Hello everyone,
I wanted to know what I can do to fix this error- it occurs when I'm running
recon-all -all -s Subject
Tue Mar 30 11:27:20 BST 2010
talairach_avi done
#
#...@# Talairach Failure Detection Tue Mar 30 11:27:20 BST 2010
/home/s0964091/Deskto
Hi Jan,
the place to look at is
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Best,
Martin
On Tuesday 30 March 2010 12:30:35 Janani Dhinakaran wrote:
> Hello everyone,
> I wanted to know what I can do to fix this error- it occurs when I'm
> running recon-all -all -s Subject
>
I'm looking through it and also looking at tkregister2 help, and I have some
questions
1)Does Recon only work on fully structural data? If you have funtional
information on it will recon fail?
2)Also- Does it matter what the files are named... for ex- if the first 50
are named JohnSmith_001_01_01.i
Is your dusk full?
On Mar 30, 2010, at 3:50 AM, "Ahmed, F, Me " > wrote:
Hello,
I have been successfully running the recon-all process on all my
subjects and have come to a problem with my last subject. I ran
autorecon1 without error but when I ran autorecon2, it exited with
errors an
Well I did run out of space in FS a while back, but I made space, and it had
been running ok, do you think I have run out of space?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 30 March 2010 14:20
To: Ahmed, F, Me
C
Hello
I tried recon-all in a patient with Huntington´s disease with severe atrophy
of caudate nucleus (visually). It seems that freesurfer subcortical
segmentation failed because the volume reported is within normal limits. How
can I correct this?
Thanks
--
Diego Herrera, M.D.
Neuroradiologist
M
I also use FS to identify subcortical atrophy with affected HD patients;
have you checked the aseg, as well as white & pial surfaces for accuracy? I
have found in some of my older data at lower resolution (1.5 T) that the
intensities do not differ much in subcortical regions and FS has problems
dif
that is usually what causes that error. If you created more space try
rerunning that subject
On Tue, 30 Mar 2010, Ahmed, F, Me
wrote:
Well I did run out of space in FS a while back, but I made space, and it had
been running ok, do you think I have run out of space?
From: freesurfer-boun..
I managed to rerun recon-all completely and get the cortex out with
tkmedit jan aparc+aseg.mgz
I wonder if there is a way of specifying particular areas like extracting
and measuring the volumes or thickness of regions like the sensorimotor
cortex or broca's area?
Thank you
On 16 March 2010 12:1
Hi,
in $SUBJECTS_DIR/any_subject_ID/mri/ there are
aparc+aseg2diff.mgz files and norm2diff.mgz files.
What does the -2diff-
mean and where does it come from?
I suspect it's the reason why we have problems with one subject that has a 90
degree turn in
fslview, since it was the only one
have you visually inspected the aseg volumes? Are the caudates accurate
or overestimated? This can certainly happen if the caudate is dramatically
smaller than any of the examples in our training set
On Tue, 30 Mar 2010, Diego
Herrera wrote:
Hello
I tried recon-all in a patient with Hunting
Hi,
I've been getting "ERROR: selfreqavg failed" for my retinotopic analysis and
would appreciate any suggestions about what might have gone wrong. The
command I was using was sfa-sess. Here's the command and the output from
freesurfer:
sfa-sess -a rtopy -sf sessid -df sessdir
---
sure, mris_anatomical_stats can do this. Look at the annot and BA*.label
files in tksurfer (in the subject's label directory) to see which ones have
areas you are interested in. Many of these are already reported by default
in the stats dir.
cheers,
Bruce
On Tue, 30 Mar 2010,
Janani Dhinakara
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