[Freesurfer] prefrontal cortex label

hi, I have tried to make prefrotnal cortex label by doing first mri_annotation2label --subject "$subject" --hemi rh --outdir "$subject"/label mri_mergelabels -i lh.caudalanteriorcingulate.label -i lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i lh.medialorbitofrontal.label -

Re: [Freesurfer] Odd thing about mris_convert? Position changed from freesurfer format to .stl

Hi Ting STL may not contain the info for ras2vox transform as it is not a medical imaging format. We've only supported it in the past for 3D printing and such. You might need to keep track of the ras2vox and restore it when you convert back (e.g. in matlab) cheers Bruce On Fri, 21 Nov 2014,

Re: [Freesurfer] qdec and recon-all crashes

I test ran it with the symbolic link. the symbolink link is: lrwxr-xr-x1 wieser admin 66 Nov 14 14:17 DROPBOX_MJMRI -> /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI I'm in the DROPBOX_MJMRI directory and have set the subjects_directory to the current directory pw

[Freesurfer] mri_glmfit-sim sim-sign

hi please explain the differece between --sim-sign abs, neg, and pos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the pers

Re: [Freesurfer] repost: recon-all failure due to header

Doug, Thanks for responding. It looks like we were feeding it obliqued data. When we used our deobliqued data, it ran just fine. Ashley Ashley N. Stillman Clinical Psychology Graduate Research Assistant University of Tulsa, T.R.A.P.T. Lab Laureate Institute for Brain Research email: anstill...

[Freesurfer] Linear Mixed Effects Models

Hi,   I am from Frankfurt, Germany and I want to use Freesurfer and matlab for the analysis of my longitudinal brain structural data. I want to use linear mixed effects modelling, however, I receive an error message when I execute    [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3);

Re: [Freesurfer] qdec and recon-all crashes

Hmmm, I was able to duplicate the issue and it looks like you might be stuck. The getcwd method resolves symbolic links to the full (real) path and in the case of using qdec, this *might* be a problem with no quick fix... other than copying the SUBJECTS_DIR onto your local machine to a path wot

Re: [Freesurfer] Odd thing about mris_convert? Position changed from freesurfer format to .stl

Hi Bruce, Thank you for your reply! Would you please give me a hint how does it work, save ras2vox or ras xform into to FS surface file? I searched the archive, googled, did not figure out yet. All the function such as read_susrf.m and write_surf.m only deal with coordinates and faces information

Re: [Freesurfer] Linear Mixed Effects Models

Hi Franziska, looks to me that for some reason it does not find the vec function which should be part of the package under ..freesurferpath/matlab/vec.m so maybe you just need to source FreeSurfer in the shell before you start matlab (from that same shell). Best, Martin On 11/21/2014 02:25

Re: [Freesurfer] Linear Mixed Effects Models

Hi Martin,   thanks a lot for your help and the quick reply! It works now!   Best, Franziska   Gesendet: Freitag, 21. November 2014 um 21:34 Uhr Von: "Martin Reuter" An: "Freesurfer support list" Betreff: Re: [Freesurfer] Linear Mixed Effects Models Hi Franziska, looks to me that for s

Re: [Freesurfer] tracula failure

Hi Alena - If you're still having this problem, try specifying the gradient table (bvecfile) and b-value table (bvalfile) in your config file. Also, there's a syntax error at the very top of your terminal output, because anything that is a list of multiple items needs to be specified between p

Re: [Freesurfer] TRACULA dwi flipping

Hi Barbara - It's converting to LAS orientation. If it the images are already in LAS orientation, that command will have no effect, as you say. a.y On Fri, 17 Oct 2014, Barbara Kreilkamp wrote: > Dear all, > > Would you please explain why TRACULA is flipping the data so often? And > what does

Re: [Freesurfer] TRACULA preprocessing: bvector rotation, negative eigenvalues

Hi Barbara: 1. The rotation component of the registration matrix from eddy_correct is extracted for each DWI and applied to the corresponding gradient vector. 2. dmri_pathstats is not a script, it's a C++ executable, so to edit it you have to download the source code, modify, and rec

Re: [Freesurfer] tracula min mid max values

Hi Cat - Would setting the max to 0.05 work? a.y On Fri, 24 Oct 2014, Cat Chong wrote: Dear Anastasia, I am trying to visualize  the tract p-values along one pathway as shown in the tutorial.http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics I have implemented the p-value

Re: [Freesurfer] From bedpostX and recon-all to tracula

Hi Kate - The -prep, -bedp, and -path steps need to be run separately, in that order. You can't run them all at once unfortunately. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula a.y On Wed, 29 Oct 2014, Katherine Damme wrote: Sorry for the delay. I signed u

Re: [Freesurfer] Tracula_average_average center

Hi Mohamad - These are explained here, "average over the entire support of the path distribution, weighted average over the entire support of the path distribution, and average over highest-probability path only": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics a.y On

Re: [Freesurfer] Tracula_critical issue

Hi Mohamad - As it's a probabilistic method that's sampling from a distribution, there is a bit of randomness built in (which should decrease as you increase the number of samples that you collect). You'll find that the the weighted average measures are the most reliable, as they are less aff

Re: [Freesurfer] TRACULA bedpost error

Hi Amanda - You can try running bedpostx directly (not through trac-all) and see if that runs fine: bedpostx /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS006/dmri a.y On Thu, 6 Nov 2014, Worker, Amanda wrote: Hello, I am trying to run the second step of the TRACULA processing

Re: [Freesurfer] TRACULA - Error: bvecs and bvals don't have the same number of entries

Hi Tadeu - The files appear to have the problem described here: https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg20513.html That's probably was causing them not to be converted correctly. a.y On Thu, 6 Nov 2014, Tadeu Kubo wrote: Dear FS Experts, I'm trying to work with the

Re: [Freesurfer] Command '-qa' in TRACULA

Hi Anri - See here, and follow the link "software update": http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments The -qa option was added after 5.3 was released. a.y On Mon, 10 Nov 2014, Anri WATANABE wrote: Dear FreeSurfer experts, I'm running pre-processing steps in TRACULA

Re: [Freesurfer] tractstats2table for dwi motion

Hi Yoon - Sorry, the tractstats2table script is for measures that are specific to each tract. The motion measures are extracted from the entire DWI data set, so they're not specific to a given tract. You can concatenate the dwi_motion.txt files like this: source dmrirc foreach subj ($subjlist)

[Freesurfer] tksurfer curvature and overlay displays

Hi all, I'm having some issues (some possibly mine, some possibly tksurfer's) getting tksurfer (5.3c6) to display curvature the way I think it should be able to. I am using the bert sample data. The Curvature display - If I use the Show Curvature button in the UI control pa

Re: [Freesurfer] Resample the surface mesh

Hi Ting, I am not an expert, but why do you want to downsample the native surface mesh? The usual way of doing this is to register the full surface mesh with the functional volume data using Doug's bbregister. Cheers, Thomas On Fri, Nov 21, 2014 at 4:08 AM, ting xu wrote: > Dear freesurfer expe