Re: [Freesurfer] Problem with recon-all

I got a skullstrippen mask from another pipeline to remove the noise in the MP2RAGE. Is it possible to give that to the recon-all? it is either a mnc or nii thanks, mads On 5 October 2015 at 23:11, Andre van der Kouwe wrote: > I think the standard MP2RAGE only

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

Hi Yun, if it is for some reason impractical to use a beta version of FreeSurfer you can also try to follow the HiResRecon (http://freesurfer.net/fswiki/HiResRecon) I put together some time ago. This solves the issues related to high resolution data and will circumvent conformation to 1 mm^3.

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, The

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

Hi Kevin, yes, FS 6.0 will make my workaround redundant. Changes have been done to mri_normalize, mri_em_register and mri_watershed enabling high resolution processing without constraints. However, as 7T data is always a bit tricky to process it does not run as smoothly as the standard

[Freesurfer] Error: cannot determine file type

Hi all, Am receiving the below error, I haven't used this scan before but have never had issues with .dcm. Sorry I'm not sure what sort of scanner they are from. Any help would be appreciated. Cheers, Will /usr/local/freesurfer/subjects/YU mri_convert

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

Hi Matthieu The easiest for you is to follow these steps: 1-Read your label eg.: lhcortex = fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');  2-Read the data file eg.: [lhY, lhmri] = fs_read_Y('lh.thickness.mgh'); 3-Fit a vertex-wise lme model with random effects for the

[Freesurfer] -hippocampal-subfields-T1T2

Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points

[Freesurfer] error with .lta files in longitudinal

Hi, I’ve not idea why a few of my longitudinal runs have started to fail. It’s saying there’s a problem with the .lta files, >From “bugr” script FREESURFER_HOME: /opt/fmrib/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.7 (Final)

Re: [Freesurfer] error with .lta files in longitudinal

I’m really sorry, I’ve just realised there is an error in the naming structure in /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ That is probably the cause – not sure why that happened will sort it out and try again – sorry! From: Justin McKee