[Freesurfer] Problem with fsgd file

Dear mailing list, I am trying to run a longitudinal 2 stage model using mri_glmfit. Here is the command I am using: mri_glmfit --fsgd long-2stage_ConAR.fsgd --glmdir long-2stage_ConAR.area.lh.spc.glmdir --y long-ConAR.lh.area-spc.stack.fwhm10.mgh dods --C me_age-all.mtx --C me_gender.mtx -

Re: [Freesurfer] Problem with recon-all

Hi Mads yes, you should be able to use mri_convert to change it to .mgz format and name it brainmask.mgz, after which I think it will look as if you've manually edited it and it will be applied cheers Bruce On Mon, 12 Oct 2015, Mads Jensen wrote: > I got a skullstrippen mask from another pipe

Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache

Hi Bhavani, when I run mris_label_calc intersect MPS-007_2mod.long.MPS-007\ rh.cortex.label MPS-\ 007\ lh.cortex.label out.label it goes through and writes the out.label file. I used fs 5.3 for that. Can you please send me the command and input files that fail for you? About your other ques

[Freesurfer] FSL GUI error message

Hello When I ran FSL GUI on the Martinos center after typing source freesurfer, I received an error message like that custom widget with id loop-button does not return a valid node on the X-window terminal. How can I solve this problem? Thanks Jung Mi I used FSL 5.0.7, FEAT tool v 6.00 for

Re: [Freesurfer] error in atlas creation

Hi Anthony feel free to email me the .gca and I'll take a look cheers Bruce On Tue, 13 Oct 2015, Anthony Dick wrote: Hello Bruce, I used the rebuild_gca_atlas.csh script (attached). I only commented out the cluster configuration options. Otherwise the script is unchanged. The process fails

Re: [Freesurfer] error in atlas creation

Hello Bruce, I used the rebuild_gca_atlas.csh script (attached). I only commented out the cluster configuration options. Otherwise the script is unchanged. The process fails in the same place when we use one subject. Thanks! Anthony On 10/13/15 12:07 PM, Bruce Fischl wrote: and how did you

Re: [Freesurfer] error in atlas creation

and how did you create the gca? On Tue, 13 Oct 2015, Anthony Dick wrote: Hello Bruce, I will try a single subject. When I run the following command line (i.e., right out of recon-all) it works: mri_em_register -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2014-08-21.gca tra

Re: [Freesurfer] error in atlas creation

Hello Bruce, I will try a single subject. When I run the following command line (i.e., right out of recon-all) it works: mri_em_register -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2014-08-21.gca transforms/ta

Re: [Freesurfer] error in atlas creation

HI Anthony what is the full command line? Does it happen if you only train on a single subject instead of 23? Bruce On Tue, 13 Oct 2015, Anthony Dick wrote: > Hello Bruce, > > We have tried running the atlas creation on newly freesurfed brains with > the latest FS version and keep getting the sa

Re: [Freesurfer] error in atlas creation

Hello Bruce, We have tried running the atlas creation on newly freesurfed brains with the latest FS version and keep getting the same error. We have essentially replicated the error we get on our own manually edited volumes by copying the aparc+aseg.mgz and renaming it seg_edited.mgz. Thus, it

Re: [Freesurfer] list of normals to triangle vertices

Thank you very much. Best regards,   Don > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, October 13, 2015 10:51 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] l

Re: [Freesurfer] list of normals to triangle vertices

Hi Don 1. I think so, yes. 2. Yes. 3. The convention is that they point outwards from wm->ctx 4. Yes. On Tue, 13 Oct 2015, Krieger, Donald N. wrote: Thanks very much, Bruce. That saves me a ton of effort. Let me confirm a few key details. The command with -n kicks out a file with 2 header lin

[Freesurfer] pial surface encircling the optical chiasm

Dear FreeSurfer experts, during inspection of reconstructions of our data, I found that in many cases the pial (and sometimes also white) surface is extending out of the brain and encircling the optical chiasm. Does this situation has any effect to the results (i.e. cortex parcellation, whole-b

Re: [Freesurfer] DEPRECATED warning in Freesurfers

Hello, The message being output to the screen regarding "?PATTERN?" is just a warning message and is not directly related to the error you are experiencing. The problem is that when using a virtual machine, the MNI software will crash when subjects directory is on a shared folder between the h

[Freesurfer] No preprocessing on FAST

Hi list, I'd like to perform FAST preprocessing for functional connectivity (seed-based analysis).Data have been already preprocessed by AFNI.Therefore, no smoothing, motion and slice timing corrections are requested. When I run:preproc-sess -sf sessid -nomc -fwhm 0 -surface fsaverage lhrh -mni

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

Hi Matthieu, 1. I think it is OK, maybe Jorge can comment, if not. 2. Not really. You could do a linear fit within each subject separately (at each location) and then do a Wilcoxon Ranksum (or a Signed Rank ) Test. The non-parametric testing will help with potential outliers, the problem still

Re: [Freesurfer] DEPRECATED warning in Freesurfers

Hi everybody. I have the same problem. When I run the "recon-all -all", the first steps warns me about a "deprecated" command when running the "nu_correct" step: nu_correct -clobber ./tmp.mri_nu_correct.mni.13923/nu0.mnc ./tmp.mri_nu_correct.mni.13923/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1392

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

Hello Martin, Many thanks for your answer ! Indeed, I didn't add age and gender as covariates according the fact of my small number of patients group. Moreover, I couldn't put the slope as a random effect because of no convergence problem... Concerning the convergence, at the end of the estimati

Re: [Freesurfer] list of normals to triangle vertices

Thanks very much, Bruce. That saves me a ton of effort. Let me confirm a few key details. The command with -n kicks out a file with 2 header lines, a list of normals, and a list of triangles for which each is defined by its 3 vertex numbers. I see the format for a "Triangle Surface File - ASCII v

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

Hi Matthieu, 1. The spatiotemporal approach is designed for surfaces, not for voxel images, so regular mass univariate (vw). 2. Yes, that can be done with LME. 1 group is a simple design: column of 1, colum of time_from_baseline, other covariates such as age (I would not include too many as yo

Re: [Freesurfer] list of normals to triangle vertices

Hi Don mris_convert -n lh.white lh.white.normals.asc should do the trick. And this is the way that the area is computed (from mrisurf.c): static float mrisTriangleArea(MRIS *mris, int fac, int n) { int n0,n1; face_type *f; float v0[3],v1[3],d1,d2,d3; n0 = (n == 0) ?

[Freesurfer] list of normals to triangle vertices

Hi everyone, I need to create the vector normal to the surface at each "white" vertex. I would like to end up with 7 fields in each entry: 1 Vertex number 2-4 RAS coordinates 5-7 RAS components of the normal vector pointed from ctx --> wm mri_annotation2label gets me the first 4. I just