Dear Fresurfers,
I'm visualizing multiple timecourses using the -timecourse window in freeview.
I'd like to specify the color of each traces through the command line.
Is there a hidden (or easy to implement) feature for that?
I use the dev version at the Martinos.
Thanks for the help and
Have
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Dear Freesurfers,
Is it possible to input an alpha channel to freeview? Otherwise said, can one
obtain a voxel-specific opacity?
I would see something like
freeview underlay.mgz overlay.mgz:opacity=opacity.mgz
where the single opacity value is
not
work with unmatched voxel grids.
Thanks for you help and
Have a great day!
Sebastien
From: Proulx, Jean Sebastien
Date: Monday, August 28, 2023 at 3:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: Copy geometry (fov position) from one header to another while
keeping voxel and matrix
complains for that second scenario:
“error: volume sizes do not match”
Thanks again a lot for your help and
Have a great day!
Sébastien
From: Greve, Douglas N.,Ph.D.
Sent: Monday, August 28, 2023 10:47 AM
To: Proulx, Jean Sebastien ;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: Copy geometry (fov
g vol2.mgz --reg yourreg.lta --no-resample --o new.vol1.mgz
On 8/18/2023 11:34 AM, Proulx, Jean Sebastien wrote:
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Dear Freesurfers!
I have two single-slice images that were acquired with different head positions.
Thanks to a fancy AutoAlign-like routine at t
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Dear Freesurfers!
I have two single-slice images that were acquired with different head positions.
Thanks to a fancy AutoAlign-like routine at the scanner (areg by Paul Wighton),
the fov of the second image tracked the movement of the head—the brain
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It worked, thanks!
I used --outvox instead if --outfsl, as --outfsl was "not implemented yet"
(using dev) and it feels safer since the m3z seems to have voxel units.
For posterity, below is a snippet of the code I used:
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Hello,
I produced an m3z warp file with mri_gradunwarp.
Now I need to 0 out all displacement in the z direction, while keeping
everything else the same since I need to combine multiple warps from images
with different geometries.
I see two
unning this with -keep-scouts
and without -keep-scouts
Let me know if this runs successfully in both situations (I'm using you as my
tester:)
On 4/18/2023 10:51 AM, Proulx, Jean Sebastien wrote:
Sorry for the late follow-up.
Yes, that is what I’m doing. With dcmunpack -auto-runseq I convert everything,
th
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Great! I happen to be doing a phantom scan session this pm and will get some
test data to test that and report back soon.
Cheers!
Sébastien
From: Greve, Douglas N.,Ph.D.
Date: Wednesday, April 26, 2023 at 6:52 PM
To: Proulx, Jean Sebastien
Dear Freesurfer Team,
The help of dcmunpack says it will ignore scout scans. Is there perhaps a
hidden flag to avoid that behavior? We are running multiple scouts throughout a
session to combat head motion. Getting those images along the rest would allow
visualizing that motion offline.
Hello,
I am trying to register a full volume to a single slice, and I follow example 3
of mri_robust_register's help. I get the following error:
Input image is smaller than min dimension: 1 < 16
Input dimensions (after conformalizing) MOV: 64 64 64
Input dimensions (after conformalizing) DST:
Hello,
Specifying a single volume frame with # is great, but how to specify a range or
multiple arbitrary choosen frames?
Something like #0..9 would be nice for the 1st to the 10th frame, and #0,2,4
for the 1st, 3rd and 5th frames.
Thanks for the help and
Have a very good day!
Sebastien
Hello,
Is there an easy way to perform fast fourier transform (fft) or other fancier
spectral analysis with freesurfer tools (e.g. with mris_calc)?
Thanks and
Have a good day!
Sebastien
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