[Freesurfer] New way of installing and running Freesurfer - containers

Dear all, I have created a Docker image with Freesurfer distribution (and all required dependencies). Features: - Only requires Docker to run (works on Linux, Mac and Windows - does not suffer from the VirtualBox bug

Re: [Freesurfer] New way of installing and running Freesurfer - containers

with the FreeSurfer license? I > know that the FreeSurfer team depends on licenses to keep track of the > number of users (a key component to justifying their work when > applying for grants). I'm looking forward to trying it out! > > Thanks, > Dan > > On Tue, Aug 9, 2016 at 12:

[Freesurfer] Support for surface data on NeuroVault.org

Dear FreeSurfer community, I am one of the developers of NeuroVault.org - an open repository for vizualizing, analyzing, and sharing of statistical and parcellation maps of the human brain. So far NeuroVault was limited only to volumetric data in the MNI space since this is the most common way of r

Re: [Freesurfer] Support for surface data on NeuroVault.org

about pysurfer? Generally inflated surfaces are easiest for viewing patterns, but it is > often helpful to include anatomical surfaces as well. > Thanks! Best, Chris > > Peace, > > Matt. > > From: on behalf of Chris Filo > Gorgolewski > Reply-To: Freesurfer support l

Re: [Freesurfer] Support for surface data on NeuroVault.org

Thank you for your comments. Some more questions below: On Mon, Aug 22, 2016 at 1:09 PM, Douglas N Greve wrote: > > > 1. In NeuroVault users are asked to upload their statistical maps in > > form of files. I'm planning to target outputs of mri_glmfit: > > preferably Z.mgh but also sig.mgh. Is thi

[Freesurfer] FTP server error

FYI - there is something wrong with the FTP server: $ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz --2016-09-15 20:04:51-- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-Linux-centos4_x86

[Freesurfer] reusing mri_surf2surf transformation

Hi, I need to convert a big number of scalar surface maps from fsaverage to one particular subject space. This means running mri_surf2surf command many times. For each execution the same transformation is calculated and then applied. Since estimating the transformation take a substantial amount of

Re: [Freesurfer] reusing mri_surf2surf transformation

e wrote: > You can use mri_concat to create a stack of overlays, then mri_surf2surf > the entire stack, then split the stack. > > > On 11/10/2016 12:28 AM, Chris Filo Gorgolewski wrote: > > Hi, > > I need to convert a big number of scalar surface maps from fsaverage

Re: [Freesurfer] reusing mri_surf2surf transformation

t; > > On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote: > > Thanks for a quick reply. I'm actually in a situation where I do not > > have all of the overlays at the same time so I cannot concatenate them. > > > > To put more contexts: I am building surface su

Re: [Freesurfer] reusing mri_surf2surf transformation

-0. -0. -0. 1. On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve wrote: > 16min is a very long time. How many frames are in rh.sig.mgh? For a > single frame it should only take 10 or 20 sec > > > On 11/10/2016 03:25 PM, Chris Filo Go

Re: [Freesurfer] reusing mri_surf2surf transformation

process? Best, Chris On Thu, Nov 10, 2016 at 12:37 PM, Chris Filo Gorgolewski < chris.gorgolew...@gmail.com> wrote: > There is only one frame in rh.sig.mgh file (see below). Most time seems to > be spent in calculating forward and reverse loops. Ideas? > > root@36ddc1c5be86:/code#

Re: [Freesurfer] integrating FSL and Freesurfer

Hi, I have run into the same problem. I have managed to partially diagnose it, got some workarounds, but no real solutions. I would greatly appreciate FreeSurfer team for some feedback. So it's all about orientations. FreeSurfer internally uses LPI and FSL (Especially FSLView) uses RAS. Try conver

Re: [Freesurfer] FreeSurfer Version 6

Congratulations! I just updated the FreeSurfer BIDS App to version 6.0.0: https://github.com/BIDS-Apps/freesurfer It's already on Docker Hub. All you need to do to grab it is to run: docker run -ti --rm bids/freesurfer:v6.0.0-1 Best, Chris On Mon, Jan 23, 20

[Freesurfer] [BUG] mri_convert help inconsistency

A tiny typo in mri_convert: filo@filo-Precision-M6500:~$ mri_convert | grep voxsize -vs, --voxsize: specify the size (mm) - useful for upsampling or downsampling filo@filo-Precision-M6500:~$ mri_convert --voxsize mri_convert --voxsize mri_convert: unknown flag "--voxsize" type mri_convert -

Re: [Freesurfer] [BUG] mri_convert help inconsistency

Did you go for backwards compatibility or between flags consistency? On 18 August 2011 20:17, Bruce Fischl wrote: > fixed, thanks > On Thu, 18 Aug 2011, Chris Filo Gorgolewski wrote: > >> A tiny typo in mri_convert: >> >> filo@filo-Precision-M6500:~$ mri_convert | gre

[Freesurfer] Nipype connectivity workshop 2012

Dear fellow neuroimagers, I am very excited to announce the second Nipype workshop which will take place on 8-9 September 2012 in Magdeburg, Germany. For those who have not heard about Nipype it is a framework which helps designing, maintaining, sharing and executing data processing workflows. It

[Freesurfer] mris_volsmooth without registration

Hi, my functional runs are already coregistered and resliced to mri/orig.mgz (I use ROI from aseg+aparc and I want to avoid downsampling) so in theory I do not need to use bbregister to prepare registration file for mris_volsmooth. However, --reg argument in mris_volsmooth is mandatory. So far I wa

[Freesurfer] Performance on brains with tumors

Hi, how does freesurfer perform on brains with tumor? Are the any specyfic options that could improve the results (like masking for example)? Cheers, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] FDR correction in FS vs. SPM

Hi Jürgen, 2010/5/27 Jürgen Hänggi : > For SPM, it has been shown that the FDR procedure based on height threshold > (FDRp) is not appropriate in the random Gaussian field theory framework > (Chumbley et al., 2010; Chumbley and Friston, 2009, both published in > NeuroImage). Sorry could you elabor

[Freesurfer] NiPyPe: Neuroimaging in Python Pipelines and Interfaces

Dear members of the neuroimaging community, We are pleased to announce release 0.3.2 of NiPyPe [nai-pipe]: Neuroimaging in Python Pipelines and Interfaces (http://nipy.org/nipype). Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides

[Freesurfer] Nipype 0.3.4 release

Dear all, I'm very happy to announce new release of nipype - the pipelining framework that allows you to combine FSL, SPM, FreeSurfer, Nipy and other neuroimaging packages. Among other changes (see the full list below) this release brings support for surface transformations, flash processing and fl

[Freesurfer] Neuroimaging Data Processing Workshop 23-24 March 2011, Edinburgh, UK

Dear all, I am delighted to invite you to a Neuroimaging Data Processing Workshop which will be held on 23-24th of March 2011 at University of Edinburgh, UK. During the workshop we will cover neuroimaging data analysis and management with reusable, scalable and reproducible processing workflows th

Re: [Freesurfer] Neuroimaging Data Processing Workshop 23-24 March 2011, Edinburgh, UK

Registration is now open. https://www.epay.ed.ac.uk/browse/extra_info.asp?compid=1&catid=42&modid=2&prodid=453&deptid=24&prodvarid=0 Best regards, Chris Gorgolewski On 18 February 2011 17:58, Chris Filo Gorgolewski wrote: > Dear all, > > I am delighted to invi

[Freesurfer] Nipype 0.4 release

Dear all, I am delighted to announce release of Nipype version 0.4. Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a