[Freesurfer] Recon-all -qcache curvature error & recon-all make -all

Hello, I have run several scans using recon-all -all -subjid subject_no -expert expert.opts where my expert.opts file changes the parameters for the mri_normalize step (this works well in my scans). I then had to edit a few of the scans by adding in more white matter and a few control points.

[Freesurfer] CSF segmentation and cortical ribbon

Dear Freesurfer users, I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels. Nevertheless, the segmentation obtained in

Re: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all

Hi Clare can you send us the screen output and also what version you are running? thanks Bruce On Wed, 25 Jul 2012, Gibbard, Clare wrote: Hello, I have run several scans using recon-all -all -subjid subject_no -expert expert.opts where my expert.opts file changes the parameters for the mri_

Re: [Freesurfer] CSF segmentation and cortical ribbon

Hi Chris that's tough to do with only a T1 image as CSF and bone look the same. We don't have any ready-made tools for doing what you want, but you could probably get close with some rules. Sounds like the voxels you are referring to are CSF or dura given their proximity to brain cheers Bruce

Re: [Freesurfer] CSF segmentation and cortical ribbon

Hi Bruce, Absolutely, the voxels I'm referring to are defined regarding their distance to the cortical ribbon (let's say within 5 mm) rather than by belonging to a specific tissue type. Using a distance criteria from the ribbon surface and collect only voxels within a certain distance (going o

Re: [Freesurfer] CSF segmentation and cortical ribbon

Hi Chris, sure, we can compute distance-to-surface transforms and such, but I don't think we have any pre-packaged binaries that will do what you want, just a set of C functions Bruce On Wed, 25 Jul 2012, Christopher Coello wrote: > Hi Bruce, > > Absolutely, the voxels I'm referring to are de

[Freesurfer] Surface number of vertices mismatch

Dear List, I am trying to show my results on Caret's F99 atlas, in Caret. For this I already managed to take my anatomical (white, pial etc) surfaces and register them to F99 in Caret, which works fine. I am trying now to get my functional p-map (initially a nifti volume) into Caret too to overlay

Re: [Freesurfer] Surface number of vertices mismatch

Hi Pablo how did you run mri_vol2surf? Note that this isn' really a surface per-se, but rather a scalar overlay on the surface. mri_vol2surf samples the functional volume onto the surface so that you have 1 number per vertex (the functional value at that point in space). We'll need all your com

Re: [Freesurfer] Freesurfer Question

Hi Doug, Sorry for all the confusion, I misunderstood what we were looking for. Right now what we want is the volume measurement in each of the subcortical regions for each subject, which you suggested with the asegstats2table command. Thanks so much for your help! Alex > > Hi Alex, what do you

Re: [Freesurfer] Surface number of vertices mismatch

Hi, Here is the mri_vol2surf I run: mri_vol2surf --src /space/data/ppolosecki/cooked/2011/110520GIZMO/bold/a2u/c13_2456/sig.nii --src_type nii --srcreg /space/data/ppolosecki/cooked/2011/110520GIZMO/t1epi/110520GIZMO_2_120509GIZMO.register.dat --projfrac 0.5 --trgsubject 120509GIZMO --surf white

Re: [Freesurfer] Surface number of vertices mismatch

Can you load the output of step 1 into tksurfer? doug On 07/25/2012 11:01 AM, Pablo Polosecki wrote: > Hi, > > Here is the mri_vol2surf I run: > > mri_vol2surf --src > /space/data/ppolosecki/cooked/2011/110520GIZMO/bold/a2u/c13_2456/sig.nii > --src_type nii --srcreg > /space/data/ppolosecki/cooked

[Freesurfer] recon-all error

Hi, We're getting the following error from recon-all: command line: pbsubmit -m etanski -c 'recon-all -s DODASD012 -all -i /cluster/archive/300/siemens/TrioTim-35006-20120718-151622-227000/391000-15-01.dcm -mail etan...@nmr.mgh.harvard.edu' output: ... ... mri_binarize --i ./tmp.

Re: [Freesurfer] Surface number of vertices mismatch

Yes, it loads just fine. On Wed, Jul 25, 2012 at 1:55 PM, Douglas N Greve wrote: > Can you load the output of step 1 into tksurfer? > doug > > On 07/25/2012 11:01 AM, Pablo Polosecki wrote: >> Hi, >> >> Here is the mri_vol2surf I run: >> >> mri_vol2surf --src >> /space/data/ppolosecki/cooked/2011

[Freesurfer] MRIread on matlab

Hi all, I am a beginner to FreeSurfer, and have been experimenting with the MRIread function on MATLAB. I am able to load .nii files using MRIread, but is there a way to display a particular slice from a nifti file on MATLAB using MRIread and its related functions? Thanks in advance, Kevin __

Re: [Freesurfer] MRIread on matlab

sure: mri = MRIread('vol.nii'); imagesc(squeeze(mri.vol(128,:,:))) would show the 128th axial slice. cheers Bruce On Wed, 25 Jul 2012, Kevin Chen wrote: > Hi all, > > I am a beginner to FreeSurfer, and have been experimenting with the > MRIread function on MATLAB. I am able to load .nii files

[Freesurfer] Converting labels to individual volumetric masks

Dear All, I want  to use cingulate bundle as ROIs more exactly mask  for fiber tracking. Can I use different aseg than the one from Freesurfer for examples can I use segmentation from JHU-WhiteMatter-labels-1mm.nii.gz and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingula

Re: [Freesurfer] Surface number of vertices mismatch

In case it helps anyone in the future, I solved the problem by setting mri_surf2vol to the "paint" output format. This stores a .w surface file that you can later convert to Caret format using caret_command -file-convert -fsf2c Thanks! Pablo On Wed, Jul 25, 2012 at 2:03 PM, Pablo Polosecki wrot

[Freesurfer] non-stationarity in CTh maps

Dear all, I have been performing cortical thickness analyses and as far as I understand the thickness maps are non-stationary (please correct me if I'm wrong). I have two questions: 1. How susceptible is Monte Carlo clusterwise correction to this (should I expect clusters at smoother areas to be b

[Freesurfer] tcsh: tailarach_avi: Command not found

Hi Freesurfer experts, I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all. Advice on how to troubleshoot this would be appreciate. Thanks, Fidel a3128u:/Applications FVila$ export

Re: [Freesurfer] Surface number of vertices mismatch

were there multiple frames ("time points") in the sig.nii file? The .w format will save only one frame. You can check with mri_info --nframes sig.nii On 7/25/12 6:03 PM, Pablo Polosecki wrote: > In case it helps anyone in the future, I solved the problem by setting > mri_surf2vol to the "paint

Re: [Freesurfer] non-stationarity in CTh maps

Hi Hugo, they are assumed to be stationary. I've never tried to figure out how much of a problem this is. doug On 7/25/12 6:03 PM, Hugo Baggio wrote: Dear all, I have been performing cortical thickness analyses and as far as I understand the thickness maps are non-stationary (please correct m

Re: [Freesurfer] tcsh: tailarach_avi: Command not found

did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug On 7/25/12 7:57 PM, Fidel Vila wrote: Hi Freesurfer experts, I recently installed FS (PowerPC architecture version available on FS website) on a Mac O

Re: [Freesurfer] recon-all error

It looks like you are using the dev environment? I fixed this problem a couple of days ago, but it must not have propagated into dev. Why are you using dev? doug On 7/25/12 2:02 PM, Yigal Agam wrote: > Hi, > > We're getting the following error from recon-all: > > command line: > > pbsubmit -m

Re: [Freesurfer] WM/Pial surfs Problem with SPGRs from 3T GE

Hi Thomas, The following message posted by Michael Harms http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20991.html has some very useful options. I recently noticed that they help us with a very similar problem... Also, I recall that for FS v5.0 there was a flag -nuintensitycor-3T f