This looks like an error inside of fmriprep to me. If you want our help,
please recreate the error using just the FS tools
On 10/11/2023 2:08 PM, Xingyu Liu wrote:
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Dear freesurfer experts,
I was trying to segment thalamic nuclei using segmentThalamicNucle
Not sure what is going wrong here. Try looking at the images and the
initial segmentation, eg,
freeview norm.mgz aseg.presurf.mgz
Does anything look off?
On 10/8/2023 11:05 AM, Massimo Valerio wrote:
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Il giorno dom 8 ott 2023 alle ore 16:58 Massimo Valerio
Do you just need to change the voxel size for that dimension? If so, you
can use mri_convert, something like
mri_convert -iis newvoxsize input.mgz output.mgz
where -iis means the change the voxel size of the first dimension. Use
-ijs or -iks for the 2nd and 3rd. You may have to play with it to g
You are on the right track. First, you need a registration matrix. You
can get this with
bbregister --mov mtr.nii.gz --reg reg.lta --s subject --t2
The above command assumes that GM is brighter than WM in MTR. If this is
not the case, then use --t1
View your registration with
tkregisterfv --mov m
have you looked here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
?
On 10/4/2023 4:20 PM, Carly McIntyre-Wood wrote:
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Hi there,
I have recently been looking at the aseg.mgz file in several of the
participants I have ran thr
That is correct for DOSS (note that you don't need to do the pos and neg
separately as you can handle that at the next stage; in the sig maps,
the pos will show up as red/yellow and neg will show up as blue). For
DODS you would need 0 0 0 0 0.5 0.5
On 10/4/2023 10:34 AM, Steve Petersen wrote:
oh, that is not due to an error in the aseg itself. That's due to the
surface being cut off, probably due to a topological defect. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 10/4/2023 5:07 AM, Krystal Xiwing Yau wrote:
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what are you trying to do? This is for viewing the registration between
two volumes. One of the volumes is obtained from the subject, but you
need to specify the other volume on the command line (eg, --mov fmri.nii.gz)
On 10/3/2023 3:18 PM, Viktorija Pratuseviciute wrote:
External Em
You can also try editing the wm.mgz or filled.mgz to remove the defect.
See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 10/3/2023 5:23 AM, Pål Gunnar Larsson wrote:
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OK.
Did make a new setup with 16Gb. Restarted. Hop
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To whom it may concern,
Hello! We are currently trying to do a ST-LME (Spatiotemporal-LME) analysis
based on bipolar disorder brain MRI images. We are having 2 problems:
1)In the lme_mass_fit_EMinit step, we get a warning that says matrix is
singular,
Hi Maya,
It looks like you need to have 'synthseg -robust' in the file instead of
"mri_synthseg -robust".
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Huang, Yujing
Sent: Wednesday, November 1, 2023 6:06 PM
To: Maya Yablonski
Cc: Freesurfer support list
Subject: R
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