-_kJw0wnWXkvlLzMnewj7RVJWE0ZyKP6Te_bsblaEFj0_W9B0HtJv3BHbTIaEK09xDOxjj1HFdS6U6mLna4w/http%3A%2F%2Fwww.jeiglesias.com
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Andrei Bieger
Date: Sunday, July 2, 2023 at 17:27
To: Freesurfer support list
Subject: [Freesurfer] Hippo subfields long
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Hello everyone,
Quick
External Email - Use Caution
Hello everyone,
Quick question.
After running the longitudinal recon-all pipeline, is it required to run
all subjects/tps through the segmentHA before running the segmentHA_long?
If no, since I already ran the segment_HA in a few subjects, if I stop an
0a7a5f.png]
Reply-To: Freesurfer support list
Date: Tuesday, 29 May 2018 at 13:00
To: Freesurfer support list
Subject: Re: [Freesurfer] hippo subfields and amygdala
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Hi Eugenio,
Thanks, I'll give that a try. Just a quick question, the correct ROI id'
http://cmictig.cs.ucl.ac.uk/
From: on behalf of Erik O'Hanlon
Reply-To: Freesurfer support list
Date: Tuesday, 29 May 2018 at 13:00
To: Freesurfer support list
Subject: Re: [Freesurfer] hippo subfields and amygdala
External Email - Use Caution
Hi Eugenio,
Thanks, I'll g
vice: RCSI Strategic Plan
2018-2022<http://www.rcsi.ie/strategy2018>
RCSI LEADING THE WORLD TO BETTER HEALTH
[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
Reply-To: Freesurfer support list
Date: Tuesday, 29 May 2018 at 11:07
To: "freesurfer@nmr.mgh.harvard.edu"
Sub
freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] hippo subfields and amygdala
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Hi FS experts,
I have run my analysis using the dev version and have all the necessary
volume.txt files. As a secondary step, I want to use some of the subfields as
s
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Hi FS experts,
I have run my analysis using the dev version and have all the necessary
volume.txt files. As a secondary step, I want to use some of the subfields as
seed volumes for tractography (using ExploreDTI). I have may diffusion data in
the
Hi Stefano,
When segmenting 1 mm scans, the position of the internal boundaries between the
hippocampal substructures largely relies on prior knowledge acquired from our
ex vivo training data and summarized in our statistical atlas. For this reason,
volumes of internal subfields (especially GC-
Hi list,I'm performing hippo-subfields analysis on T1 having the followed
parameters:
data_type INT32dim1 170dim2 256dim3 256dim4
1datatype 8pixdim11.25pixdim21.00pixdim3
1.00pixdim41.00cal_max
freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, May 20, 2015 9:14:05 PM
Subject: [Freesurfer] Hippo-subfields visualization
Hi list,
I'm using version 5.3 and I have performed hippo-subfields analysis.
A- I'd like to visualize the mask of each subfield on the T1.
In subid/mri, I run th
Hi list,
I'm using version 5.3 and I have performed hippo-subfields analysis.
A- I'd like to visualize the mask of each subfield on the T1.
In subid/mri, I run the command line above:
freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz
-p-labels posterior_right_* posterior_
Hi, Greg
I use to process my subjects with:
recon-all -s subjid -all -hippo-subfields
The -all flag makes the program run all the 3 stages (autorecon1,
autorecon2 and autorecon3) in sequence. Only after this it starts the
hippo-subfields stage. If you do not have any special reason to run each
au
-
From: "Gregory Kirk"
To: "free"
Sent: Thursday, August 7, 2014 5:05:27 PM
Subject: [Freesurfer] -hippo-subfields
we have freesurfer set up on our big condor cluster, i asked that the
-hippo-subfields be added. they have it set up to run in 3 stages
autorecon1 autorec
we have freesurfer set up on our big condor cluster, i asked that the
-hippo-subfields be added. they have it set up to run in 3 stages
autorecon1 autorecon2 autorecon3
they added the flag to all 3, i think it would only be needed on autorecon3,
but don't think it would
cause harm, just be ign
Gari, can you send us the log of the hippo subfield module (or the
screen output; they should be the same)
Cheers,
/Eugenio
On 10/16/2013 10:22 AM, Garikoitz Lerma-Usabiaga wrote:
Hi,
I had a subject already run through recon-all.
After making recon-all -s ID -hippo-subfields
or
recon-all -s ID
Hi,
I had a subject already run through recon-all.
After making recon-all -s ID -hippo-subfields
or
recon-all -s ID -hippo-subfields -make all
it is failing.
It is the first subject ever failing with the hippo-subfields. The rest of
the subjects are ok. This subject is properly segmented (tkmedit
Hi Marcos,
the subfields of the left and right hippocampi are defined on different
voxel spaces. If you want to combine them, you first need to reslice them
to a common voxel space (for instance using -rl in mri_convert)
Cheers,
/Eugenio
On Fri, April 19, 2013 9:57 pm, Marcos Martins da Silva wro
TYVM, Juan Eugenio and Bruce.
I am a neurologist and Professor in Federal University of Rio de
Janeiro. I am confortable with Linux and scripts but, as a physician,
eigenvectors will be really hard. I will try to get some help inside
University. But if I correctly understood, it seems an elegant w
I agree with Bruce. You can use MRIread.m to read in the data.
Regarding the other question: first you need to combine the posteriors
of all the subfields into a single posterior for the whole hippocampus.
You can do that like this:
mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum --o
Hi Marcos
I would do it in matlab. Compute the spatial eigenvectors then divide the
hippocampus up along the primary eigenvector
cheers
Bruce
On Thu, 18 Apr 2013, Marcos
Martins da Silva wrote:
Thank you for your answer, Juan.
Yes, I want a surface of the whole hippocampus and I thought
Thank you for your answer, Juan.
Yes, I want a surface of the whole hippocampus and I thought I had just
obtained that using freeview and adding all hippo-subfield files. That
resulted in the screenshot I previously attached. I just do not know how I
can save the resultant surface.
After I check
Dear Marcos,
> 1- How do I save the combined 3D view I got as a surface?
Do you want a surface of the whole hippocampus? In that case I would
suggest adding up the probability volumes from all the subfields and
thresholding the resulting volume.
> 2-I know the hippo-subifields .mgz files are pr
Hi Inge
I think this is a question for Koen (ccd)
cheers
Bruce
On Fri, 14 Oct 2011, Inge Knudson wrote:
> Hi Bruce et al.,
>
> I have a problem with the -hippo-subfields segmentation not creating some
> files for the left side when I run it on our Linux box located at the
> Martinos Center, w
Hi Bruce et al.,
I have a problem with the -hippo-subfields segmentation not creating some files
for the left side when I run it on our Linux box located at the Martinos
Center, with Freesurfer sourced to /usr/local/freesurfer/nmr-stable51-env.
Specifically, it runs to apparent completion and
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