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Hi!
Jumping in on this, since it has come up many times but is without a
solution so far: the issue is that the color code is now mapped onto a
straight color bar, not a circle. At the same time, it is not documented
what color refers to which angle.
Hi Fleur,
It’s definitely running with tcsh. Can you provide a bit more context for the
error? Like is there any terminal output preceding it?
Andrew
From: on behalf of Fleur Warton
Reply-To: FS Help
Date: Wednesday, May 20, 2020 at 6:13 AM
To: fsbuild
Cc: FS Help
Subject: Re: [Freesurfer]
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Open Postdoctoral Scholar Position
The University of Washington Institute for Learning & Brain Sciences (I-LABS;
http://ilabs.washington.edu/) located in Seattle, WA is seeking a Postdoctoral
Scholar to conduct analyses of human MRI brain imaging
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Yeah that works, thanks a lot.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Friday, 22 May 2020 1:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_register intermediate results display
I
Typo
yhat = X(:,[1 2 3])*beta([1 2 3],:)
On 5/21/2020 2:12 PM, Hua, Jessica wrote:
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I apologize for resending all of this info, but my email is acting up
and every time I try to respond to the other email, my Outlook freezes.
Here is info from our
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I apologize for resending all of this info, but my email is acting up and every
time I try to respond to the other email, my Outlook freezes.
Here is info from our thread. I modified it to include the analysis in which I
found significant clusters
You can try using --rbv. In theory, you can use mueller-gaertner
(--mgx), but I don't have it set up to look at WM or CSF. And be careful
because the extracerebral CSF segmentation is often not very good.
On 5/21/2020 1:07 PM, Barletta, Valeria wrote:
Yes I need the lh and rh cerebral WM for
Yes I need the lh and rh cerebral WM for sure, but not just the values, also an
image.
And I need also a corrected image for the extra cerebral CSF. How can I get
that?
Thank you very much,
Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823
I don't know what is wrong. Can you upload the hires run? Instructions below
From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user
Hi Chris
if you specify -w on the command line it will write out a surface
every n iterations of the minimization (-n 1 will write out every step).
You can then write a script to turn those into tiffs with freeview
cheers
Bruce
On Thu,
21 May 2020, Chris Adamson wrote:
External
I would just map the ?h.curv from one subject to another and then
display them on a single surface and flip back and forth. Would that
work for you?
On 5/21/2020 9:30 AM, Chris Adamson wrote:
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Freesurfer devs,
Apologies if this has already been asked.
Yes, CSF and vents
On 5/21/2020 9:48 AM, Vicky Shi wrote:
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Hi Douglas,
Thank you so much for your quick response. That is what I am looking for.
By the way, I found another file,global.gmwm.dat, in aux. Is this file
the mean suv intensity for grey matter
We don't have tools to do this. I guess you could use BV to do the
correction and feed the output into recon-all. For 7T, we often run SPM
VBM or segmentation to get a bias corrected output, then feed that into
recon-all
On 5/21/2020 3:50 AM, Tali Weiss wrote:
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Sorry, one of the reasons we stopped supporting QDEC was because it
became impossible to debug these kinds of things. Please use the command
line stream (ie, create an FSGD file and contrast matrices, run
mris_preproc, mris_fwhm, and mri_glmfit). I can help you once you
recreate the error
On
It is not clear what is failing. Can you check two things?
1. Check the talairach.lta with
cd $SUBJECTS_DIR/subject/mri/transforms
tkregisterfv --mov ../orig.mgz --reg talairach.lta --targ
$FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca
This does not have to be perfect, but it
You can just run
recon-all -s x autorecon2-wm -autorecon3 -T2pial
When you ran it the first time, your volT2.nii was copied into the
subject's folder and will be used when the pial surface is placed when
you include -T2pial
On 5/16/2020 1:12 PM, Octavian Lie wrote:
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If I understand, you run two analyses, one with an FSGD file with only
two classes and one where the FSGD file has the same two classes but you
include two variables. You are doing the same test (group1-group2) and
are wondering why the results are different.
They are different because you
You can use these commands
From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for
When you say it is "linear" do you mean it does not wrap-around?
On 5/19/2020 8:47 PM, Devavrat Vartak PhD wrote:
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Hello freesurfer community,
I am trying to setup a retinotopy pipeline. I have analysed pRF data
generating polar angle and eccentricity
I'm still confused as to what you are trying to do. If you just want to
sample your data onto the surface, then you do not need to resample it
at all. You just run mri_vol2surf with the appropriate registration and
projection fraction. If I'm misunderstanding, please clarify.
On 5/19/2020
It will certainly do cortex. We do not have a segmentation for
subarachnoid spaces. Or are you just talking about extra cerebral CSF?
We do have a segmentation for xCSF, but it is not the most beautiful
thing in the world. For WM, the GTM will give you a PVC corrected value
for the entire lh
On 5/15/2020 8:17 PM, Lab of Autism and Developmental Neuroscience, Lab
of Autism and Developmental Neuroscience wrote:
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Dear Freesurfer experts,
Hope everyone is doing well! Could someone please clarify some things
about mris_anatomical_stats, done
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Hi Douglas,
Thank you so much for your quick response. That is what I am looking for.
By the way, I found another file,global.gmwm.dat, in aux. Is this file the
mean suv intensity for grey matter and white matter? Which ROIs does it
remove compare to
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Freesurfer devs,
Apologies if this has already been asked. I'm looking for a way that I can look
at the progress of mris_register to investigate the accuracy of registration.
Given that the registration is done on the 2D parameterisations of the
Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect in the
cortex, white matter and subarachnoid space. Is Freesurfer's partial volume
correction working on all these areas or only the grey matter volume and
surface? Is there a way to use gtmseg on the white
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Dear all,
1. BV have a tool:
https://www.brainvoyager.com/bv/doc/UsersGuide/HighResDataAnalysis/UsingPDScansForInhomogeneityCorrection.html
Is freesurfer have something similar for MPRAGE (i use recon-all)
2.Is PD is suitable also to correct
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Hi,
I was running longitudinal trac-all. After the 3rd step -path was finished,
I found that multiple pathways were missing (e.g. fminor). I traced back,
realizing outputs from its first step trac-prep were missing corresponding
pathways in
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