hi Qiongmin try making the output format .mgz (or maybe .nii) and see if that fixes the problem cheers Bruce On Tue, 13 May 2014, Caka wrote: Dear Doug and All, I want to register the individual subject surface into the fsaverage surface. I used mdi_surf2surf command. But one error occur

Re: [Freesurfer] Cannot allocate memory

can you send us the recon-all.log? On Tue, 13 May 2014, Mayer Kristina wrote: > Dear Bruce, > > I was running: > recon-all -autorecon2-cp, after adding control points. > When I then look at the surfaces using tkmedit -surfs or inflated surfaces > using tksurfer, everything seems to fit and I can

Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

Hi Emil I would need the entire subject dir plus the T2-space volume cheers Bruce On Tue, 13 May 2014, Emil H.J. Nijhuis wrote: Dear Bruce & Matt, thank you for your help. @Bruce: I would be happy to send you the data, just let me know by e-mail which files you wo uld need. @Matt: Could

Re: [Freesurfer] white matter surface (tkmedit -surfs) vs wm.mgz

Hi Kristina are you running: recon-all -autorecon2-cp -autorecon3 ... after adding control points and editing the wm? Bruce On Tue, 13 May 2014, Mayer Kristina wrote: > Dear all > > I am segmenting data of 2 year olds and as freesurfer fails on segmneting > inferior parts of the temporal lo

Re: [Freesurfer] LME Matlab toolbox

Hi Victor As explained in the wikifs_read_surf.m andfs_read_Y.m depend on Freesurfer's scripts so you need to have installed Freesurfer software package and included the Freesurfer's matlab subdirectory in your Matlab's search path. Best -Jorge El Martes 13 de Mayo de 2014 4:40, Victor

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, Just to clarify, when you say "average the thickness along each A/P coordinate" do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P->A, or is there another way to find the average thickness of each slice and then see

[Freesurfer] R: R: R: R: Filipping issue

Dear Doug, I am trying to run "mris_preproc" as you indicated, but it fails with the following error: MRISread($SUBJECTS_DIR/fsaverage/surf/lh.fsaverage_sym.sphere.reg): could not open file. Why is target file searched in the "fsaverage" folder? I was expecting it is searched in the "fsaverage_s

[Freesurfer] lme and survival (time-to-event) analysis tools on github

Hi everyone Just wanted to point out that all the technology required to implement the statistical methods used in our last paper: "Event time analysis of longitudinal neuroimage data. Neuroimage. doi: 10.1016/j.neuroimage.2014.04.015". is available on github: https://github.com/NeuroStats I

Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

I don’t know if recon-all will pass those flags in or not. Probably best to let Bruce take a look. Peace, Matt. On 5/13/14, 7:36 AM, "Bruce Fischl" wrote: >Hi Emil > >I would need the entire subject dir plus the T2-space volume > >cheers >Bruce >On Tue, 13 May >2014, Emil H.J. Nijhuis wrote:

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Panos I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate cheers Bruce On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi Bruce, > > Just to

[Freesurfer] bbregister surf2vol

Dear Freesurfer I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , th

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, I see, that's really helpful, thank you! Best, Panos > Hi Panos > > I would make an average thickness map in fsaverage space, then in matlab > divvy up the a-p direction into bins (say 100 of them) and compute the > average in each bin based on the a/p coordinate > > cheers > Bruce >

[Freesurfer] how to save an intensity contour?

Hello, I am using the intensity contour tool for defining a white/gray matter border of my ROI. I can adjust my ROI according to this contour and save it. However, the contour itself is not saved (to the same layer as the ROI) and will not be loaded when opening the ROI layer again later. Is the

Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

Hi doug Thanks doug. My mask and input mgh file are all fsaverage space. I try the mri_segstats, and I cannot get what you mean clearly. So I read the help of mri_segstats, but neither do I get the information. Then I have to try to run this: mri_segstats --i ./rh.36sb.10.mgh --mask ./cluster1.m

Re: [Freesurfer] how to save an intensity contour?

Hi Sarah what tool are you using to draw the contour? Bruce On Tue, 13 May 2014, Burke, Sarah wrote: > Hello, > I am using the intensity contour tool for defining a white/gray matter > border of my ROI. > I can adjust my ROI according to this contour and save it. However, the > contour itself i

Re: [Freesurfer] how to save an intensity contour?

Hi Bruce, in Freeview, I am using the voxel edit tool called "Contour". Sarah Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@nmr.mgh.harvard.edu] Verzonden: dinsdag 13 mei 2014 17:29 Aan:

[Freesurfer] question about surf2vol

> > Dear Freesurfer > I want to use surf2vol to get volume files of gray > thickness.And the --volreg Contains the matrix that maps XYZ in the reference > anatomical to XYZ in the functional volume. So I use bbregister.Why I need > not invert the BBR registration matrix with sur

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, Sorry, I had a last follow up question. I just realized that the resulting bins will be in the fsaverage space, and hence I wouldn't be able to use mris_anatomical_stats to calculate the average thickness of the bins, since the fsaverage "subject" does not have a wm.mgz file. Did you hav

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Panos no, mris_anatomical_stats won't do it. I would map the average thickness to fsaverage coords, then load that into matlab and go from there using the [xyz] coords of fsaverage for the binning, which is pretty much MNI305 cheers Bruce On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wro

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, I was having issues with the part after that, that is how to calculate the average thickness of those bins, after I create them. Thanks again Best, Panos > Hi Panos > > no, mris_anatomical_stats won't do it. I would map the average thickness > to fsaverage coords, then load that into ma

Re: [Freesurfer] NHP surface reconstruction in FS5.3

Just to follow up, it looks like mris_thickness needs to be run, but mris_curvature is unchanged by changes to the pial surface. Thanks again for the help! stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Sun, May

Re: [Freesurfer] Quesion about lobar volumes

Just use mri_binarize doug On 05/07/2014 05:08 PM, pfot...@nmr.mgh.harvard.edu wrote: > Hi Doug, > > That sounds great! I'll go ahead and do that. I would just be interested > in coming up with the binary maps of the lobes, not their associated > stats. Should I still go ahead and use mri_segstats

Re: [Freesurfer] LOOK FOR HELP

surf2vol understands which direction the registration goes and applies it appropriately. Use --outvol thicknessvolume.nii to get a single nifti file output On 05/07/2014 10:22 PM, 刘东博 wrote: > Dear Greve > Thank you for your reply > I want to use surf2vol to get volume files of gray thickness.

Re: [Freesurfer] Fwd: extracting rois for connectivity analysis

This is a very vague request. What kind of connectivity analysis? fMRI or DTI? What software are you using? On 05/08/2014 05:43 AM, Jutta Ernst wrote: > > > Dear Freesurfer's > > I draw a roi to extract the cortical thickness for my two groups and > that worked fine. > Now I'm trying to export

Re: [Freesurfer] Fwd: extracting rois for connectivity analysis

Sorry, I was going through "old" emails and did not see this had already been addressed. Please ignore, which I'm sure most of you were doing anyway :-) On 05/13/2014 01:37 PM, Douglas N Greve wrote: > This is a very vague request. What kind of connectivity analysis? fMRI > or DTI? What softwar

Re: [Freesurfer] NHP surface reconstruction in FS5.3

the pial curvatures will change, but you probably don't use them anyway cheers Bruce On Tue, 13 May 2014, S.V.Shepherd [work] wrote: Just to follow up, it looks like mris_thickness needs to be run, but mris_curvature is unchanged by changes to the pial surface.  Thanks again for the help! st

Re: [Freesurfer] Subcortical volume calculation from aparc+aseg.mgz?

The partial volume correction is done based on the intensity and label of the surrounding voxels. By using aparc+aseg you change the label of the surrounding structures and it changes the PV correction. Use aseg.mgz and not aparc+aseg doug On 05/09/2014 05:27 AM, Schreiber, Stefanie wrote: > D

Re: [Freesurfer] mri_surf2surf

You can't use analyze for this. mgh format will work. nii might work On 05/13/2014 04:37 AM, Caka wrote: > Dear Doug and All, > > I want to register the individual subject surface into the fsaverage surface. > I used mdi_surf2surf command. But one error occurred. Could you please help > me with

Re: [Freesurfer] Viewing functional data on the inflated brain

Sorry, I've totally lost the thread on this one. Can you send the command line, the terminal output, and the log file again? doug On 05/12/2014 04:11 PM, Sherryse Corrow wrote: > Hi Douglas, > > I don’t receive any emails from anyone, I only receive the the digest > which is what I “reply” t

Re: [Freesurfer] nonlinear models in longitudinal analysis

Hi Jodie, are you familiar with mixed effects models? If not I would recommend you include a biostatistician. What I mean (and you can do this in the matlab code, no need to include it in the qdec file) is to use a piecewise linear model. So for a subject with visits at 0, 0.4 and 0.9 years you

Re: [Freesurfer] Coomand not found

Not exactly sure why your getting a permission denied error. Can you please try the following and provide us with the relevant output? 1) What is the output of the following: ls -ld $FREESURFER_HOME/bin 2) After sourcing FreeSurfer, what happens when you type: tkmedit -f $SUBJECTS_DIR/sample-001

[Freesurfer] Freeview/Freesurfer Version Compatibility

During the Spring Freesurfer workshop the newest version of Freeview was used as the primary viewing tool. Are there compatibility issues with using the newest version of Freeview while running analyses in an older version of Freesurfer (v5.1.0)? That is, if you run recon-all through v5.1.0, can

Re: [Freesurfer] R: R: R: R: Filipping issue

Sorry, in both of those mris_preproc commands add --target fsaverage_sym doug On 05/13/2014 09:48 AM, Paola Valsasina wrote: > Dear Doug, > > I am trying to run "mris_preproc" as you indicated, but it fails with the > following error: > > MRISread($SUBJECTS_DIR/fsaverage/surf/lh.fsaverage_sym.

Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

There are a lot of things that I don't understand about your command line. Why are you passing the thickness as the segmentation? The mask only limits the computations to be inside the mask. What precisely are you trying to do? On 05/13/2014 11:27 AM, charujing123 wrote: > Hi doug > Thanks

Re: [Freesurfer] Freeview/Freesurfer Version Compatibility

You can use the new version of freeview with older versions of FS. doug On 05/13/2014 03:10 PM, Sarah Blankenship wrote: > During the Spring Freesurfer workshop the newest version of Freeview > was used as the primary viewing tool. Are there compatibility issues > with using the newest version

Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere

Hi Christopher -- Indeed, you can use 'mris_pmake' to calculate the shortest distance along the surface between arbitrary mesh points. Given a valid FreeSurfer environment, $SUBJECTS_DIR, etc: $>mris_pmake --subj 101 --hemi lh --surface smoothwm --mpmProg pathFind --mpmArgs vertexStart:0,verte

[Freesurfer] freeview segmentation fault

Hello- We’re having a problem with our Freesurfer 5.3 install: freeview exits with a Segmentation fault. No windows open, and there is no other other output. strohm::funcserv1:=>freeview Segmentation fault All I have been able to find is that it appears to be making an ina

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Hi, The same result! the last is insula ! Best regards, Amirhossein Manzouri On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve wrote: > Try this version > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ > greve/aparcstats2table > > > On 05/12/2014 03:41 AM, amirhossein manzouri wrot

Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

Hi doug, I read your last e-mail again. After changed my command, it worked. Thanks doug. Rujing Zha 2014-05-14 charujing123 发件人：Douglas N Greve 发送时间：2014-05-14 03:14 主题：Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specifi

[Freesurfer] Registration and Surface flatten

Dear Doug and all, I have already done two things: (1) 'recon-all’ to the segmentation for 140 subjects; (2) surface registration to fsaverage template for 1 subject using: mri_surf2surf --hemi lh --srcsubject sub001 --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval ./su

[Freesurfer] change background color in tksurfer

Hi FS experts and users I want to change the background color of tksurfer from black to white. However I cannot find the drop-down list. Is there anyone who can tell me to desolve this? Thanks. All the best. Rujing Zha 2014-05-14 charujing123 ___ Fre