Hi Fernando,
Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to
take advantage of multiple images with higher resolution, but it hasn’t been
thoroughly tested and it’s not publicly availa
Hi Matt,
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 9 Jun 2016, at 19:31, Matt Glasser mailto:m...@ma-tea.com>>
wrote:
I would be intereste
boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Iglesias, Eugenio
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation
FreeSurfer 6.0 is not available yet, but you can download the development
version to take advantage of this functionality.
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 10 Jun 2016, at 18:10,
Hi!
I actually sent out an email yesterday regarding this. The way that the
subfield module is set up, you cannot take advantage of your full res T1 and
your T1. We are working on a solution.
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.j
after cortical surfaces.
Matt.
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Iglesias, Eugenio"
mailto:e.igles...@ucl.ac.uk>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, June 10, 2016 at 12
If you mean the new subfield module, then the answer is: cubic mm.
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 27 J
Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 27 Jun 2016, at 15:32, pierre deman
mailto:deman.pie...@gmail.com>> wrote:
I tried that. but didn't work.
Cheers,
Pierre
On Mon, Jun 27, 2016 at 4:32 P
Jun 2016, at 15:43, Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
Hi Pierre,
Due to some technical problems, it might take me a couple of days to figure out
what’s going on. But it definitely sounds funny that it is asking for the CTF,
since this is supposed to be embedded
Dear all,
We are working on this; I'll write again when the problem is solved (hopefully
soon!)
Cheers
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: freesu
Hi Jim,
the latter command uses a new, higher resolution atlas based on ex vivo scans.
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 6 Jul 2016, at 15:39, Alexopoulos, Dimitrios
mailto:alexop
.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Iglesias, Eugenio
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Friday, June 10, 2016 3:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of th
I think I identified the problem; hopefully this will be sorted out very soon.
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis
mailto:rpereac
).
You can downloaded the latest development version from our website.
Thanks everyone for your feedback.
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 8 Jul 2016, at 12:14, Iglesias, Eugenio
And thanks to Zeke, of course ;-)
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 13 Jul 2016, at 11:19, Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
Dear all,
our expert developer Zeke K
Hi Mojmir,
ASEG typically gives a larger estimate of the volume, though highly correlated
with that from the subfield package. We have found the measurements from the
subfield package to be a bit more reliable, though.
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University
Dear Fernando,
Are you using the MAC version? I haven’t finished fixing the bugs in that one
yet.
If you’re using the Linux version: Zeke, can you please shed some light on what
the problem might be?
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
ht
://cmictig.cs.ucl.ac.uk/
On 14 Jul 2016, at 10:05, Fernando Pérez-García
mailto:fepe...@gmail.com>> wrote:
I am using Ubuntu 14.04.4.
Please let me know if you need some more info.
Cheers,
Fernando
2016-07-14 10:59 GMT+02:00 Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>>:
Dear F
ake more precise measurements? For
example by using T1 from the same subject / different time instead of T2 in
subfields?
Thanks!
Mojmir
On Wed, Jul 13, 2016 at 5:15 PM Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
Hi Mojmir,
ASEG typically gives a larger estimate of the volume, th
lear (line 11)
Error in segmentSubjectT1_autoEstimateAlveusML (line 133)
MATLAB:invalidMEXFile".
Does anyone have any idea about a solution ?
Cheers,
Pierre
On Wed, Jul 13, 2016 at 12:22 PM, Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
And thanks to Zeke, of course ;-)
Juan Eugenio I
It need to run some additional tests, but I'm almost sure it is solved. The
fixed code will be in the development version very soon, with some other
updates. Stay tuned!
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
h
Hi Daniel,
the problems was that I accidentally compiled the module against dynamic rather
than static libraries. The code will be fixed in the development version very
soon.
Also, I introduced some changes in the code so that it can handle high
resolution T1s, but the behaviour on standard reso
Dear Xiaowei,
That beta version was taken down because it had several problems. I would
recommend that you wait until the next beta comes out (hopefully in 2 weeks or
so), or that you download the development version (in that case, I’d do it next
week because we currently fixing an error I accid
Hi Daniel,
The issue is fixed, but I don’t know if the updated version is already in dev.
Zeke, can you shed some light on this?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 1 Aug 2016, at 1
Dear users,
Many of you have recently experienced problems with the hippocampal subfield
and brainstem substructure segmentation modules. These modules have been broken
in the dev version for a couple of weeks. All the problems have now been fixed
internally. The updates will be incorporated to
You can always run mri_convert with the -rl (“reslice like”) flag to achieve
this. Something like: mri_convert input.mgz output.mgz -rl reference.mgz -odt
float
If it’s a segmentation volume, you should add -rt nearest, in order to use
nearest neighbor interpolation.
Cheers,
Eugenio
Juan Eugeni
Hi Erik,
there’s no FreeSurfer program to do this in a straightforward manner. But you
can:
1. read in the hippocampal subfield segmentation into matlab with the MRIread
function in the $FREESURFER_HOME/matlab directory.
2. extract the major axis with the hippocampus using PCA.
3. Subdivide th
You can! It just makes your results harder to reproduce (running recon-all with
one version, and the subfields with the other).
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 24 Aug 2016, at 17:01, Douglas Gr
Hi Mohamad,
For now, our brainstem module separates this structure into midbrain, pons,
medulla and SCP - please see this link:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
If you want to segment more specific nuclei, we don’t have a tool capable of
doing that yet.
Cheers,
/Eu
Hi Renata,
In general, mixing’n’matching is not a good idea, since different sequences
bias the volumes in different directions. Now, if the differences in sequences
were independent of whether subjects are patients or controls, it wouldn’t be
*that* bad. But, if patients have different sequence
The same one; just change the input file and the analysis ID
- T2: recon-all -s mySubject -hippocampal-subfields-T1T2 myT2scan.nii.gz
T2
- FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 myFLAIRscan.nii.gz
FLAIR
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior Research Fellow
2 + 3D FLAIR). Is that option at all possible
with the available FS version or in the works?
Best,
Jorge
On 05/09/2016 16:13, Iglesias, Eugenio wrote:
The same one; just change the input file and the analysis ID
- T2: recon-all -s mySubject -hippocampal-subfields-T1T2 myT2scan.nii.g
elds (MPRAGE + high res 2D T2 + 3D FLAIR). Is that option at all possible
with the available FS version or in the works?
Best,
Jorge
On 05/09/2016 16:13, Iglesias, Eugenio wrote:
The same one; just change the input file and the analysis ID
- T2: recon-all -s mySubject -hippocampal-su
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