[Freesurfer] equivalent for fslmaths -mas option in freesurfer

I have a question about the equivalent of fslmaths -mas option in freesurfer. I have several manually defined labels in .label form that I want to use to extract specific regions of functional data from a flat patch. Ordinarily in fsl I would just use fslmaths -invol {functional_data} -mas {bin

Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

valent for fslmaths -mas option in freesurfer Hi Sarah have you used mri_vol2surf to sample the data onto the surface? When you say "extract specific regions of functional data from a flat " do you want to average within the ROI? cheers Bruce On Thu, 26 Feb 2015, Sarah Finnegan wrote: >

Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

urfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sarah Finnegan [sarah.finne...@stcatz.ox.ac.uk] Sent: 26 February 2015 15:12 To: Freesurfer support list Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer Hi Bruce Thanks for your re

Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

occipital cortex with a V2 mask to only see activation within V2 on the inflated surface. I have a V2.label file and a V2_colour_lh.mgz file overlaid onto an inflated surface using mri_vol2surf. thanks S From: Sarah Finnegan Sent: 03 March 2015 14:41

Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 03 March 2015 16:00 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer On 03/03/2015 10:43 AM, Sarah Finnegan wrote: > The command I used to visualise the label converted to volume f

[Freesurfer] Taking a measure of cluster width and length on flat surface

Dear all, I am looking to take two measures within the visual cortex. 1) A measure of width and length for each activation cluster overlaid onto the flattened cortical surface. 2) A measure of spacing between each cluster I can find how to take measures of area but I specifically want to know th

Re: [Freesurfer] Taking a measure of cluster width and length on flat surface

think? Thanks again! Sarah From: Sarah Finnegan Sent: 11 May 2015 17:13 To: Freesurfer support list ‎[freesurfer@nmr.mgh.harvard.edu]‎ Subject: Taking a measure of cluster width and length on flat surface Dear all, I am looking to take two measures within the visual

Re: [Freesurfer] Taking a measure of cluster width and length on flat surface

as MATLAB starts there rather than 0 and attempt to visualise the patch using >> p=patch('faces',faces(:,[1 3 >> 2]),'vertices',vertices,'facecolor','flat','edgecolor','none','facealpha',1); Error using patch Verti

Re: [Freesurfer] mris_pmake update

Hi, Is it also possible to get an updated version for the mris_pmake binary? This is freesurfer-i386-apple-darwin11.4.2-stable5-20130514 version. Thanks! Sarah ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/

[Freesurfer] Recon reprocessing control points error

be located. Can anyone offer any advice on what might be going on? The same error is also being experienced by a colleague here. Thanks a lot! Sarah Finnegan Nuffield Department of Clinical Neurosciences University of Oxford, John Radcliffe Hospital Oxford, OX3 9DU Email: sarah.finne

[Freesurfer] Recon reprocessing control points error

Hi Bruce, Thanks for your email. I have uploaded the two examples. The first subj001_fs.zip has the control points added but has not been rerun yet. The second subj001_fs_cp.zip has been rerun and the segmentation looks incorrect. Thanks for your input! Sarah