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Hi Bruce,
1) Free-surfer output is always 256*256*256, regardless of any input dimensions.
2) I have a doubt, while doing this re-sampling from input dimension to
256*256*256. Does free-surfer change the origin of image?
3) My input is an MRI dicom im
yes, I believe so. Where did the red overlay come from?
On Thu, 2 Aug 2018,
jahanvi patel wrote:
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Hi Bruce,
Thanks a lot, here is the figure. We want to know the annotation of the red
cluster.
When we check the cache.th30.pos.sig.culster.summary
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Hi Bruce,
Thanks a lot, here is the figure. We want to know the annotation of the red
cluster.
When we check the cache.th30.pos.sig.culster.summary, we got this cluster
info.
MNIX -8.8,
MNIY -89.2,
MNIZ 21.4
What are these coordinates? are they in MN
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Dear Dr Bruce, thank you!!
Hi John
you can try a morphological close using mri_morphology.
cheers
Bruce
‐‐‐ Original Message ‐‐‐
On August 2, 2018 3:15 PM, John Anderson wrote:
> Dear Freesurfer experts,
> I would like to inquire if there
External Email - Use Caution
Dear Freesurfer experts,
I would like to inquire if there is any command/method in FS6.0 that can help
to fill holes in a brain mask without dilating it?
I would appreciate any advice!
John___
Freesurfer mai
but the cluster scheduling software might have other ideas
Bruce
On Thu, 2 Aug 2018, Ortal Nakash wrote:
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on the log it says that cpu time is unlimited.
On Thu, Aug 2, 2018 at 12:58 PM, Ortal Nakash wrote:
Do you mean that I should have use
you need to specify the SUBJECTS_DIR. And yes, you might have needed more
ram as the free is a lot less than the used at the start of recon-all, but
some clusters also have limits on the length of time a job is allowed to
run
cheers
Bruce
On Thu, 2 Aug 2018, Ortal Nakash wrote:
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on the log it says that cpu time is unlimited.
On Thu, Aug 2, 2018 at 12:58 PM, Ortal Nakash
wrote:
> Do you mean that I should have used higher memory?
>
> Is there a way to continue running it from where it stopped or should I
> start it all over a
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Dear All,
I have a problem with the Freesurfer hippocampal longitudinal segmentation
results , when i have done segmentation using following algorithm (
https://github.com/CobraLab/antsRegistration-MAGeT) with no
anterior/posterior partitioning ( Head/
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Do you mean that I should have used higher memory?
Is there a way to continue running it from where it stopped or should I
start it all over again?
On the Freesurfer Archive there's a suggestion to use the following
command: recon-all -make all -s Ho
hmmm, it looks like it just stopped in the middle of a process. DId it
exceed some wall time limit perhaps?
On Thu, 2 Aug 2018, Ortal Nakash wrote:
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Sure, here it is.
On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl
wrote:
can you send it as a
can you send it as a text file (not converted to .docx)?
On Thu, 2 Aug 2018,
Ortal Nakash wrote:
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I copied it in the attached file.
Thank you,
Ortal
On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl
wrote:
Hi Ortal
you need to send us t
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I copied it in the attached file.
Thank you,
Ortal
On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl
wrote:
> Hi Ortal
>
> you need to send us the recon-all.log, otherwise we don't have the
> information we need to help you
>
> cheers
> Bruce
> On Thu,
Hi Ortal
you need to send us the recon-all.log, otherwise we don't have the
information we need to help you
cheers
Bruce
On Thu, 2 Aug 2018, Ortal Nakash wrote:
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Hi,
I tried to run the recon-all command on a single participant on a high memory
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Hi,
I tried to run the recon-all command on a single participant on a high
memory cluster by typing:
qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G
recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/
-all
- Most of th
Awesome, thanks Bruce!
Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of B
yes, use vol2surf. I'm not sure what you want to do with the results, but
certainly matlab will give you the max flexibility
On Thu, 2 Aug 2018,
Fotiadis, Panagiotis wrote:
Hi Bruce,
That's actually great for visualizing the new surface as well, thanks! And to
calculate the actual
intensit
Hi Bruce,
That's actually great for visualizing the new surface as well, thanks! And to
calculate the actual intensity at that distance, would I need to resample with
mri_vol2surf and then use MATLAB or should I go another way?
Thanks again,
Panos
Panagiotis Fotiadis
Senior Imaging Researc
Hi John
you can try a morphological close using mri_morphology.
cheers
Bruce
On Thu, 2 Aug 2018, John Anderson wrote:
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Dear Freesurfer experts,
I would like to inquire whether there is (are) any command(s) in FS6.0 that can
help to fill holes
in
Hi Panos
we typically use mri_expand to move the surface inwards and outwards, then
sample with the resulting surfaces.
cheers
Bruce
On Thu, 2 Aug 2018, Fotiadis, Panagiotis
wrote:
Hi Bruce,
I had a follow-up question concerning measuring the signal intensity of the
gray and white ma
Hi Jahanvi
did you mean to attach a figure? If you did it did not make it. Definitely
look at the annotation on the surface (inflated probably) if you want to
judge its accuracy
cheers
Bruce
On Thu, 2 Aug 2018, jahanvi patel wrote:
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Dear List,
External Email - Use Caution
Dear Freesurfer experts,
I would like to inquire whether there is (are) any command(s) in FS6.0 that can
help to fill holes in a brain mask without dilating it?
I would appreciate any advice,
John___
Freesur
Hi Bruce,
I had a follow-up question concerning measuring the signal intensity of the
gray and white matter in those ex vivo brains:
I used mri_vol2surf to create an mgh surface that goes 1mm outside the white
matter (to estimate intensity in the gray matter) and another surface that goes
1m
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Dear List,
We have a question about the annotation of this MNI coordinate (-8.8,
-89.2, 21.4).
Freesurfer's report summary showed it is -- left superior parietal lobule,
while we see from the figure it seems not very much correct. It seems more
occipit
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