What is the name of FreeSurfer subject? This is not necessarily the same
as SUBJ01 in your command line below. That is the session (which may or
may not be the same as the "subject name"). What ever the subjectname
is, does $SUBJECTS_DIR/subjectname exist?
On 10/31/2012 03:07 PM, Zhou, Wei wr
Hi, Doug
Thank you for your reply. I have tried exporting SUBJECTS_DIR to the directory
of upper fold, retinotopy or SUBJ01 But none of them works. Still the same
error msg.
So what should SUBJECTS_DIR be exported to for this analysis?
Best
Wei
>Hi Wei, this is a bug in the error msg. It
The lines are as follows
Computing Initial Surface Statistics
-face loglikelihood: -9.5176 (-4.7588)
-vertex loglikelihood: -7.1428 (-3.5714)
-normal dot loglikelihood: -3.5493 (-3.5493)
-quad curv loglikelihood: -6.1889 (-3.0944)
Total Loglikelihood :
I have a MRI data which has a lesion on the left side .
recon-all fails with errors . I was hoping to recover from this error .
The last few lines of the log file is as follows'___
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The command line was: recon-all -make -s CON1
I am not sure why the log said it was: recon-all -s
/usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel
I am running it again right now and it said the command line was:
recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1
-careg
If FSL isn't happy with the directions, that's going to be fatal b/c
trac-all relies on bedpostx running properly. I'm going to look into this
further to try to figure out what it is about this data that's causing
the discrepancy.
On Wed, 31 Oct 2012, Fernando Ventrice wrote:
Dear Anastasia
Is the last item in the list "lh_MeanThickness_thickness" This is the
mean thickness across the hemisphere.
doug
On 10/31/2012 05:16 AM, Daniel Ferreira wrote:
> Hi Douglas,
>
> Well, I usually use aparcstats2table with -m thickness, but what I get
> is the thickness for all those 34 hemisphere
Hi,
I did a SPM VBM (using dartel) analysis as well as a freesurfer group
analysis. After correcting for multiple comparisons. Both maps give me
pretty different results. From the literature review both sets of results
make sense but the fact that the results don't agree is troubling me. I
have ch
Bruce, thanks a lot. I will look forward for Jonathan's reply.
On 31/10/2012 13:11, "Bruce Fischl" wrote:
>Hi Lena
>
>sorry, I havne't heard of Phase-Sensitive Inversion Recovery. I'll cc Jon
>Polimeni who might have some thoughts.
>
>cheers
>Bruce
>
>
>
>On Wed, 31 Oct 2012, Lena Palaniyappan
>
Hi Lena
sorry, I havne't heard of Phase-Sensitive Inversion Recovery. I'll cc Jon
Polimeni who might have some thoughts.
cheers
Bruce
On Wed, 31 Oct 2012, Lena Palaniyappan
wrote:
Hi all
Our local team of physicists recommend Phase-Sensitive Inversion Recovery
instead of MPRAGE for ana
Hi Efrat
if it's not messing up the surfaces or the aseg then you don't have to
worry about it
cheers
Bruce
On Wed, 31 Oct 2012, Efrat Kliper wrote:
Dear Freesurfer expert,
I am using Freesurfer version 5.1.0.
After I ran the freesurfer recon-all -autorecon-all and checked the data I
saw
Thanks Ed
It wasn't as bad here as elsewhere
Bruce
On Oct 31, 2012, at 5:53 AM, Ed Gronenschild
wrote:
> Hi Bruce and colleagues,
>
> I hope you did survive Sandy without too much damage.
>
> Cheers,
> Ed
>
> ___
> Freesurfer mailing list
> Frees
Hi all
Our local team of physicists recommend Phase-Sensitive Inversion Recovery
instead of MPRAGE for anatomical imaging in 7T. So far, I have had no issues
with 7T MPRAGEs with regard to freesurfer processing. I am not sure about PSIR
and freesurfer compatibility.
Does anyone have experience
Hi Bruce and colleagues,
I hope you did survive Sandy without too much damage.
Cheers,
Ed
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The information in this e-mail is intend
Hi Douglas,
Well, I usually use aparcstats2table with -m thickness, but what I get is
the thickness for all those 34 hemisphere regions, but not that measure of
mean thickness for the hemisphere. Could I be missing something?
thanks
Daniel
Message: 15
Date: Tue, 30 Oct 2012 11:17:56 -0400
From:
Hi,
For your information: for version 5.1.0 we have
found no differences in the results between
MacOSX 10.6 and 10.7 (53 subjects).
Cheers,
Ed
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Dear Freesurfer expert,
I am using Freesurfer version 5.1.0.
After I ran the freesurfer recon-all -autorecon-all and checked the data
I saw that the skull wasn't removed as a whole (yet it is not part of the
pial or white matter margin).
I was wondering if it just doesn't look good or that part
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