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FYI: Connectome Workbench is comparable with NIFTI/GIFTI/CIFTI formats. GIFTI
includes .surf.gii, .label.gii, .shape.gii, .func.gii.
Matt.
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Dinicola, Lauren"
mailto:lmd...@g.harva
Hi Dayea
probably, but I wouldn't recommend it. Most of the surfaces are clamped
in those regions, meaning the thickness (and hence volume) will be zero.
I guess surface area might have some meaning. You could get it using
mris_anatomical_stats (or maybe it is listed in the ?h.aparc.stats file
also double check your path with
which freeview
On Thu, 6 Sep 2018, Ruopeng Wang wrote:
Were they loaded with the same command? Can you check freeview's build time to
make sure they are
the same build? You can check it from menu Help->About.
Ruopeng
On 09/06/2018 09:15 AM, Sofia Rodriguez
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HELP
-- Forwarded message --
From: Rebecca Ray
Date: Thu, Sep 6, 2018 at 12:05 PM
Subject: longitudinal hippocampal aseg editing
To: freesurfer@nmr.mgh.harvard.edu
I have 2 time points on 60 subjects with most being in some form of AD
I have not tried to compile it, sorry.
On 09/06/2018 03:45 PM, Thomas, Adam (NIH/NIMH) [E] wrote:
>
> External Email - Use Caution
>
> We’d like to calculate the Local Gyrification Index (LGI) on several
> thousand scans, but our HPC cluster does not have the necessary Matlab
> licenses
The Mathworks offers runtime distribution that contains the libraries you can
build your code against w/o needing a Matlab license; you just cannot
re-distirbute the files from the distribution w/o permission from The
Mathworks. I’ve used it to build code that links against libmat etc. You ca
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We’d like to calculate the Local Gyrification Index (LGI) on several thousand
scans, but our HPC cluster does not have the necessary Matlab licenses to do
this in a reasonable amount of time.
Has anyone managed to compile the LGI code such that it c
Hi Doug,
I actually got this to work by just changing .aparc.gii to .label.gii &
opening using the workbench; please disregard, and I apologize for taking
your time.
All the best,
Lauren
On Thu, Sep 6, 2018 at 2:47 PM, Dinicola, Lauren
wrote:
> Hi Doug,
>
> I have successfully converted an in
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Dear Freesurfer experts,
I would appreciate any help regarding my previous question:
I need to transform a bunch of MNI coordinates to subject's space. I have
already registered my subjects to cvs_avg35_inMNI152 using
mri_cvs_register. How can I use t
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Hello,
I read on the website FAQ that "if you use the values in the ?h.aparac.stats,
it already factors out the 'unknown' region, so you don't have to do it
yourself". Is there a way to view stats (ex. thickness, area, volume) for these
unknown regi
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I have 2 time points on 60 subjects with most being in some form of AD.
There are considerable differences in hippocampal volume between time
points. I edited the raw images before making the template. I then had to
edit the aseg template image and the
Hi Doug,
I have successfully converted an individual BA label to a .label.gii file
and opened it; I have not been able to open the Gifti .aparc.annot file
after attempting to convert the .annot file in Connectome Workbench. So I
am wondering if a full parcellation already exists in dlabel.gii form
Canyou give more info on how you arrived at those numbers? Eg, are those
the numbers after you imported into SPSS? If you look in an individual's
aseg.stats file, do you see the same value?
On 09/06/2018 12:41 PM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
> H
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Hello Freesurfer developers,
Did hoy have chance to read this question?.
Thank you very much for your help!
Best regards,
-- Forwarded message -
From: Miguel Ángel Rivas Fernández
Date: mar., 4 sept. 2018 20:37
Subject: strange eT
what is the compatible format?
On 09/06/2018 11:54 AM, Dinicola, Lauren wrote:
> Hi all,
>
> I have been searching for the Freesurfer label or annot files for
> fsaverage in the formats compatible with Connectome Workbench and have
> not yet found them. Are these available?
> If not, is there a
Hi all,
I have been searching for the Freesurfer label or annot files for fsaverage
in the formats compatible with Connectome Workbench and have not yet found
them. Are these available?
If not, is there a way to convert all the BA labels to then convert them to
borders for viewing on fsaverage? I
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Hi FS Experts
I've run my data through the brainstem, hippocampus and amygdala following the
usual Recon_all and using the developmental version downloaded and stalled
around Jan2018. I'd like to use the new thalamus tool and am wondering if I
need
Were they loaded with the same command? Can you check freeview's build
time to make sure they are the same build? You can check it from menu
Help->About.
Ruopeng
On 09/06/2018 09:15 AM, Sofia Rodriguez Penuela wrote:
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Hello team!
We are trying to load t
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The Child Mind Institute is seeking a Data Analyst to support a collaborative
study with Dr. Amy Roy at Fordham University. The Data Analyst’s role is to
assist with the analysis of functional MRI data, as well as reporting results.
In particular, th
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Hi,
I'm working on data from different sites, scanned with different
MRI-Scanners ans slightly different parameters (all in the range of 1x1x1
to 1.2x1.2x1). I wonder if you would recommend to run recon all and
segmentation of HC sub-fields in differen
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Hi Maedeh,
The human cerebral cortex is a highly folded sheet of neurons the thickness
of which varies between 1 and 4.5 mm, with an overall average of
approximately 2.5 mm (1–3). Regional variations in the cortical thickness
can be quite large. For ex
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