Hi Doug,
Thanks! Now recon-all is processing well.
Regards,
Falk
-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 06, 2009 6:25 PM
To: Falk Lüsebrink
Cc: 'Nick Schmansky'; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Measuring cortic
hello
i'm running the LGI for all my subjects, and i have no problem with almost all,
but, i recibe an error message with one subject, and just with the right
hemisphere no problem when making Left hemisphere, does anybody knows what can
i do for correcting that error and to calculate the LGI?
Gabriel,
Have you tried to relaunch the lgi computation once? Sometimes it
crash the first time but when you launch it again it finishes properly.
If it still fails, the next thing to do is to check mris_euler_number
and visually check for any defects in the cortical surface. If there
is
Are you loading the one created by mri_glmfit (in the output
directory)?
doug
On Mon, 6 Apr 2009, Jeff Sadino wrote:
Thank you for the advice Sid. I added those lines, and now my errors
disappear, but I still get a blank screen where there should be a scatterplot.
Is this a graphics is
Hello list,
I would like to create a mask on fsaverage/surf/?h.pial that masks out
the areas where the surface does not follow the cortex, but is just
cutting across the mid line or across the brain stem. I know
Freesurfer does this to maintain the surface toplogy, and I think it
only does this in
Hi Mishkin,
yes, the ?h.cortex.label should be created for every subject that labels
the cortical regions of the surface.
cheers,
Bruce
On Tue, 7 Apr 2009, Mishkin Derakhshan
wrote:
Hello list,
I would like to create a mask on fsaverage/surf/?h.pial that masks out
the areas where the surfa
Hi Freesufer folks-
I was just about to start constructing a custom aseg atlas and I
wondered if there were any recommendations for any of the optional
flags? Any parameters yield better results (especially for specific
brain regions)? I was focused on improving amygdala segmentation for
my struc
Hi Martin, I don't know as I don't use fslswapdim on a regular basis.
Sounds like the geometry is not being computed correctly in the new
file. In any event, it seems more like an fslswapdim issue that a
freesurfer one.
doug
Martin Kavec wrote:
Hi Dough,
I took another subject, which was an
Hi Dough,
I took another subject, which was analyzed recently with the latest FS and the
result of the masking is gook!
I found another issue in my experimenting!
Here is exactly what I did:
1. mri_convert -i brainmask.mgz -o brainmask.nii.gz
2. fslswapdim brainmask.nii.gz x z -y brainmask.axia
Thanks. After reading up on the wiki it seems that a more general
solution I'm loking for would be to somehow get the contents of
?h.aparc.annot into ascii form. I know mris_annotation2label will kind
of do this, but it creates one file for every label. What I'm loooking
for is a single file with n
10 matches
Mail list logo
