Hi Freesurfer experts,
I installed CentOS 7 on my computer and tried running freeview in the terminal
window after ssh’ing into a remote computer. The software opened up correctly
and I was able to see the toolbars; however, the main screen where the images
should be showed a distorted backgrou
How can I get the the position of a tkr voxel in terms of the native voxel
space?
My guess was:
pos = Torig*[C R S ones(size(S))]';% orig CRS to tkrRAS
pos = P*pos;% tkrRAS to native RAS
pos = W*bmsk;% native RAS to native CRS
Where,
Torig is given by mri_info --vox2ras-tkr orig.mgz
P is qive
You should also know that the memory management during openmp
mri_em_register execution is not optimal (as found by the HCP group. If
you are oversubscribing your processors (ie, have 20 cpus, but run 3
jobs each with 8 cpus), then mri_em_register will slow way down. This
appears to be due to s
Thank you - this is very useful!
On Tue, May 2, 2017 at 12:05 PM, Bruce Fischl
wrote:
> Hi Chris
>
> we have found an almost linear speed improvement up to 4, then it starts
> to fall off, with not much at all after 8.
>
> cheers
> Bruce
>
> On Tue, 2 May 2017, Chris Gorgolewski wrote:
>
> Hi,
>
The Vascular Risk and Cognition laboratory in the Neuroimaging Research Center
at VA Boston and Harvard Medical School is recruiting a full-time postdoctoral
fellow with expertise in magnetic resonance imaging (MRI) and strong data
processing skills. The postdoctoral position will focus on the a
Just bumping to the top to see if anyone has ideas about comparing 0.8mm
vs. 1mm data using the long stream.
Dear FS Experts,
I’m trying to compare multiple T1-weighted sequences taken across multiple
scanners in the same day in 15 individuals using the longitudinal stream.
One question we had
Hi Chris
we have found an almost linear speed improvement up to 4, then it starts
to fall off, with not much at all after 8.
cheers
Bruce
On Tue, 2 May 2017, Chris
Gorgolewski wrote:
Hi,
We are running freesurfer as part of a bigger pipelines with other steps
that can be performed in paral
Hi,
We are running freesurfer as part of a bigger pipelines with other steps
that can be performed in parallel to freesurfer reconstruction. So far we
have set the openmp flag to the number of all available cores. However, our
experience with ANTs and AFNI which also capitalize on the OpenMP
paral
Would it be possible for you to update to Freesurfer v6.0? On my macOS
Sierra + FS 6.0, freeview appears to work well.
Best,
Ruopeng
On 05/02/2017 12:18 PM, Kevin Japardi wrote:
Hello Freesurfer!
I'm working with someone in our group on some Freesurfer QA, and she's
having some issues with u
It is hard to say. As Anderson said, we have the improved method for
computing volume. But just because something is improved does not mean
that results will be more significant!
On 5/2/17 1:17 PM, John Anderson wrote:
Dear Doug,
Thank you very much for the clarification!! I highly apprecia
Dear Doug,
Thank you very much for the clarification!! I highly appreciate your science
and help.
I received an answer about my question from your colleague Dr Anderson Winkler
(Below) who directed me to review the paper (link also bellow).
My last question is: can Freesurfer 6 address "better
By noise, I just mean variability, which could come from those sources,
but more likely come from intersubject variability. No good way to check
those. It is looking like volume analysis has much higher false positive
rates than thickness too.
On 5/2/17 12:29 PM, John Anderson wrote:
Thank y
Thank you Doug,
One more question please.
Noise: does this mean low quality /high quality T1 images regarding SNR and
contrast between white and gray matter.
What is the correct approach to check noise effect on the reconstructed T1
images to avoid these controversies between cortical and volumet
Hello Freesurfer!
I'm working with someone in our group on some Freesurfer QA, and she's
having some issues with using the freeview gui.
She's using a Mac with OS Sierra, with X11 2.7.8.
Some of the issues she's having are:
1) The Mac red-yellow-green 'exit/hide/extend' buttons are blackened out
oh, that must of been it. I did not keep edits in brainmask
On 5/1/17 4:39 PM, Antonin Skoch wrote:
Doug,
did you process from scratch or did you retain edits to brainmask.mgz
and wm.mgz?
The -cubic should not be necessary, since recon-all (which I primarily
obtained from
https://surfer.n
It will probably crash. I does nothing to find NaNs and handle them in
an appropraite way
On 5/2/17 7:37 AM, Ladan Shahshahani wrote:
Hi Douglas,
Thanks for the reply.
One more question, Qdec excludes subjects with NaN values, right? How
will mri_glmfit treat subjects with NaNs?
For each sub
You are speaking statistically, I assume? Ie, you see a sig change in
volume and not thickness, or vice versa? If so, it can easily be
explained by differences in noise
On 5/2/17 5:00 AM, John Anderson wrote:
Hi Doug,
Thank you for the detailed explanation!
Please I have one follow-up questio
Doug,
I tried to replicate again v5.3 results of subject 1.
I checked wm.mgz, orig.mgz, ?h.orig, ?h.pial, ?h.white and found everything
identical (by using mri_diff and mris_diff) except FLAIR.mgz and ?h.pial (after
FLAIRpial refinement).
The difference was small, I have traced it to the level
Dear John,
you can prepare expert options file with the entry:
mri_gcut -T
and run recon-all -skullstrip -clean-bm -gcut -subjid -expert
expert_opts_file.txt
The mri_gcut help page reads:
-T
set threshold to value (%) of WM intensity, the value should
be >0
Hi Knut
I didn't see a 100% below. They look like what we usually see - low
contrast small structures (e.g. the pallidum) or ones with poorly
definied boundaries (the segments of the callosum, also quite small) show
large % changes (which typically correspond to not very many voxels).
cheers
Hi Douglas,
Thanks for the reply.
One more question, Qdec excludes subjects with NaN values, right? How will
mri_glmfit treat subjects with NaNs?
For each subject, there are some vertices with NaN values (These vertices
are not the same in all subjects).
Bests,
Ladan
_
Hi Doug,
Thank you for the detailed explanation!
Please I have one follow-up question and I highly appreciate your input
How can we explain results related to reduce cortical thickness and normal gray
matter volume. Are these parameters two different thing or they are related to
each other.? In o
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