Can you send the actual command you ran and all the terminal output?
On 9/10/2020 12:58 AM, vittal korann wrote:
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Yes, I did replace question marks with left and right.
Thank you so much, Douglas.
With regards
Vittal
*/
/*
On Thu, Sep 10, 2020 at 1:11 AM
Assuming these are cortical lesions, you can use mri_vol2surf to map
them as overlays onto the surface. Use the --regheader flag since they
are already in the conformed space. You can even specify the target
subject to be fsaverage to have the overlay be on the fsaverage surface
(if not, then u
My guess is that changes in the anatomy over a year will be pretty
small, unless there is something extreme about your population
On 9/9/2020 7:36 PM, Zeng, Qi wrote:
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Hi,
I was conducting a longitudinal DTI analysis. However, MRI and DTI
brain scans were
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Hi:
Why I got a big ICV difference between MPRAGE of the same patient (2019:
1775887.317631, 2020: 1566398.53576 mm3), one-year difference acquisition,
and the same MRI Skyra 3T equipment? I used freesurfer 5.1.0 on the same
computer, and operating s
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Hello,
I noticed tksurfer disappeared in the new 7.1 version of freesurfer. While it's
still present in older versions of course, it no longer runs on 64-bit only
operating systems (e.g. OSX Catalina). Is tksurfer going to be updated? It
seems to be
Hi Jesse,
Freeview does support surface-based ROI drawing. There is a Path/Custom Fill
tool button on the left pane. Once it is checked, you should see a bunch of
tool buttons similar to what tksurfer had for ROI drawing.
Best,
Ruopeng
On Sep 10, 2020, at 10:27 AM, Jesse Gomez
mailto:jessego.
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Hi FS community,
I started using FS 7.1.0 for cortical and subcortical
parcellation/segmentation.
As I found information that FLAIR data could improve pial surfaces
creation, I decided to try it on since I have FLAIR images besides
MPRAGE, by using
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Thanks Ruopeng. Is surface-based or tksurfer coming back? The surface-based
label drawing was much more powerful than drawing slice by slice in volume
space.
On Sep 10, 2020, at 10:35 AM, Wang, Ruopeng
mailto:rwa...@mgh.harvard.edu>> wrote:
Hi
Thanks so much Douglas.
Many of the lesions are in the white matter, and many span across WM and GM. In
the case where the lesions on not strictly cortical, is this surface mapping
not possible? Or perhaps a representative surface map showing the occurrences
of lesions in any lobe/ROI?
Best,
M
I believe tksurfer will be depreciated if not already. But like I said in the
previous email, freeview does support surface-based label drawing.
On Sep 10, 2020, at 10:49 AM, Jesse Gomez
mailto:jessego...@princeton.edu>> wrote:
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Thanks Ruopeng. Is surface-b
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My apologies, I totally read "does not". I see it now (it's a feature in the
new version of freesurfer it seems, I was pointing to version 6). Thank you so
much!
Best,
Jesse
On Sep 10, 2020, at 11:10 AM, Wang, Ruopeng
mailto:rwa...@mgh.harvard.
Hi Doug
Thanks for your reply.
I did so, I'm getting the error below:
line 43: 8101 Segmentation fault (core dumped) mri_volsynth --template
$SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 -12.2 -10.3 --pdf delta
--delta-crsf 150 138 116 0 --dim 5 5 5 5 --o delta.mgh
I appreciate
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Sorry if cross-posted. See the attachment for the job detail. Thanks.
_
Xiangrui Li, Ph.D.
Center for Cognitive and Behavioral Brain Imaging
The Ohio State University
Phone: 614-292-1847
MRI Senior Research Specialist.pdf
Description: Ado
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Finally, it worked. Thank you, Douglas.
My question is regarding the mean gyrification similar to what we get for
thickness as a whole-brain mean thickness.
If there is a way to calculate, please let me know.
Here is a command that I executed and got t
On 9/10/2020 12:08 PM, vittal korann wrote:
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Finally, it worked. Thank you, Douglas.
My question is regarding the mean gyrification similar to what we get
for thickness as a whole-brain mean thickness.
I'm not sure what you are asking here. gyrification a
The question is more for you. The lesions are not on the surface but
you want to display them on the surface. How do you want to do that?
ps. please remember to post to the list
On 9/10/2020 10:25 AM, Horn, Mitchell Jacob wrote:
Thanks so much Douglas.
Many of the lesions are in the white ma
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Sorry, Douglas, I might have confused you.
Freesurfer will provide mean thickness for the whole-brain. similarly, can
I have mean gyrification for the whole brain (not individual values for
left and right hemisphere)?
*Finally, it worked. Thank you, D
rh.pial.T1 is the T1-based surface, rh.pial.FLAIR is the FLAIR-based
surface refined from the T1 surface. rh.pial is the final surface and is
a symbolic link to rh.pial.FLAIR
On 9/10/2020 10:40 AM, Otília C. d'Almeida wrote:
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Hi FS community,
I started us
please send the full terminal output
On 9/10/2020 11:24 AM, Nasiriavanaki, Zahra wrote:
Hi Doug
Thanks for your reply.
I did so, I'm getting the error below:
line 43: 8101 Segmentation fault (core dumped) mri_volsynth
--template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8
-
It all comes down to the registration. See
https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV
The image may have more-or-less neck and that can change the
registration and ICV. The contrast may be different. The scanner may
have had software updates. You might be comparing dewarped vs not dewarped.
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Thank you Douglas.
So, as far as I understood, the estimates (cortical thickness for
example) are estimated from rh.pial surface (that comes from FLAIR pial
surface). Since the use of FLAIR decreased the quality of pial
segmentation (GM is underestima
Can't you just average the lh and rh values? You can weight by the
surface area or number of vertices
On 9/10/2020 12:53 PM, vittal korann wrote:
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Sorry, Douglas, I might have confused you.
Freesurfer will provide mean thickness for the whole-brain. simila
Sure, sorry for the inconvenience.
Here is the full output:
[bee:ROI_analysis] (nmr-stable6-env) ./make_flabels.sh
voliddelta.mgh
volfmt (null)
Using
/autofs/space/oprah_001/users/zn025/looming_3T/SUBJECTS_DIR/fsaverage/mri/brainmask.mgz
as template
fwhm = 0, gstd = 0
seed 1600286417
pdf
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Thank you so much, Douglas.
On Thu, Sep 10, 2020 at 10:20 PM Douglas N. Greve
wrote:
> Can't you just average the lh and rh values? You can weight by the surface
> area or number of vertices
>
> On 9/10/2020 12:53 PM, vittal korann wrote:
>
>
I think if you delete the ?h.pial files then run
recon-all -s subject -autorecon3 -nosphere -nosurfreg -nowhite -nocortparc
It should regenerate everything with the T1-only pial
On 9/10/2020 12:50 PM, Otília C. d'Almeida wrote:
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Thank you Douglas.
So, as f
remove --dim 5 5 5 5
this tells it to make the output volume 5 voxels
On 9/10/2020 12:53 PM, Nasiriavanaki, Zahra wrote:
Sure, sorry for the inconvenience.
Here is the full output:
[bee:ROI_analysis] (nmr-stable6-env) ./make_flabels.sh
volid delta.mgh
volfmt (null)
Using
/autofs/space/opr
thanks for you reply.
So, how should I define the size of the sphere around that coordinate?
I am trying to make a subcortical 5 mm sphere ROI around that talairach
coordinate.
Thanks
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hos
Try using --pdf sphere --sphere-center 150 138 116 --radius 5
instead of delta
On 9/10/2020 2:22 PM, Nasiriavanaki, Zahra wrote:
thanks for you reply.
So, how should I define the size of the sphere around that coordinate?
I am trying to make a subcortical 5 mm sphere ROI around that
talairach c
Thanks for your reply.
So I did these steps to get the values from the spherical ROI that I created
and got the below error:
mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --pdf sphere
--sphere-center 150 138 116 --radius 5 --o
/autofs/space/oprah_001/users/zn025/looming_3T/
I found the answer to my question.
Thanks anyway
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
On Sep 10, 2020, at 6:06 PM, Nasiriavanaki, Zahra
mailto:znasiriavan...@mg
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Hi,
Here is my log, deid'd, and attached should be a simple txt file for the config
file. Any thoughts on why I'm receiving this error?:
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMA
Hi Pilar,
You can update freesurfer to 7.1 by installing the rpm (on linux), running the
mac installer, or by extracting the tar archive. The rpm and mac installers
will download freesurfer distributions to appropriate version subdirectories,
so they will not overwrite an earlier version. If yo
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