[Freesurfer] Problem in loading .mgz into MATLAB

Hi I have been trying to load .mgz file that is generated after the recon -all process into MATLAB using load_mgh.m but have been unable to do so. ERROR - ' 'zcat' is not recognized as an internal or external command, operable program or batch file. SWITCH expression must be a scalar or string c

Re: [Freesurfer] Cortical Segmentation

​ SE8RECON.tar.gz ​​ SE19RECON.tar.gz ​​ SE20RECON.tar.gz

Re: [Freesurfer] Problem in loading .mgz into MATLAB

Hi Raunak you should be able to use gunzip to unzip it outside of matlab and give it the extension .mgh instead of .mgz, then everything should work fine. I'm not sure why zcat isn't working but this should be a reasonable work-around cheers Bruce On Tue, 16 Dec 2014, Raunak Mundada wrote: >

Re: [Freesurfer] Cortical Segmentation

are they really .46 x .46 x .4? That is very high resolution, and typically will be quite noisy unless you average a lot. My guess is that's why the inflated looks spikey - the underlying data is quite noisy. To get good surfaces that kind of resoution is not needed, and is usually counterprodu

[Freesurfer] Tracula Question

?Hello, I was wondering what the difference was between the dwi.nii.gz and thd data.nii.gz files. I know based on the website description that the dwi.nii.gz file is the DWI after all corrections have been made but I was unsure about the data.nii.gz file. I am

Re: [Freesurfer] TRACULA dwi flipping

Thank you Anastasia. Best wishes, Barbara On 21/11/2014 21:45, Anastasia Yendiki wrote: > 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: > >

Re: [Freesurfer] study specific template or fsaverage and LME analysis?

Thanks! On Mon, Dec 15, 2014 at 11:55 AM, Douglas N Greve wrote: > > It is not possible to know whether this is a good idea or not. If you > want to do it, here are the instructions > doug > > # Create an average subject (Creates $SUBJECTS_DIR/newtemplate) > make_average_subject --out newtemplate

Re: [Freesurfer] longitudinal statistics LGI

Jorge, We are interested in examining the impact of cannabis exposure (time-varying continuous variable) on local gyrification index over 3 time points (baseline, 18 month, 36 month)- so this is a time-varying random effect. I apologize in advance if these are student questions… we are novice

Re: [Freesurfer] retinotopy in subject volumetric space

Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these

Re: [Freesurfer] Fwd: Errors in recon-all

Hi Bruce, I can view the file using "*freeview -v file.mnc*" but I think that won't solve my problem as I need to switch from 2D to 3D and vice versa. I will be thankful if you could be a bit specific about "preserving the direction cosine information" as I am facing difficulty to process these vo