[Freesurfer] .mgh to .label ??

Hello All, How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ? Is there an automated way other than drawing ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

Re: [Freesurfer] .mgh to .label ??

Hi Ri, I think you can use mri_cor2label with flag --id set to 1. Sita. On Mon, 16 May 2011, Ritobrato Datta wrote: > Hello All, > > How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ? > Is there an automated way other than drawing ? > > Thanks > > Ri >

[Freesurfer] two questions

Hi there, First the simple question - is there a way to run mris_anatomical_stats on all my subjects at once generating a single output file? Second - actually comprised from several questions: when looking a the unthresholded group analysis on cortical thickness (in the averaged space), the

Re: [Freesurfer] visualization after cluster correction

Hi Heidi, I think this is what you need: csdbase.sig.cluster.mgh - the sig volume corrected for multiple comparisons on a cluster-wise basis. The value at each voxel is the -log10(p), where p is the pvalue of the cluster at that voxel. If that voxel does not belong to a cluster, its value will be

Re: [Freesurfer] mri_surfcluster and the color table

Hi Elisa, how was the slt file created? Can you send it and the summary file to me (don't send to the group). doug Elisa Golfinopoulos wrote: > Hi all, > > I wanted to follow-up on my previous e-mail, which may have been a bit > too vague. > > I am using the command: > > mri_surfcluster --in ./o

Re: [Freesurfer] discrepancy between p-values computed from t.nii and those stored in sig.nii

Those residuals are actually whitened, but there is still a problem in that you need to include the whitening matrix in the equation for the t ratio below. I don't know any easy way to do it from there. You can save the unwhitened residuals with -svres-unwhitenen, then compute the average of t

Re: [Freesurfer] Load normalized thickness into Matlab

Hi Rene, you can load these with MRIread.m doug René Besseling wrote: > Dear all, > > I'd like to analyse some Freesurfer outputs in Matlab. I know it is > possible to load ./surf/lh.thickness into Matlab using read_curv, but > is it also possible to load normalized (and smoothed) thickness maps,

Re: [Freesurfer] Segmentation Fault

Hi Chinduri, is this still happening? I can't replicate. doug Chindhuri Selvadurai wrote: > Hi all, > > We are trying to run individual analyses on several subjects, and we keep > getting a 'Segmentation Fault.' We have run other subjects with the same > command a while ago, and the command work

[Freesurfer] sliver problem with tksurfer over VNC

Hi all, I am experiencing the infamous sliver problem in tksurfer over VNC. I tried solving it by installing VirtualGL, but it doesn't work, I get the following error message: [VGL] WARNING: VirtualGL attempted and failed to obtain a Pbuffer-enabled [VGL]24-bit visual on the 3D X server :

[Freesurfer] [Major Upgrade] - iSurf Brainview 3.0.0

Today it was released the version 3.0.0 of iSurf Brainview, it's a major version release for IPad, IPhone and IPod Touch. Major New Features - Quiz for Brain structures (you can take a Quiz with 10 random questions about structure locations. The current database has more than 40 questions) - Selec

Re: [Freesurfer] two questions

Hi Ilana, I'll let the first question to the FS experts to answer. For the second: > 1. Is it legitimate toconclude from this that the regressor's overall effect > is that it's associated with a thinner cortex (e.g., older subjects have a > thinner cortex), eventhough most of the cortex does no

[Freesurfer] mri_segstats error

Hello, I'm trying to use mri_segstats to obtain some subcortical volume stats. When running the command line both in the tutorial data or in my own data, I have the follow error: ERROR: could not open stats/aseg.stats for writing [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analys

Re: [Freesurfer] mri_segstats error

does the stats directory exist? doug Fernanda Palhano wrote: > Hello, > > I'm trying to use mri_segstats to obtain some subcortical volume > stats. When running the command line both in the tutorial data or in > my own data, I have the follow error: ERROR: could not open > stats/aseg.stats for

Re: [Freesurfer] mri_segstats error

And do you have write permissions? Can you touch stats/aseg.stats doug Fernanda Palhano wrote: > Yes. > > [Fernanda-Palhanos-Mac-Pro:group_analysis_tutorial/004/stats] > fernandapalhano% ls > aseg.statslh.aparc.a2009s.statslh.supramarg.stats > rh.aparc.a2009s.statswmparc.stat

Re: [Freesurfer] two questions

Hi Ilana, Normality isn't a requirement for FDR to work. However, if the distribution of your statistic isn't normal **under the null hypothesis**, neither follows t, F or any other well known parametrizable distribution, then you have to obtain p-values in a different way, not from the cdf/p

Re: [Freesurfer] mri_segstats error

yes, that is fine. doug Fernanda Palhano wrote: > Doug, > > I have another question about doing a volumetric group analysis. I > used the command: > asegstats2table --subjects V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 > V14 V15 V16 V17 V18 V19 V20 V21 V22 V23 V24 V25 V26 V27 V28 V29 V30 > V31

Re: [Freesurfer] Segmentation Fault

Hi, I am experiencing the same problem. When I try to do the motion correction on fmri data it stops with a segmentation fault in mri_convert. This used to work until this week. Best Marcus On 13.05.2011 12:48, Chindhuri Selvadurai wrote: > Hi all, > > We are trying to run individual analyses

[Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

I'm having this error in the recon-all # #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

Re: [Freesurfer] Segmentation Fault

OK, I've verified and fixed this. It will be in dev in the next build (probably overnight). Are you using dev? doug Marcus Belke wrote: > Hi, > I am experiencing the same problem. When I try to do the motion > correction on fmri data it stops with a segmentation fault in > mri_convert. This use

[Freesurfer] freeview: creating ROIs, measuring volume

Hello All, I think I am missing a key step in creating an ROI in freeview. I have been tracing an ROI by hand in freeview, and saving as a label. Then I use mri_label2vol followed by mri_label_volume, and this works GREAT... except the output has far too few voxels to be the whole volume of my ROI

Re: [Freesurfer] freeview: creating ROIs, measuring volume

When you say tracing an ROI by hand in freeview, did you fill it or just traced the outline? In any case, you will need to do this on each slice by hand. However, there're various options and tools in freeview that may help speed up the process dramatically. Ruopeng On 5/16/11 5:12 PM, Lynette

Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

PPJ, Hi, mri_info /space/incoming/ga_2010.nii shows that the image is 0.5 x 0.5 x 0.5. but when viewing in freeview or tkmedit, the brain seems 'squashed', as if there is a slice gap. do you know the details of how this was acquired? N. On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Ma

Re: [Freesurfer] freeview: creating ROIs, measuring volume

Thanks Ruopeng, I tried tracing the outline with the freehand tool, and I also tried setting waypoints around the surface area of my ROI. What tools would you recommend? Thanks again! Lynette On Mon, May 16, 2011 at 3:46 PM, Ruopeng wrote: > When you say tracing an ROI by hand in freeview, did

Re: [Freesurfer] freeview: creating ROIs, measuring volume

You can try use the flood-fill tool to fill the ROI you outlined. On 5/16/11 5:58 PM, Lynette Silva wrote: > Thanks Ruopeng, > > I tried tracing the outline with the freehand tool, and I also tried > setting waypoints around the surface area of my ROI. What tools would > you recommend? > > Thanks

Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

The images are: 0.5 x 0.5 x 1.0 Can mri_convert fix it or should I edit the Nifti header? 2011/5/16 Nick Schmansky > PPJ, > > Hi, > > mri_info /space/incoming/ga_2010.nii > > shows that the image is 0.5 x 0.5 x 0.5. but when viewing in freeview > or tkmedit, the brain seems 'squashed', as if