Re: [Freesurfer] Hippocampal Subfields Segmentation

Hi everyone, you need to install the Matlab 2012b runtime as explained in the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 27

Re: [Freesurfer] registering to fsaverage

Hi Trisanna we need more information if you want us to help you. What does "very odd mean"? If you do it in .mgz do you get a different answer than in .mnc? If so, why not just compute them in .mgz and convert to .mnc at the end? cheers Bruce On Mon, 27 Jun 2016, Trisanna Sprung-Much

Re: [Freesurfer] Hippocampal Subfields Segmentation

Hi Pierre, Due to some technical problems, it might take me a couple of days to figure out what’s going on. But it definitely sounds funny that it is asking for the CTF, since this is supposed to be embedded in the executable… I’ll get back to you as soon as possible. Cheers, Eugenio Juan

Re: [Freesurfer] visualizing statistical maps in FreeView

Hi Lars, Freeview currently does not have this feature. We will add it in the future. Best, Ruopeng > On Jun 27, 2016, at 10:21 AM, Bruce Fischl wrote: > > Hi Lars > > > I'll leave this for Ruopeng. > > cheers > Bruce > > On Mon, 27 Jun 2016, Lars Morten Rimol

Re: [Freesurfer] visualizing statistical maps in FreeView

Hi Lars I'll leave this for Ruopeng. cheers Bruce On Mon, 27 Jun 2016, Lars Morten Rimol wrote: Hi Bruce,   Yes, now it works (my guess is I loaded a single subject surface as template before…) but I don’t find an FDR correction button in the Configure Overlay interface. The fdr

Re: [Freesurfer] visualizing statistical maps in FreeView

As to the color bar, would it be possible to send me a screenshot of it? Thanks, Ruopeng > On Jun 27, 2016, at 10:21 AM, Bruce Fischl wrote: > > Hi Lars > > > I'll leave this for Ruopeng. > > cheers > Bruce > > On Mon, 27 Jun 2016, Lars Morten Rimol wrote: >

Re: [Freesurfer] Hippocampal Subfields Segmentation

I tried that. but didn't work. Cheers, Pierre On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio wrote: > Hi everyone, > you need to install the Matlab 2012b runtime as explained in the wiki: > https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime > Cheers, > Eugenio >

Re: [Freesurfer] FSFAST- Cerebellum

Hi Thomas and Doug- Thanks for you suggestions. Per your suggestions I performed following recon-all -i $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz -subjid Yeo2011_MNI152_FS recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS

Re: [Freesurfer] Freesurfer/Freeview help

Hi Abbie you just use the recon-all script from the command line: recon-all \ -i \ -sd \ -s \ -all this will take 5-20 hours and at the end will create and populate a directory tree with segmented volumes and surfaces cheers Bruce On Mon, 27 Jun

Re: [Freesurfer] Freesurfer/Freeview help

Hi Abbie what are you trying to create a mesh of? We supply meshes for the gray/white interface and for the pial surface. We supply voxel segmentations of lots of other things that you could mesh, but we don't by default. cheers Bruce On Mon, 27 Jun 2016, Abbie McNulty wrote: > Hello, > I am

Re: [Freesurfer] Stuck on “CORRECTING DEFECT”

Hi Bruce, Thanks for the tips. I tried playing around with the files for a bit but didn’t make much progress. Here’s a link to the full tar/gz’ed subject dir: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=4ej948sa49s Thanks! Dan On Fri Jun 24 22:22:17 EDT 2016, Bruce Fischl

Re: [Freesurfer] Freesurfer/Freeview help

Hi Bruce, I am trying to create a mesh of the MRI scans, eventually with imported scans, but for now just using the information available through the software. How do you work these voxel segmentations? I'm just very new with the software. Say I import an MRI scan, and I want to cortically

Re: [Freesurfer] Freesurfer/Freeview help

Essentially, once segmentation is achieved, how do you mesh the scans? On Mon, Jun 27, 2016 at 3:41 PM, Abbie McNulty wrote: > Hi Bruce, > > I am trying to create a mesh of the MRI scans, eventually with imported > scans, but for now just using the information available

[Freesurfer] Freeview nightly / dev / beta

Hello Freesurfer developers, I am looking for a version of Freeview that recognizes the -noquit flag. V 1.0 Build Aug 24 2015 14:50:08 allows this, but is no longer available from "ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev

Re: [Freesurfer] FSFAST- Cerebellum

Hi Thomas- On second thought is it valid to simply do if I want average time series of the cerebellum regions? fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >> avgCerebellum.txt Is this correct? Cheers, Sabin Khadka On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka

Re: [Freesurfer] Question about FreeSurfer

Hi, I am graduate student at the University of Michigan and I am performing research on deep brain stimulation. I want to warp an anatomical brain atlas to individual patient MRIs to get the patient specific brain models out of it. I chose FreeSurfer to do this and I have installed it on my

Re: [Freesurfer] Question about FreeSurfer

Hi Dorsa what specific models do you need? The 10-20 hours is to process the data from a single subject at a single timepoint. If you check out our wiki (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of tutorials and sample datasets and such cheers Bruce On Mon, 27 Jun 2016, Dorsa

Re: [Freesurfer] Question about FreeSurfer

Hi, I need patient specific brain models created by warping atlases to individual MRIs. I want the model to include the Subthalamic Nucleus, Gpi, Thalamus and their surrounding organs. (Cortical segmentation is not necessary). When I use the" recon all "command on one MRI image, I get the error

[Freesurfer] Freesurfer/Freeview help

Hello, I am trying to segment a MRI brain in order to create a mesh of the image into finite elements, but I am very new with Freesurfer/Freeview and am not familiar with the tools. So far, I have only uploaded brain.mgt from the bert file that comes with the program. If I wanted to mesh this

Re: [Freesurfer] Hippocampal Subfields Segmentation

Hello, I have similar problem. " "Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf" the file is here but when I try to execute it, it's always missing some library (libmwi18n.so for example, it was missing others before that

Re: [Freesurfer] registering to fsaverage

any ideas? Thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 22, 2016 at 10:22 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > thanks Bruce - I had found that option for my fsaverage maps and it worked. >

[Freesurfer] Hippocampal Subfields Segmentation

Hello FreeSurfer Developers, I’m having issues with the hippocampal subfields segmentation using OS X Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: