Re: [Freesurfer] Processing 7T data

Hi Damien, I have tested using the HighResRecon vs Freesurfer beta on 0.7 mm^3 data and have preferred the segmentations on the beta version. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School

Re: [Freesurfer] question white matter

I believe they are mean and Gaussian curvature respectively. Cheers, Kevin Aquino > On 13 Dec 2016, at 17:23, tom parker wrote: > > Dear Freesurfers, > > Could anyone tell me what the white.H and white.K measures in Qdec are? > &

[Freesurfer] Re-running recon-all in V6 {Disarmed}

to keep all the corrections. Cheers! *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu

[Freesurfer] mris_surf2vol

don't need. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Imaging Center, School of Physics & astronomy, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney. *E* kevin.aqu...@nottingham.ac.uk, aqu...@

Re: [Freesurfer] mris_surf2vol

? Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W

Re: [Freesurfer] mris_surf2vol

Hi Doug, Thanks for the file, do you happen to have one that is compiled for a 64bit mac installation of freesurfer? Cheers! Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics

Re: [Freesurfer] mris_surf2vol

Hi Doug, sorry to be a bother, this doesn't work on my machine, running: file mri_surf2vol.mac64 gets me: mri_surf2vol.mac64: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.4.0, not stripped Cheers, *Dr Kevin Aquino* Res

Re: [Freesurfer] high resolution data using recon-all

Hi Falk, Just to jump on this as well – does FS 6.0 make HiResRecon redundant? – I've been using HiResRecon [working like a charm :) ] and wondering if FS 6.0 will cut the need for that workaround. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center

[Freesurfer] Freesurfer V6 (beta) and MacOS 10.11 (El Capitan)

Dear all, I was wondering if many users have had freesurfer 6 (beta) working (well) with Mac OS 10.11? (or Freesurfer V5.3) Thanks! *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics

[Freesurfer] Using freesurfer on a partial brain

? Not necessarily the parcellations and the full set-up, but other tools such as segmentation, creating a white and pial surface and topology fixes. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow

Re: [Freesurfer] FS 6.0 Freeview

I've had the same problem, the only solution I have is to only open Freeview from terminal Cheers, Kevo > On 23 Feb 2017, at 10:58 pm, peng wrote: > > Dear Ruopeng, > >I have the same problem even before the current version 6 release, and it > was "solved" by invoke freeview from the co

Re: [Freesurfer] Smooth overlay in command line {Disarmed}

You can use mri_surf2surf with the -nsmooth flag but just remember to set the target and source subject as the same subject, [check out the info in --help :) ] Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary

Re: [Freesurfer] Re. display SPM results on inflated surface? {Disarmed}

Hi Douglas, I am wondering, where did you find the mini 152 T1 map? :) Regarding this... Would it be better to instead run recon-all on a higher-res MNI atlas? and then run mri_vol2surf for that segmentation? Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic

[Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

ise corrections described with Eklund et al. (Cluster failure paper). Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* kevi

Re: [Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

s, or is there a mri_glmfit-sim version for data that has passed through selxavg3 ? Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydne

Re: [Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

ues on a single subject level? - since the permutation test won't be applicable. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* k

Re: [Freesurfer] mac mghread and freeview error {Disarmed}

Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W* https

Re: [Freesurfer] 7T recon {Disarmed}

Does adding control points help? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science

[Freesurfer] FS-FAST outputs is X.mat used? {Disarmed}

s, is there a way to parametrically modulate each run? e.g. to model behavioural changes per run etc. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of S

Re: [Freesurfer] FS-FAST outputs is X.mat used? {Disarmed}

s) There are slight differences between the two (so it doesn't matter in the long run) but I just want to know which one is being used. On a quick look of selxag3-sess, the matlab files look like compiled mex files, so I can't access them. Thanks! *Dr Kevin Aquino* Research fell

Re: [Freesurfer] FS-FAST outputs is X.mat used? {Disarmed}

Thanks for that Doug! Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W

[Freesurfer] Fixed effects fMRI {Disarmed}

lace but I can't seem to find it. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.u

Re: [Freesurfer] Tilting / orienting brain slices

Something quick: mricro http://www.cabi.gatech.edu/mricro/mricro/ Cheers, Kevo > On 23 Nov 2017, at 9:05 pm, Sam Norman-Haignere wrote: > > I would like to tilt/rotate a brain image so that I can see multiple > activations in a single slice. I don't believe this is possible in Freeview, >

[Freesurfer] Pial surface running into white surface

could find is that this could be fixed with FS v6). The build stamp is: freesurfer-Linux-centos6_x86_64-dev-20170915- what kind of edits should I be doing? I have added the necessary files to https://github.com/KevinAquino/errorPial if you could be so kind to have a look! Cheers, *Dr Kevin Aquino