[Freesurfer] Cannot save edited label

Dear FS experts I used mri_annotation2label to extract the superior frontal gyrus label from the aparc annotation. I edited (cut plane) this label in tksurfer and then tried to save it using Save Selected Label. However, the whole label is saved including also the part that I have cut away. Any i

Re: [Freesurfer] Cannot save edited label

Hi Jürgen it wounds like you edited the surface, but did you edit the label? Did you remove part of it in the fill dialog box? You might be better off just creating a new one using the same procedure, then using custom fill cheers Bruce On Thu, 25 Oct 2012, Jürgen Hänggi wrote: Dear FS expe

[Freesurfer] make_face_parcellation ambiguous color table

Dear Freesurfers, I have performed make_face_parcellation on fsaverage (with ic5) (Darwin-leopard-i686-stable-pub-v5.1.0). I read_annotation ed the parcellation into matlab an noticed that while colortable.table has 10242 rows (as expected), length(unique(colortable.table(:,5))) produce

Re: [Freesurfer] residual after mri_glmfit

Hi Minjie, if you run mri_glmfit with --help, you will see: --eres-save : save residual error (eres) This will create a file called eres.mgh with the residuals for each voxel. doug On 10/25/2012 01:05 AM, Minjie Wu wrote: > Dear FreeSurfers, > > I have a question regarding mri_glmfit: Is it pos

Re: [Freesurfer] make_face_parcellation ambiguous color table

Hi Franz, this was noted and addressed a few weeks ago. You can download a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux doug On 10/25/2012 10:33 AM, Franz Liem wrote: > Dear Freesurfers, > > I have performed make_face_parcellati

Re: [Freesurfer] znzTAGskip error using mri_em_register

Hi Bruce, Thanks for the tip on bert, I tried running the compiled version of mri_em_register on fsaverage and it seems to run without giving the error. I've been scavenging through the fswiki to find the latest version of bert but to no success.. could you maybe help me find the url to it? Tha

Re: [Freesurfer] Files

And the input is already TimePoint2-TimePoint1? If so, then you will need two more contrasts: [1 0 0 ] and [0 1 0 ]. The first tells you if controls are thinning (blue) or thickening (red), the 2nd tells you if the training is doing the same. doug On 10/25/2012 03:34 PM, Ryan wrote: > D

[Freesurfer] Surface-based normalization, smoothing and averaging

Dear Freesurfer experts, I would like to have your help. I have a volume data of a certain parameter on white/grey matter boundary (X.nii). What I want to do are as follows: Step 1: I want to register it onto a standard space using surface-based alignment and smooth it. Step 2: I want to generat

[Freesurfer] recon-all crash

Hello experts, Wonder if you could help me with the following error after running "recon-all -all -subjid BT6403 -qcache": -- unfolding failed - restoring original position 0581: dt=0.112000, rms=0.602 (0.000%), neg=0, invalid=766 writing output transformation to tran

Re: [Freesurfer] Cannot save edited label

Hi Bruce Thanks for the advise. It works with the fill dialog box Cheers Jürgen On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: > Hi Jürgen > > it wounds like you edited the surface, but did you edit the label? Did > you remove part of it in the fill dialog box? You might be better off > just cr