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Thank you so much! It works.___
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When you set a variable to a list of multiple things, you need parentheses
around them (see the example config file for this). My recommendation to make
things simpler for yourself is to remove any variables where you are just using
the default settings, and only keep the ones where you define
Yes, but threshold it first, eg
mri_binarize --abs --i sig.cluster.mgh --min .01 --o newmask.mgh
On 12/4/19 1:38 PM, cody samth wrote:
>
> External Email - Use Caution
>
> Thanks, for your input. It's interesting that there isn't a more
> standard way of approaching it. If i wanted
Try using this instead
lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz
On 12/4/19 5:09 PM, Marcel Heers wrote:
>
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>
> Dear all, (dear Eugenio),
>
> I would like to use hippocampal subfields as masks for mri_segstats to
> retrieve intensity values. I am having
try setting your SUBJECTS_DIR to the full path instead of "./"
On 12/4/19 2:48 PM, Rellick, Stephanie wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am having an issue with the mri_label2label command.
>
> What I did was mri merge of the BA4 a and p labels for each hemisphere
>
I believe the problem is that they live in different voxel spaces (Doug, can
you please clarify?)
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Marcel Heers
Reply-To: Freesurfer support list
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Dear all, (dear Eugenio),
I would like to use hippocampal subfields as masks for mri_segstats to
retrieve intensity values. I am having problems loading the subfields file
although it works fine with aseg.mgz.
Does anyone know the cause?
Thank you
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The Neuroimaging Research Group of the Alzheimer's Prevention Program of
the Barcelonabeta Brain Research center is seeking a Post-Doctoral
researcher (open to Ph.D. students), a Neuroimaging Data Analyst and a
Scientific Project Manager.
For further
Hi Jason,
Can you try this command in a terminal on your Mac:
defaults write org.macosforge.xquartz.X11 enable_iglx -bool true
Then make sure to restart XQuartz and ssh -X to your linux box. It works
for me on macOS 10.12.
Ruopeng
On 12/4/19 10:59 AM, Stockmann, Jason wrote:
Hi,
I have
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Hello,
I am having an issue with the mri_label2label command.
What I did was mri merge of the BA4 a and p labels for each hemisphere from the
fsaverage files, ending up with a lh.BA4.label and a rh.BA4.label.
I am wanting to now map the fsaverage
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Dear Freesurfers experts,
I'm a beginner in the diffusion imaging preprocessing. I was following the
freesurfer/dti tutorial with my own data when i get stuck in the trac-all
step. I have created the configuration files trying to follow the tutorial
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Thanks, for your input. It's interesting that there isn't a more standard
way of approaching it. If i wanted to constrain my post-hoc to be within
the cluster(s) from the main effect how would I go about running this
through mri_glmfit? Would I include
This is actually a problem with mri_label2vol. I have fixed it and put a
new copy here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_label2vol
run it like this
mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o
sc.nii --tkr-template orig.mgz
On 12/3/19 8:23 AM, ZORO
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Hi FreeSurfer Experts,
I had a question regarding contrasts for univariate LME models.
I am interested in looking at the interaction of alcohol with change in volume
across two time-points. Included in my model are covariates Gender, ICV, and
yes, that is correct
On 12/4/2019 5:30 AM, Ferraro, Pilar wrote:
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>
> Yes, absolutely, this should work! Many Thanks!
> I have just one last question concerning the colors in FreeView.
> I have a fsgd file with class 1 (patients) coming first and then class
Hi,
I have been having trouble running freeview from the Mac OS terminal via
XQuartz on my laptop. I have seen the problem with both Mac OS 10.15.1
(Catalina) and the previous version of Mac OS. I get the error copied below.
I am however able to run other GUIs such as fslview. The problem
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Thank you Andrew, that did it.
-Dustin
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Hoopes, Andrew
Sent: Wednesday, November 27, 2019 10:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] freeview parallelized binary
Hi
Hello Freesurfer,
We would like to distribute Freesurfer through our BioGrids tool (
biogrids.org) with a license file already in place. I've read the previous
message that asks individual users to obtain licenses even if using a
single central license.
I have requested a license ad filled in
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MRC-funded Doctoral Position in Brain Microstructure Imaging Analysis using MRI
and light sheet microscopy - Sir Peter Mansfield Imaging Centre, School of
Medicine, University of Nottingham, UK
Application Deadline: 5.00 pm Friday 17 January 2020
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Yes, absolutely, this should work! Many Thanks!
I have just one last question concerning the colors in FreeView.
I have a fsgd file with class 1 (patients) coming first and then class 0 (hc)
after.
The contrast matrix is 1 -1 0.
Among the results I
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