05
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields
Oh, now I understand.
Yeah you can add the head, body and tail segments of each subfield to get 6.0
type of measurements ;-)
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and
: Friday 27 August 2021 22:02
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Hippocampal subfields
Dear Erik
I’m not sure I understand. What does your output file look like?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
C
...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez, Juan
E.
Sent: Friday 27 August 2021 22:02
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields
Dear Erik
I’m not sure I understand. What does your output file look like?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior
Dear Erik
I’m not sure I understand. What does your output file look like?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On Aug 27, 2021, at 16:14, Erik O'Hanlon
mailto:ohanl...@tcd.ie>> wrote:
External Emai
External Email - Use Caution
Hi Philipp,
Thank you very much! This was very helpful!
Best,
Yiota
On Mon, Jun 21, 2021 at 3:38 PM Saemann, Philipp
wrote:
> External Email - Use Caution
>
> Hello Yiota,
>
>
> the whole hippocampus value is a sum of all subregions except
External Email - Use Caution
Hello Yiota,
the whole hippocampus value is a sum of all subregions except for the
hippocampal fissure - best try to reproduce this in an example.
The recon-all pipeline also delivers a total hippocampal volume, but it is an
entity/result of its o
n a step directly (both with ""
> empty value and the values below)
..."
Hope to that helps!
Regards,
Chester
--
Message: 4
Date: Fri, 11 Jun 2021 11:43:21 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Hippocampal
edit your Subject line so it is more specific
>> than "Re: Contents of Freesurfer digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Re: Hippocampal Subfields error "no such file or
>> directory"/"dyld library not loaded" (Iglesias Gonzalez, Juan E.)
t; (Iglesias Gonzalez, Juan E.)
> 2. Ill-Conditioned/Badly Scaled Matrix Error (Lurie, Lucy)
> 3. LGI FS 7.1 (Del Re, Elisabetta)
> 4. mri_glmfit with pvr (std...@virgilio.it)
> 5. Re: FW: WM or Pial edits to correct surfaces (Fischl, Bruce)
>
>
>---------
Dear Chester,
What command did you exactly run? There seems to be a mix of T1 and
T1+additionalMRI segmentation commands in there.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
> On Jun 9, 2021, at 00:23, Chester Ka
: Re: Hippocampal Subfields
Okay, Thank you very much Philipp.
Best,
Saurabh
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Saemann, Philipp
Sent: Thursday, April 22, 2021 2:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
: [Freesurfer] Hippocampal Subfields
* External Email - Caution *
External Email - Use Caution
Hi Saurabh,
you have to run (and QC) recon-all before,
Best,
Philipp
Von: freesurfer-boun...@nmr.mgh.harvard.edu
im Auftrag von Jindal, Saurabh
External Email - Use Caution
Hi Saurabh,
you have to run (and QC) recon-all before,
Best,
Philipp
Von: freesurfer-boun...@nmr.mgh.harvard.edu
im Auftrag von Jindal, Saurabh
Gesendet: Donnerstag, 22. April 2021 20:55
An: freesurfer@nmr.mgh
: fsbuild , freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
External Email - Use Caution
External Email - Use Caution
Hi 'E' / 'R',
I even tried changing the resolution to 1.0 with no success rulin
Thank you both! On Linux, 8GB is insufficient, and 16GB is normally
sufficient; I wonder if the requirements are a bit higher on MAC?
Could you please try the following?
1. Edit $FREESURFER_HOME/bin/segmentHA_T1.sh (might require sudo)
2. Replace the line:
set RESOLUTION="0.33
: Ramtilak Gattu
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
Maybe you could let us know if the system integrity protection feature is
turned on the Mac (which is the default). The following command will report if
it is enabled or disabled, e.g., when enabled
ay.com>Sent: Tuesday, March 23, 2021 11:00
PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Ramtilak
Gattu <rg...@med.wayne.edu>Subject: Re: [Freesurfer] Hippocampal
Subfields Segmentation Violation-error [EXTERNAL]I”m wondering if this is
an issue with the version of
00:59:59 EDT 2021
For more details, see the log file
/Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1.log
tilak@tilak Hipps %
From: fsbuild
Sent: Tuesday, March 23, 2021 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu
External Email - Use Caution
I”m wondering if this is an issue with the version of Java installed on the
machine and Matlab. I’ve seen the latest MCR Matlab installer try to make
changes to java installed on a Mac. So maybe updating or re-installing
the Matlab software on your
Hi Steve,
Thank you very much for the interest in our tool!
Q1. Yes, mm^3.
Q2. I’ll defer to Doug Greve (CCed) 😉
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Steve Petersen
Reply-To: Freesurfer supp
with an
older dataset we need to be able to extract the older hippocampal subfields,
starting with the recon-all hippocampal subfields processing.
Thanks,
Emily
Date: Wed, 9 Sep 2020 21:21:41 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Hippocamp
External Email - Use Caution
The whole log message:
#
#@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT
2020
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/
Dear Courtney,
You can safely ignore “This file does not contain MRI parameters”. If the
output files are not created, there must be another error further down. Could
you please send us the whole output?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSA
Dear Hae Won,
Normalizing by ICV and whole hippocampal volume simply attempt to answer two
different questions:
Is the volume of subfield X, accounting for head size, [insert analysis
question here]?
Is the % of hippocampal volume covered by subfield X, [insert analysis question
here]?
(where [a
Dear Ioana,
This is tricky because the volumes are computed from soft segmentations, which
are not the ones you’re editing. In general, editing outputs is a bad idea; it
may be better to simply discard the cases for which quality control fails.
Having said that: if you want to use corrected cases
20 19:07
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal-subfields-T1 error
This email from jiglesiasgonza...@mgh.harvard.edu originates from outside
Imperial. Do not click on links and attachments unless you recognise the
sender. If you trust the sender, add them to your
Dear Aleks,
Please try: chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/*
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Duvnjak,
Aleksandar"
Reply-To: Freesurfer support list
External Email - Use Caution
To clarify, upon copying the entire FreeSurfer 6.0 package to our personal
directory, we have then downloaded the matlab runtime MCRv80 folder to that
directory and the issue does not appear to be the hippocampal-subfields-T1
pipeline accessing that.
: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool
(incl Amygdala) FreeSurfer_dev version
External Email - Use Caution
Dear Juan,
Thank you very much for you answer! However, I ran into another issue using the
new tool: It
External Email - Use Caution
Dear Juan,
Thank you very much for you answer! However, I ran into another issue
using the new tool: It is stated: 'Using the additional scan in
isolation is advised when it is of higher resolution than the T1 while
covering the whole hippocampi an
Hi Rene,
The atlases are slightly different so the outputs will be a bit different. But
the segmentations will indeed be comparable.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Rene Seiger
Re
fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Steve Petersen
Reply-To: Freesurfer support list
Date: Wednesday, 11 December 2019 at 10:28
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Hippocampal subfields: exporti
External Email - Use Caution
Dear Eugenio,
I noticed what was the problem. I used freesurfer dev version with the
following command:
segmentHA_T2.sh
I tried to export the hippocampal and amygdala results of several subjects
with these commands and now everything works fine.
qua
Dear Steve,
Can you please send us:
- The segmentation command you used for a sample subject
- A list of the files under the mri directory for that subject.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on be
Try using this instead
lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz
On 12/4/19 5:09 PM, Marcel Heers wrote:
>
> External Email - Use Caution
>
> Dear all, (dear Eugenio),
>
> I would like to use hippocampal subfields as masks for mri_segstats to
> retrieve intensity values. I am having pro
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
D
Are you using fsfast?
On 9/25/19 7:00 AM, ZZY wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Dear ?0?2Doug??
>
> ?0?2 ?0?2 ?0?2I have a group of multimode MRI data, including functional MRI,
> T1WI and diffusion MRI. We want to analyze the functional and
> structual
glad it worked out
Bruce
On Fri, 13 Sep 2019, 3 6 wrote:
External Email - Use Caution
Hi Bruce,
I checked the alias, I really aliased mv to “mv -i”, and it worked
automatically, after I unaliased.
Thanks for your help.
Best regards,
Guodong
在
2019年9月13日，上午12:00，f
External Email - Use Caution
Hi Bruce,
I checked the alias, I really aliased mv to “mv -i”, and it worked
automatically, after I unaliased.
Thanks for your help.
Best regards,
Guodong
> 在 2019年9月13日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu 写道：
>
> Re: Hippocampal-subfie
Hi Guodong
Hmmm, not sure what is doing that, but my guess is you have mv aliased. Can
you type:
which mv
and see if you have it aliased to "mv -i" or some such?
cheers
Bruce
On Thu, 12 Sep 2019,
3 6 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempt
support list
Date: Friday, 9 August 2019 at 01:19
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields
External Email - Use Caution
Dear /Eugenio,
Here is the log files and all results for one subject as the attachments. I
have run a lots of subjects and all result
External Email - Use Caution
Dear /Eugenio,
Here is the log files and all results for one subject as the attachments. I
have run a lots of subjects and all result directories didn't include
l(r)h.hippoSfLabels-T1.v10.mgz file.
Sincerely,
Zheng
At 2019-08-08 09:49:30, "Ig
Dear Zheng,
Can you please send us the log files?
Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of 郑凤莲
Reply-To: Freesurfer support list
Date: Wednesday, 7 August 2019 at 21:19
To: "frees
pport list
Date: Monday, 17 June 2019 at 10:11
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields error
External Email - Use Caution
Dear Eugenio,
attached you’ll find the picture. Looks as though the left hippocampus has
erroneously been
attribut
) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Mennecke,
Angelika"
Reply-To: Freesurfer support list
Date: Monday, 17 June 2019 at 10:11
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields error
External Email - Use Caution
De
External Email - Use Caution
Dear Angelika,
Can you please send us a screenshot of the inaccurate T1 segmentation?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Mennecke,
Ang
External Email - Use Caution
Dear Wu,
The “templates” are probabilistic atlases with no image intensities. All you
can look at is images like the ones in the top panel of Figure 5 in the paper.
If you want to generate these, let me know and I’ll show you instructions (it’s
a bit
External Email - Use Caution
Thanks, Marcel. Can you please send us the whole output (can be found in the
log file)
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://
External Email - Use Caution
That sounds pretty weird… Did you get any error messages on the Linux server?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmic
http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of 오진영 <
> jinyoung.oh...@gmail.com>
> *Reply-To: *Freesurfer support list
> *Date: *Monday, 30 July 2018 at 09:29
> *To: *Freesurfer support list
> *Su
: Freesurfer support list
Date: Monday, 30 July 2018 at 09:29
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields segmentation error
External Email - Use Caution
Dear Eugenio,
Thanks for your reply.
I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2b
External Email - Use Caution
Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing
eesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Hippocampal Subfields Module, output error
Hi Eugenio,
Thank you for replying so quickly to my lengthy message. I correct some of my
statements,
1. Matlab 8.4 was used (not 8.2)
2. When I ran the cross-sectional subfiel
://cmictig.cs.ucl.ac.uk/
From: on behalf of "Hurtado, Aura
Maria"
Reply-To: Freesurfer support list
Date: Friday, 23 March 2018 at 05:28
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Module, output error
Hi Eugenio,
Thank you for replying so quickly to my lengt
Dear Arsenije
The atlas is encoded in a tetrahedral mesh, so there is no nifti file for it.
Having said that, it is possible to rasterize the atlas at a target resolution.
The command is the following:
kvlRasterizeAtlasMesh $FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz
$FREESURFER_HOME/ave
Hi Aura,
1. What do you mean by “loading Matlab 8.2”? It should be Matlab 8.4 (2014b).
2. “Some still did”: what error did you get?
- Also, I’m confused by what you wrote, that subfields worked but hippocampal
module didn’t (aren’t they the same thing?)
- Finally: can you please send us a screen
Hi Alexis,
Yes please send me the images!
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of Alexis Guyot
Reply-To: Freesurfer support list
Date: Monday
Dear Christian,
They atlas is built using subfield segmentations on scans of older adult
brains, but:
1. it’s also built with whole hippocampus segmentations of scans of subjects of
a wider age range.
2. the deformation model should be able to account for large parts of the
anatomical differenc
Dear Donatas,
I believe that mri_segstats is just counting voxels using the hard
segmentation, whereas the volume in lh.hippoSfVolumes-T1.long.v20.txt is
obtained using a soft segmentation. If you’re interested in this, look up the
WRITE_POSTERIORS option in the wiki.
Cheers,
/Eugenio
--
Juan
Great question!
El 26/10/2017 17:09, "NIELS JANSSEN ." escribió:
> In the mri output folder, I noticed that both the 0.33 mm and 1 mm
> (voxelspace) maps have subfields that do not overlap in space, meaning that
> each subfield occupies a unique location in space that does not overlap
> with oth
Hi Niels,
The code works at .33 mm and ends up with a soft segmentation for each voxel,
i.e., each voxel has a vector of probabilities corresponding to the different
structures. So, they DO overlap. However, we don’t write those probabilities by
default. Instead, we take the most likely label a
Hi Guido,
I think you should wait until recon-all is done. Running 2 recon-all commands
on the same subject simultaneously: a) would need hacking recon-all; b) it’s a
bad idea. Moreover, the subfields make use of wmparc.mgz, which is produced
towards the very end of recon-all -all anyway.
Cheers
2017 11:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability
Hi Prad,
The final probabilities are in the posterior files. There’s no need to binarize
?h.hippoSfLabels if what you’re interested in is the soft segmentations.
Or maybe I’m missing so
:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>>
Sent: Tuesday, March 21, 2017 2:22 PM
To: Freesurfer support lis
genio
Sent: Wednesday, March 22, 2017 11:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability
Hi Prad,
The final probabilities are in the posterior files. There’s no need to binarize
?h.hippoSfLabels if what you’re interested in is the soft segmenta
esurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>>
Sent: Tuesday, March 21, 2017 2:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability
Dear Prad,
There is a “secret” way of getting the
-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez,
Eugenio
Sent: Tuesday, March 21, 2017 2:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability
Dear Prad,
There is a "secret" way of getting the posteriors. You need
Dear Prad,
There is a “secret” way of getting the posteriors. You need to set the
environment variable WRITE_POSTERIORS to 1 before you call recon-all.
In (t)csh:
setenv WRITE_POSTERIORS 1
In bash:
export WRITE_POSTERIORS=1
And then call recon-all -hippocampal-subfields-T1(T2) as usual.
The discr
: Re: [Freesurfer] hippocampal subfields - T1
Hi Batool,
It’s not ideal, but if FreeSurfer does a decent job with the recon, something
decent should come out of the subfields.
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
Hi Batool,
It’s not ideal, but if FreeSurfer does a decent job with the recon, something
decent should come out of the subfields.
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl
Hi Lauri,
it depends on what you mean by template. If you mean an intensity averaged
image, then no. But if you mean probabilities in a reference space, then yes.
You can visualize the atlas with (warning: the viewer is a big buggy):
cd $FREESURFER_HOME/average/HippoSF/atlas
kvlViewMeshCollection
gh.harvard.edu>
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Iglesias Gonzalez, Eugenio
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Monday, February 13, 2017 11:49 AM
To: Freesurfer support list
Subject: Re: [Frees
rvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Iglesias Gonzalez, Eugenio
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Monday, February 13, 2017 11:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields analysis command
Hi Batool
Wh
du
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez,
Eugenio [e.igles...@ucl.ac.uk]
Sent: Monday, February 13, 2017 11:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields analysis command
Hi Batool
What are the contents of hippo.txt? Just empty?
Cheers,
/E
Hi Batool
What are the contents of hippo.txt? Just empty?
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 13 Feb 2017, at 16:41, Rizvi, Batool
mailto:br2...@cumc.col
du>>
namens Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>>
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error
Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virt
ens Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>>
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error
Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine
running o
nstall ...
Sincerely,
Michel hu
Van: freesurfer-boun...@nmr.mgh.harvard.edu
namens Iglesias Gonzalez, Eugenio
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error
Dear
Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine
running on Windows 10?
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 24
Dear Ferdi,
It is really hard for us to know why you‘re getting such a weird error
(segfault of kvlAutoCrop) in a submitted job when you don’t get it in an
interactive session … You will have to look into the peculiarities of the
submission system to see what is changing from one setting to the
Wow, longitudinal segmentation is absolutely awesome! It reduced our
measurement error by more than 30%. I can't wait when the hippocampal
longitudinal segmentation is ready.
By the way, I want to run (cross-sectional) hippocampal subfields on
longitudinal data using additional T2 with lower resol
ok thanks a lot for the quick answer.
let me know when it works.
our mri voxel size is 1 mm isotropic.
(if it changes anything, I am working on ubuntu 14.04).
Cheers,
Pierre
On Wed, Jul 20, 2016 at 11:15 AM, Iglesias, Eugenio
wrote:
> Thanks a lot, Pierre.
> I’ll get this sorted out as soon as
Thanks a lot, Pierre.
I’ll get this sorted out as soon as possible. I’m in the process of modifying
the module so it supports data with resolution >1mm, and also incorporating the
longitudinal segmentation method described in
https://doi.org/10.1016/j.neuroimage.2016.07.020
Cheers,
Eugenio
Jua
Hi,
I downloaded the new freesurfer development version and I still have the
same problem when running the hippocampal-subfields
"Invalid MEX-file
'/tmp/MCR_4195017647/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64':
libkvlGEMSCommon.so: cannot open shared obj
Dear Mojmir,
using ~400 subjects, we found that the subfield module was a bit better than
the ASEG volumes at discriminating Alzheimer’s patients from controls (see the
Neuorimage paper). But, in any case, the difference is small.
Regarding longitudinal segmentation: we just got a paper about thi
Hi Juan,
Thanks! You're right, they really are tightly correlated (although their
absolute values differ by 30%). We tried it on couple of subjects, but
didn't find subfields to be significantly better than aseg stats though. By
the way, is Freesurfer capable of using multiple scans from the same
The MAC version is now fixed as well. It should be available for download in
the next couple of days (Zeke can provide a better estimate).
Thanks again to all of you for your feedback.
/E
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http:/
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
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
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 Kaufman fig
Dear all,
our expert developer Zeke Kaufman figured out what the problem was. We have now
fixed the Linux version; the MAC version will hopefully be ready as well in a
couple of days. I have also fixed other bugs (including the problem that caused
the code to get stuck every once in a while).
Yo
Thanks. Only for FS 6.0 and later, correct?
Jim
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias, Eugenio
Sent: Wednesday, July 06, 2016 9:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields command
.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
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
, Eugenio
[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 the input?
Hi Matt,
Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t
crash when you run
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of pierre deman
Sent: Tuesday, July 5, 2016 7:04:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation
Hi,
I still have a problem as well with the subfields segmentation (ubuntu 14.04,
with the files
Hi,
I still have a problem as well with the subfields segmentation (ubuntu
14.04, with the files .ctf)
Cheers,
Pierre
Hello FreeSurfer Experts,
I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp:
freesu
I could finally look into this. It is indeed weird. The CTF is indeed embedded
in the executable…
Zeke/Nick, 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 27
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 in the executable… I’ll get back to you
as soon as possible.
Cheers,
Eugenio
Juan Euge
I tried that. but didn't work.
Cheers,
Pierre
On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio
wrote:
> 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 Igle
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