[Freesurfer] Simple_Surface_labels2005.txt

I'd like to identify the voxel locations of each vertex within each aparc label. I found the command "mri_annotation2label" and thought it might do the trick. However, I noticed that the examples http://surfer.nmr.mgh.harvard.edu/fswiki/mri_5fannotation2label?action=h ighlight&value=mri_annotation2

Re: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm]

Nevermind, it works fine now with after i added "--sign < >" flag to the mri_volcluster ..command. thanks pratap Original Message Subject: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm From:[EMAIL

[Freesurfer] anatomical weirdness?

Greetings, Is the subcollosal gyrus included in the ACC label from the cortical parcellation of Fischl, 2004? We are using the ACC label to constrain Monte Carlo simulations to the ACC. A max vertex for an ACC cluster has the annotation G_subcollosal, but is listed in the ROI-constrained

Re: [Freesurfer] legacy data and FDR

You can get brain.mgz by converting the COR files in /space/ventzl/1/users/SUBJECTS_DIR/mano001/mri/brain to mgz using mri_convert --in_type cor --out_type mgz Robert Levy wrote: Hi Doug, I just got around to looking at this problem again and trying what you had suggested (link brain.mgz to

Re: [Freesurfer] Some methodological questions

1. As long as your groups are balanced you are probably ok, although ideally you would scan the same subject on both scanners to assess the differences. 2. Not easily, although we have some tools for doing this. They aren't packaged and distributed though. 3. Yes, this probably makes a diffe

[Freesurfer] Some methodological questions

I have some methodological doubts and I think somebody can give a hint. 1) I have read the paper from Neuroimage 2006 comparing Scanner, Field Strength, etc in thickness measurements. Is it possible to assume that we can mix in our study group images that come from different MRI Scanners?

Re: [Freesurfer] legacy data and FDR

Hi Doug, I just got around to looking at this problem again and trying what you had suggested (link brain.mgz to brainmask.mgz), and the problem is, there is no brain.mgz either. I would expect to see it in $SUBJECTS_DIR/$subject/mri/brain.mgz, but instead what I see, both in individual subj

Re: [Freesurfer] convert mnc->analyze->mgz

p.s. and how did you create the .mnc in the first place? The safest thing by far is to go right from the dicoms. Does the .mnc show up properly in tkmedit and/or scuba? On Fri, 28 Sep 2007, Doug Greve wrote: How do they look in tkmedit? How do you know the problem is not in neurolens? What do

Re: [Freesurfer] convert mnc->analyze->mgz

It does not require neurological/radiological. It only requres that the geometry in the input file be accurate. Is it? You can test it by viewing it in tkmedit. doug Olivier Coulon wrote: Doug Greve a écrit : How do you know it is left-right swapped? What tool are you using to visualize it

Re: [Freesurfer] convert mnc->analyze->mgz

Doug Greve a écrit : How do you know it is left-right swapped? What tool are you using to visualize it? Do you have a fiducial? Hello, the surface reconstruction (visualised with scuba) gave a left hemisphere that should be the right one (I am using icbm data that have also been processed by o