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Dear Freesurfers,
gray matter volume of the entorhinal cortex (EC) can be obtained either in
the ?h.aparc.stats or ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files.
Considering that all our T1 images were manually edited on a slice-by-slice
basis to
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hey,
is there any update regarding the release of the FreeSurfer 6
HCP-compatible version?
cheers,
Shachar
On Mon, 14 Jan 2019 at 14:58 Shachar Gal wrote:
> thanks,
> hope it'll work
> anyway, looking forward for the version 6 release
>
> cheers,
>
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There is a little more testing we are doing.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, February 4, 2019 at 3:32 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.e
Hi Jose
the threshold is set so that the EC label has the average surface area of
the labels that went into the average. It is probably more accurate than
the aparc as it is based on actual cytoarchitectural landmarks that are
visible in ex vivo mri.
cheers
Bruce
On Mon,
4 Feb 2019, Labor
Hi Emma
the dimensions (163842 x 1 x 1) mean that these are overlays on the
fsaverage surface. Can you remind me what issue you are trying to solve?
cheers
Bruce
On
Mon, 4 Feb 2019, Bunting, Emma wrote:
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Hi Bruce,
I ran the mri_info command o
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Thank you!
El lun., 4 feb. 2019 a las 15:29, Bruce Fischl ()
escribió:
> Hi Jose
>
> the threshold is set so that the EC label has the average surface area of
> the labels that went into the average. It is probably more accurate than
> the aparc as it
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I have recently installed the free surfer software and when testing that it is
installed correctly using the examples listed on the website I get a permission
denied message.
How can I go about fixing this?
Attached is the terminal output from try
Can you just paste the message rather than attaching an image?
On 2/4/19 11:33 AM, Jordan Fowler wrote:
>
> External Email - Use Caution
>
> I have recently installed the free surfer software and when testing
> that it is installed correctly using the examples listed on the
> website I g
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Here is the message displayed:
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/sub
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Dear FreeSurfer Developers,
Prior to extracting the gray volume numbers of the entorhinal and
perirhinal cortex from ?h.BA_exvivo.thresh.stats file, I was examining the
entorhinal and perirhinal cortex on the ?h.BA.thresh.annot on
Freeview. However, I
Hi Yi-Leng
the annot file contains the label with the max p-value at each location.
The thresholded .label files are computed to have the surface area that
matches the average of the training labels, so they will not be the same.
cheers
Bruce
On
Tue, 5 Feb 2019, Yi Leng Fung wrote:
Hi Jorgan
do you have read permission for that file/directory? It looks like not
cheers
Bruce
On Mon, 4 Feb 2019, Jordan Fowler wrote:
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Here is the message displayed:
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /A
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Hi Bruce,
How can I get read permission for that file/directory?
Jordan
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Monday, February 4, 2019 12:27:48 PM
To: Freesurfer support li
Hi Jordan
that is something you need to talk to your local sys admin about.
cheers
Bruce
On Mon, 4
Feb 2019, Jordan Fowler wrote:
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Hi Bruce,
How can I get read permission for that file/directory?
Jordan
__
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Hello Bruce,
Thank you very much for your quick response.
I do have another point of confusion regarding the BA.thresh.annot file.
When visualised in Freeview (using Bert as the example), the BA.thresh
annotation file labelled the medially located str
Hi Yi-Leng
can you send us an image of the parcellaton on an inflated surface so we
can see?
thanks
Bruce
On Tue, 5 Feb 2019, Yi Leng Fung wrote:
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Hello Bruce,
Thank you very much for your quick response.
I do have another point of confusion
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Hello Freesurfer experts,
I am interested in running an along the tract analysis with the outputs
from tracula. I am interested in using
https://www.nitrc.org/projects/fadttster/ to do so. I was wondering where
to find the 'arc length' for the fibers a
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Hi all,
I'm hoping to get some input on clustering, multiple correction, smoothing
preferences, and (if available) best practices. Please correct me if I'm
wrong, but it seems that the amount of attention given to multiple
correction and spatial depend
Hi Yi-Leng
eek! Can you verify that the lh.entorhinal_exvivo.thresh.label is
correct? Does it overlay on the perirhinal annotation?
thanks
Bruce
On Tue, 5 Feb 2019,
Yi Leng Fung wrote:
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[3f1a37b0d4514e4a90a5d3340afcefe6c789830e.png?u=328927]
H
thanks. It is almost certainly a bug in recon-all. I'm testing a fix
tomorrow and hopefully we can have one out to you (and the rest of the
list) by tomorrow.
Sorry!
Bruce
On Tue, 5 Feb 2019, Yi Leng Fung wrote:
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[3a1715320c6fbab489126e656ad6e765d
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Thank you!
Cheers,
Yi Leng
On Tue, Feb 5, 2019 at 1:05 PM Bruce Fischl
wrote:
> thanks. It is almost certainly a bug in recon-all. I'm testing a fix
> tomorrow and hopefully we can have one out to you (and the rest of the
> list) by tomorrow.
>
> S
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