[Freesurfer] full-time PhD position available -- DTI

The Laboratory of Functional Neuroscience at the Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, Seville (Spain) invites applications for one full-time PhD student position to investigate on cerebral white matter integrity markers of healthy and pathological agin

Re: [Freesurfer] (no subject)

you can load it in tkmedit from the file menu and probe it one voxel at a time, or you can use mri_convert atlas.gca#0 means.mgz and mri_convert atlas.gca#1 priors.mgz labels.mgz to look at the most likely label and it's mean cheers, Bruce On Thu, 29 Oct 2009, Guang Zeng wrote: > > Hi, the

Re: [Freesurfer] Temporal lobe part is missing

Hi Evert, one thing you can try if the patterns of loss are stereotyped is to take 10 or 20 subjects or so and correct them by adding control points, then use mri_compute_bias to compute the common component of the bias field. You can then apply that to the other subjects in your study with mri

Re: [Freesurfer] problem starting qdec

Hi Zonglei, The problem was related to the fact that I was accessing another computer remotely to run FreeSurfer, and I needed something to support the graphics. I assume you are also accessing a remote computer? I was using Exceed, which was working fine for tkmedit and tksurfer, but for s

[Freesurfer] mri_glmfit AR1 warning

Hello, I am noticing a warning message with mri_glmfit (no voxels in AR1 computation): Fit completed in 0.06015 minutes Computing spatial AR1 in volume. fMRIspatialAR1(): hit 0 voxels WARNING: no voxels in AR1 computation Residual: ar1mn = (nan,nan,nan) fwhm = (nan,nan,nan) nan Writing results

Re: [Freesurfer] Statistical output

I can't tell from your description what you did. Can you be more specific? Did you use DODS or DOSS? Did you demean the ages? doug mmoay...@uhnres.utoronto.ca wrote: > Hi everyone, > > I was hoping you can clarify something for me. > > I'm comparing two groups using CTA (in freesurfer). When I

Re: [Freesurfer] GLM question

Mehul Sampat wrote: > Hi FS folks, > > I have a basic GLM question. I went through the tutorials online but I > was not sure and wanted to check with someone. > > I am trying to compare the cortical thickness between a group of > patients (n = 166) and controls (n = 76). > > For patients mean a

Re: [Freesurfer] question about load_segstats

That program is for loading "seg stats", ie, anything created by mri_segstats, which creates aseg.stats. Unfortunately, it does not create ?h.parc.stats. We don't have a program to read that in. doug Mehul Sampat wrote: > Hi FS folks > > I was trying to use the load_segstats function to read as

Re: [Freesurfer] mri_glmfit AR1 warning

It looks like the input is a surface and not a volume, but mri_glmfit does not know this, so it interprets it as a volume, and so the neighbor relations need to compute the spatial AR1 are messed up. Try running it with --surf subject hemi, eg, --surf fsaverage lh doug muet0...@umn.edu wrote:

Re: [Freesurfer] Recon-all exited with ERRORS

Hi, I'm trying to run the command: recon-all -subjid -autorecon1. I'm getting the an error message during skull stripping and the error log reads as follows: #...@# Skull Stripping Wed Oct 28 12:29:47 PDT 2009 /space/raid7/data/london/data/ mri/other/angie/Freesurfer/SUBJECTS_DIR/5003/mri mri_

[Freesurfer] WM hypointensities in aseg vs wmparc

Hello all, I was curious as to whether it is preferable to use the wm hypointensities output from wmparc.stats or from aseg.stats or if there is no real difference. Also, I believe I've seen this answered elsewhere, but just to be clear, is it the case that there is currently no way to visuali

Re: [Freesurfer] WM hypointensities in aseg vs wmparc

Use the ones in aseg.stats. When you load aseg.mgz into tkmedit, the hypo intensities show up as segmentations. Dankner, Nathan (NIH/NIMH) [F] wrote: > Hello all, > > I was curious as to whether it is preferable to use the wm hypointensities > output from wmparc.stats or from aseg.stats or if th

Re: [Freesurfer] GLM question

Thanks Doug, I have two follow-up questions. 1. I am using QDEC and my discrete variables are: (a) TYPE (PATIENTS/CONTROLS) and (b) GENDER I include age as a continous co-variate and then select all of the variable before running the design. I believe QDEC is generating the various possible con

Re: [Freesurfer] effect of the radius on lGI

Hi, As explained in the paper, the radius of the sphere correspond to the region of interest in which you analyze gyrification: if you take 25mm, you will measure all the amount of cortical surface enclosed in a 25 mm radius from each of the cortical point (that is the default). You can

[Freesurfer] PostDoc Positions at UCSD MultiModal Imaging Laboratory (MMIL)

Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego The Multimodal Imaging Laboratory (MMIL) at the University of California, San Diego invites applications for multiple postdoctoral research scholar positions under the directi