Hi Jacob,
whenever there is is systematic difference, there is also potential for a bias.
In your specific situation no one knows how large this bias could be. I would
think it will not really be measurable, as the base is only used for
initialisation and within such a small time frame, the
What version of Freesurfer are you using? Would it be possible to send us the
volume files before and after the rotation?
Best,
Ruopeng
On Dec 14, 2021, at 6:10 PM, Christopher Panks
mailto:cpa...@uw.edu>> wrote:
External Email - Use Caution
I’m trying to get images of post-mortem
External Email - Use Caution
I'm trying to get images of post-mortem brains, some from cadavers, some
excised, into standard space. I'm new to Freeview, so I'm not sure if I'm doing
something wrong, or my expectations are wrong. I find the Transform Volume tool
easy to use to
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Hi Doug,
I’m trying to do two different things but let’s focus on the one which does not
involve dilation.
I have a pair of vertices in a “white” label.
I want to compute the shortest distance from one vertex to the other along the
“white” surface.
This contrast will do it: [1 -1 0 0]
But I would first test [0 0 -1 1] to see if the slopes are different. If
not, then use [1 -1 0] with DOSS instead of DODS
On 12/14/2021 5:07 PM, Laura Willers de Souza wrote:
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Yes! Sorry for that.
And I'm resending my
Can you include the previous emails in your current email?
On 12/14/2021 3:46 PM, Laura Willers de Souza wrote:
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Dear Douglas,
Thank you so much for your answer!
Sorry, but I don't think I explained myself correctly in the previous
email.
I want to
There is an automatic topology fixer in the stream. While sometimes it
fixes an topo error properly, it does not always do so, so you will need
to see whether it has fixed is or not. It is the white surface that is
in error, which is created from the wm.mgz (or filled.mgz), so you will
need to
use the asegstats2table command in
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
You will have to add command line options to specify the subjects you
want. You can then pass the output file with the --table option to
mri_glmfit
On 12/13/2021 3:56 PM, Laura
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Dear Douglas,
Thank you so much for your answer!
Sorry, but I don't think I explained myself correctly in the previous email.
I want to analyze the difference in cortical thickness between two groups (CU
and CI), adjusting for a covariate (cortisol
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Good day Anastasia,
Thank you for replying back. It worked like a charm, I also had to add set
epifactor, but after that, it started to run, and a dmri folder was created in
subject directory as well. However, I'm getting this error right now:
Yes, here it is:
Volume information for data.nii.gz
type: nii
dimensions: 120 x 120 x 69 x 132
voxel sizes: 2.00, 2.00, 2.00
type: SHORT (4)
fov: 240.000
dof: 0
xstart: -120.0, xend: 120.0
ystart: -120.0, yend: 120.0
Is there a dmri/data.nii.gz? Can you run mri_info on it please?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra,M.D.
Sent: Tuesday, December 14, 2021 12:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error
How much space would I need to run this?
Thanks,
Mona
On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Any chance you're low on disk space?
From:
Any chance you're low on disk space?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra,M.D.
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error
Yes.
dmri.bedpostX has
Yes.
dmri.bedpostX has these files in it:
diff_slices empty
xfms empty
bvals
bvecs
monitor
nodiff_brain_mask.nii.gz
logs:
monitor empty
bedpostx_pre.e9769
bedpostx_pre.e47281
bedpostx_pre.o9769
bedpostx_pre.o47281
Hard to tell from the two lines. Did any files get created in bedpostX
Hard to tell from the two lines. Did any files get created in bedpostX output
directory?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra,M.D.
Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list
Subject: Re:
Hello,
I was running the "trac-all -bedp” section, when I got the below error. I
appreciate it much if you please let me know what the issue is.
Thanks,
Mona
- Bedpostx Monitor -
An error ocurred. Please check file
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