Re: [Freesurfer] How to tackle large segmentation errors

Hi Richard You can't put control points in the lesions or it will make everything too bright. The wm edits. Old work. Ideally they won't have to be perfectly accurate - just start the orig surface close enough so that the white surface ends up in the right place Cheers Bruce On Jun 26, 2012,

[Freesurfer] Problem with mri_glmfit ill-conditioned matrix

Dear Freesurfer, We have a recurrent problem with an ill-conditioned matrix. Could someone shed some light on our problem. Here is the command line: mri_glmfit --y lh.ELS-CON.thickness.10.mgh --fsgd CAT-SP_June26.FSGF dods --C ELSvsCON_COV-Gen-Age-ICV.mtx --surf fsaverage lh --cortex --glmdi

Re: [Freesurfer] pars triangular and BA44 segmentation bug?

We have data from 200 college students using Freesurfer 4.5 Mac 10.6.8. We looked at both surface area and volume asymmetries. For surface area for Triangularis, there is a small leftward asymmetry averaged over the whole sample. 113 participants have leftward asymmetry and 85 have rightward as

Re: [Freesurfer] trac-all: error during trac-paths due to tract missing

Hi Torben - I just scrolled to the end of your log file. The last invocation of trac-all -prep is the one that failed b/c of the bvecs error. Did you rerun trac-all -prep after you fixed the bvecs? Thanks, a.y On Tue, 26 Jun 2012, Torben Prokscha wrote: > Hi Priti, > > thank you for your repl

Re: [Freesurfer] trac-all: error during trac-paths due to tract missing

Hi Priti, thank you for your reply, but I'm afraid you didn't scroll to the end of the log file: Yes, we had that bvecs/bvals error in the first run, but we corrected it and got the error I reported in my previous mail (it is also printed at the end of the log file): ERROR: Could not open /Users/

[Freesurfer] skull strip (ss) and pial/wm/orig surf

hi FS users; have two questions which i am having issue across ss and pial/wm/orig surf boundaries 1- it has happened that sometimes the sagittal view of individual was flipped from left to right. but the pial/wm boundaries look good. was wondering why this happened only for countable ppl? i t

Re: [Freesurfer] qdec_glmfit problem

You have to make it manually. See the tutorial for an example. doug On 06/26/2012 01:01 PM, Nicolai Grüner-Hegge wrote: > Hi Doug, > > Thank you for the link. I was able to get up to pre-smoothing my > fsaverage surfaces but do not know how to continue to the > qdec.table.dat section. Is this a

Re: [Freesurfer] mri_vol2surf and Spherical Surfaces

Hi Luis, yes there is a more efficient way. Specify the native res functional as the --mov argument and specify the registration that you used to create the hires_functional as the --reg argument (instead of --regheader). While you can use a .w file, I would recommend instead a .mgh file (we're

[Freesurfer] mri_segstats: reported volume depends on voxels size

Hello all, I found volume size reported by mri_segstats is changed very much depending on voxel size when partial volume correction (--pv option) is used. The difference was much larger than that can be explained by the difference of image resolution. (mri_segstats version is 1.75.22 2011/4/27 in

Re: [Freesurfer] is it a bug of freeview? or wrong segmentation?

Can you try re-run that freeview command again? I remember I saw similar problem once, but somehow I could not reproduce it when I re-run the same command. If you can positively reproduce it, would it be possible to send us all the files that are used in the command? Best, Ruopeng On 6/26/12