External Email - Use Caution
Dear Daniel,
Such a script doesn’t exist yet (it’s in the to-do list). The reason why it’s
not a straightforward extension of segmentHA_T1.sh is that resampling the
anisotropic T2s to a common space is not a good idea, given the differences in
orient
ou in advance.
Best,
CC
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez,
Eugenio
Sent: Friday, July 26, 2019 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error
External Email - Use Caution
Dear CC,
You need the development version of FreeSurfer, since the amygdala was added to
the atlas after the 6.0 release.
Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesia
from brainstemSsLabels.v10.mgz, I need the real pixel
size of it, than I can calculate the real area size. Many Thanks!
Best
Jackie
On Tue, Jul 16, 2019 at 11:16 AM Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
External Email - Use Caution
Dear Jackie,
You may want
External Email - Use Caution
Dear Jackie,
You may want to use the soft segmentations; you can obtain them by setting the
environment variable WRITE_POSTERIORS to 1 before running the code, see:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
Also: you can obtain t
External Email - Use Caution
Thanks, Antonin.
The ASEG has definitely oversegmented the hippo. Those large regions were ASEG
and the subfield module disagree are mostly partial voluming of the lateral
ventricle and the cerebral white matter or the fimbria, and are thus NOT
hippo
External Email - Use Caution
Dear Antonin,
It is difficult to see what’s going on in the images you sent. Would you mind
uploading the subject, or at least sending us the image without the
segmentation overlaid (and ideally, a sagittal view as well)?
Cheers,
/Eugenio
--
Juan Eug
External Email - Use Caution
1x1x3 is a no-no.
The 1x1x1 FLAIR may or may not help; it’s hard to tell (especially without
seeing the images!).
But I would try both T1 and T1+FLAIR, and see what happens ;-)
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and
External Email - Use Caution
Dear David,
These are all great questions.
ASEG covers more voxels: the segmentations from the HA module are leaner than
their ASEG counterparts (the volumes are very highly correlated, though). This
is because the HA module operates at higher resol
External Email - Use Caution
Dear Gwang-Won,
What version are you using? What’s the output of “recon-all –version”?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Gwang-Won Kim
ar Eugenio,
attached you’ll find the picture. Looks as though the left hippocampus has
erroneously been attributed to gray matter.
Cheers, Angelika
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Iglesias
Gonzalez, Eugenio
Gesendet: Montag
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
Yes! The changes will probably be tiny, though.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Boris Rauchmann
Reply-To: Freesurfer support list
External Email - Use Caution
Dear Jaime,
This is indeed a funny error. The left side runs to completion, and then the
right side dies right away…
Is the problem reproducible? Does it happen with other subjects, too?
Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
Senior research
External Email - Use Caution
Hi Dusan,
Volumes are computed from soft segmentations, which ameliorates the problems
with partial voluming with the surrounding CSF.
Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://
External Email - Use Caution
Dear Zheng,
The reticular nucleus is in the atlas and we use it to fit it to the image, but
its segmentation is not always reliable and that’s why we don’t provide it (nor
its volume).
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
External Email - Use Caution
Dear all,
We are looking for a postdoc in our ERC project, with two main purposes. First,
to improve the 3D histology reconstruction tools that we have been developing
to build an ultra-high resolution atlas of the brain using histology. And
second,
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
Dear Zheng
One of the other developers can help you with Freeview.
But, as a workaround, you can always use an earlier version of Freeview, and
load the lookup table of the Dev version.
Cheers
Eugenio
Sent from mobile, please excuse brevity and typos
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez,
Eugenio [e.igles...@ucl.ac.uk]
Sent: Thursday, April 04, 2019 5:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfield version
External E
External Email - Use Caution
Hi Emily,
You need to download the dev version, but run the subfield/amygdala volume on
cases reconned with FS6.0.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From:
External Email - Use Caution
How about quantifyHAsubregions.sh?
Cheers,
/E
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Daniel Callow
Reply-To: Freesurfer support list
Date: Monday, 1 April
External Email - Use Caution
Dear Daniel,
This is weird. Can you please send us
lh.hippoAmygLabels-T1.long.v21.*.mgz
for a sample subject?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on b
Laboratory (CSAIL)
Massachusetts Institute of Technology
Lecturer on Radiology
Harvard Medical School
http://www.jeiglesias.com
From: Valentina Mancini
Date: Wednesday, 27 March 2019 at 10:08
To: "Iglesias Gonzalez, Eugenio" , Freesurfer support
list
Subject: Re: [Freesurfer] Con
gt; Sent from mobile, please excuse brevity and typos
>
>
> From: Valentina Mancini
> Sent: Wednesday, March 27, 2019 5:56:34 AM
> To: freesurfer@nmr.mgh.
: Wednesday, March 27, 2019 5:56:34 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Iglesias Gonzalez, Eugenio
Subject: Conversion of thalamic nuclei labels
Dear all,
I ran the thalamic segmentation implemented in FreeSurfer and, according to
visual inspection, I got nice results with a good delineation of
External Email - Use Caution
Dear Zheng,
Did the segmentation run to completion?
Can you please send us the output?
Cheers
Eugenio
Sent from mobile, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of 郑凤莲
External Email - Use Caution
Hi Daniel,
Can you please give us some more information? How did you call the script? Did
you get any other output? Did the running case complete without errors?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical
External Email - Use Caution
Dear Antti,
There’s no specific longitudinal version of the thalamic nuclei yet (hopefully
one day…)
You could naively segment the subjects in a cross-sectional fashion, but I’d
highly recommend that you run the main longitudinal stream first
(https:
External Email - Use Caution
Dear Zheng,
You’ll need a more recent dev version to use the thalamic nucle segmentation.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
Research staff
Martinos
External Email - Use Caution
Dear Yixin,
Yes, give segmentHA_T1.sh a shot. You need to install the development version
of FreeSurfer, though.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
External Email - Use Caution
Dear Manoj,
First question:
The one without the suffix is defined at higher resolution, on a voxel grid
that does not correspond to the standard FS space (where norm.mgz, aseg.mgz,
etc. live).
The one with the suffix lives on the voxel grid of norm.m
External Email - Use Caution
Thanks, Yixin.
It just ran to completion on my machine with FreeSurfer 6.0. Let me know if you
want me to send you the output.
Did you notice this problem on other subjects?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre
External Email - Use Caution
Thanks! Can you please upload one of the subjects that fail?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
Research staff
Martinos Center for Biomedical Imagin
External Email - Use Caution
Hi Yixin,
Does this happen for all subjects, or only one?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
Research staff
Martinos Center for Biomedical Imaging
M
External Email - Use Caution
Thanks a lot for your email, Saskia.
Does this happen for more than one subject? Can you reproduce the error?
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
Research
Hippocampal Subfields - error during
segmentation {Disarmed}
External Email - Use Caution
Version 6.0
Thanks,
Rachel
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez,
Eugenio
Sent: Monday, January 7, 2019 2:50:57 AM
To
External Email - Use Caution
Hi Rachel
This is very weird. What exact version are you using? 6.0 or dev?
Cheers
Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
Research staff
Martinos Center for Biomedi
External Email - Use Caution
Dear Corinna,
The reason for this is that the volumes correspond to two different analyses.
The volumes from the two sources are highly correlated, though, so it shouldn’t
make almost any difference to use one or the other – but it you’re doing any
an
y, 10 December 2018 at 16:31
To: "freesurfer@nmr.mgh.harvard.edu"
Cc: "Iglesias Gonzalez, Eugenio"
Subject: Classification of amygdala subregions using Freesurfers new Algorithm
Dear Eugenio and experts,
I have run the segmentation of the hippocampus subfields and nuclei of the
External Email - Use Caution
Dear K
1. No
2. No, just the subject name; the subjects directory is specified separately.
3. Points at a file.
4. Yes.
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University C
External Email - Use Caution
Nope, please don't rerun the recon-all with dev. Just run the hippo+amyg module
on the 6.0-reconned data.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
External Email - Use Caution
Dear Arkadiy,
Technically you should do it after, but the changes will be tiny, so it’s
probably fine to do it before (as long as you’re consistent across subjects).
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Im
data of patient A to recon-all and T2 data
of another patient B to segment ?
Thank you very much.
Confused beginner.
Qimo
At 2018-11-26 23:45:17, "Iglesias Gonzalez, Eugenio"
wrote:
External Email - Use Caution
Dear Qimo,
You do need a T1 volume
External Email - Use Caution
Dear Qimo,
You do need a T1 volume to run the main recon-all; sorry if the wiki wasn’t
clear enough. It is true that segmenta_T2.sh only uses the intensities of the
FLAIR scan, but a recon-all processed T1 is still necessary.
Cheers,
/E
--
Juan Euge
External Email - Use Caution
Dear Zhac,
Apologies for the mistake in the wiki. As explained in the error message, the
subjects directory is the second argument. Also, if you are using a T2 scan, I
would replace t1 by t2 in the last argument.
The call should be:
(For a T1 addition
External Email - Use Caution
Hi Erik,
If you render labels >7000, you shouldn’t see a rendering of the subfields –
but they will indeed remain visible in the orthogonal views. If you want to get
rid of them, you can use mri_threshold:
mri_threshold
lh.hippoAmygLabels-T1-HippoAMY
External Email - Use Caution
Hi Niels,
There is, but not in the short term. For the time being, you can run the module
on longitudinally processed subjects.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biome
External Email - Use Caution
Hi HSK
We use it in the model fitting but do not segment it due to the absolute lack
of contrast with the white matter.
Kind regards,
Eugenio
--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedic
External Email - Use Caution
Hi Jaime,
Can you please send us the output you get between calling the command and the
error?
Cheers,
/E
--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College Lo
External Email - Use Caution
It seems it could be a version conflict. Please try unsetting DYLD_LIBRARY_PATH.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http
sue, ERROR: cannot find transform
file
Hi,
Looks like the input is a multi frame image. Should only be single frame.
Best Martin
On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
It seems like a problem with mri_robust_register.
Martin, any ideas?
External Email - Use Caution
Dear J
How much RAM memory do you have?
Andrew: do you think this might be the problem?
Cheers
E
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of 오진영
Se
External Email - Use Caution
Dear Lauren,
This is a very interesting question!
Site harmonization matters aside (there’s a vast literature on it), whether you
correct by ICV or whole hippocampal volume essentially answers to different
questions:
- ICV: you’re asking whether there
External Email - Use Caution
No worries! Your LD_LIBRARY_PATH configuration made my day 😃
--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com
From: on b
External Email - Use Caution
It seems like a problem with mri_robust_register.
Martin, any ideas?
--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com
From
for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: Niels Bergsland
Date: Wednesday, 10 October 2018 at 15:42
To: "Iglesias Gonzalez, Eugenio"
Subject: Re: [Freesurfer] Disjointed thalamic nuclei segmentation
Hi Eugen
External Email - Use Caution
Thanks, Niels.
I suspect the problem is that, for some reason, such voxels have much brighter
intensity than their surroundings, and are classified as white matter /
reticular nucleus. But that shouldn’t be happening that far from the lateral
boundar
.
- Regarding the second question: it is a really good one. Would you mind
posting it on the FreeSurfer list? Short answer is: same machine.
Best
-- Forwarded message -
From: Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>>
Date: mié., 10 oct. 2018 a las 11:53
Subje
External Email - Use Caution
Hi Vasudev,
What lookup table are you using to visualize the results? Are you using
FreeView from the development version, and visualizing the segmentation with
the default lookup table?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Centre for Medical
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://
with the additional high
resolution scan works!
Thank you for all the help!
Pradeep
On Thu, Oct 4, 2018 at 11:28 AM Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
External Email - Use Caution
Thanks!
Did you check whether the T2 and the T1 were correctly registere
External Email - Use Caution
Hi Sally,
It is indeed the linear registration used to initialize the atlas deformation
that is going crazy. Do you think you could upload the subject, so we can take
a look?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre
scan
ERROR kvlGEMSMatlab
External Email - Use Caution
I have tried this for two subjects and got the same error.
Thanks,
Pradeep
On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
External Email - Use Caution
Dear Pradeep,
D
External Email - Use Caution
Dear Pradeep,
Did you get this error on several subjects, or only one?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.
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
London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: "Dr Rajendra Morey, M.D."
Date: Monday, 1 October 2018 at 21:53
To: "Iglesias Gonzalez, Eugenio" , Freesurfer support
list
Subject: RE: [Freesurfer] amygdala segmentation atlas influence
Hi Eugenio
Thanks
, 30 September 2018 at 22:15
To: Freesurfer support list
Subject: Re: [Freesurfer] cannot stat volumesAmygdala.txt
External Email - Use Caution
Hi
it is
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
John
On Sun, Sep 30, 2018 at 2:50 PM Iglesias Gonzalez, Eugenio
External Email - Use Caution
Dear Raj,
A few years ago, we published a paper on how Monte Carlo sampling could be used
to quantify this. Unfortunately, the method was incredibly slow and difficult
to tune, and the performance gain was tiny, so we never put it in FreeSurfer.
But
External Email - Use Caution
Hi Jon,
What exact version are you using? Is it a recent development version?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmic
External Email - Use Caution
Hi Carme,
This has to do with the CentOS version.
Please try the version compiled on CentOS6 (that should fix the problem).
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University Colleg
the log file
/Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log
What could be the problem?
Thanks in advance,
Best wishes,
El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio
(mailto:e.igles...@ucl.ac.uk>>) escribió:
External Emai
External Email - Use Caution
Hi Miguel Angel,
This bug was recently fixed in the dev version. If you download the most recent
one, you won’t have this problem.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
Universit
External Email - Use Caution
Hi Niels
5.1 should do but please let us know if it doesn't!
Cheers
E
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Niels Bergsland
Sent: Wednesday, S
-dev.tar.gz
Thanks in advance,
Best,
El mar., 11 sept. 2018 a las 17:47, Iglesias Gonzalez, Eugenio
(mailto:e.igles...@ucl.ac.uk>>) escribió:
External Email - Use Caution
Dear MA
Please download the latest dev version and the command will be there
Cheers
Eugenio
Sent from my
External Email - Use Caution
Dear MA
Please download the latest dev version and the command will be there
Cheers
Eugenio
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Miguel Ángel R
Very much appreciated.
Cheers
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez,
Eugenio
Sent: 10 September 2018 18:00:20
To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
Subject: Re: [Freesurfer] Using the new Tha
External Email - Use Caution
Hi Vinny,
The anatomical definitions can be found in the paper, which is open access (see
Table 2):
https://www.sciencedirect.com/science/article/pii/S1053811918307109
Kind regards
Eugenio
Sent from my phone, please excuse brevity and typos
Fr
External Email - Use Caution
Hi Jinyoung
Sorry for the slow response but I'm traveling these days
I believe this is a bug that was fixed in the dev version 2-3 weeks ago. Would
you mind trying the latest dev, and checking whether that solves the problem?
Cheers
Eugenio
Sent from
External Email - Use Caution
Dear Erik,
Installing only the thalamic tool is technically possible but requires a level
of hacking that i don't want to encourage or support ;-)
Please install the new dev on a separate directory, and make FREESURFER_HOME
point to that the directory
External Email - Use Caution
Um this is an empirical question. I would try with and without, and then
decide.
Cheers
Eugenio
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alexo
is all log file within
script directory. Would you please help me to figure out what was wrong?
Thank you so much
Best wishes
Shize
在 2018-08-24 15:50:44,"Iglesias Gonzalez, Eugenio" 写道:
External Email - Use Caution
I am really confused. There are no errors in the subfield
:08:35,"Iglesias Gonzalez, Eugenio" 写道:
External Email - Use Caution
Thanks! Can you please send us the log of the hippocampal subfield
segmentation? It should be in the same directory as the recon-all log.
Cheers,
/E
Juan Eugenio Iglesias
Centre for Medical Image Compu
External Email - Use Caution
Hi Eugenio,
Yes, If I run without the hippocampal subfield flag. Recon-all complete without
any error. So I am confused what is wrong with this.
Thank you
Shize
在 2018-08-24 00:02:32,"Iglesias Gonzalez, Eugenio" 写道:
External Email - Use C
External Email - Use Caution
Hi Shize,
Does recon-all complete when you run it without the hippocampal subfield flag?
It doesn’t look like an error in the subfield module to me …
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computi
External Email - Use Caution
Hi Ryan,
Is it possible that you're mixing versions of FreeSurfer in your PATH and/or
LD_LIBRARY_PATH? Maybe you could try unsetting them before you source
FreeSurfer?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Centre for Medical Image Computing (CM
External Email - Use Caution
Dear Antonin,
Thanks again for letting us know you had this problem; it turned out to be a
small, silly bug in the code. I will fix it ASAP, and the updated code should
be on the dev version in the next few days.
Cheers,
/Eugenio
--
Juan Eugenio Igle
External Email - Use Caution
Without having seen your FLAIR scans, I’d say probably not, but it’s an
empirical question; give them a go! ;-)
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesi
External Email - Use Caution
Dear Antonin,
Can you please send me a listing of the files in:
/hydra-db/hydra_io/vypocty/freeSurfer/A_analysis_HPC_PFC/A_links_all/ESO_C00577_20160303_1246_1/tmp/hippoSF_T1_v21_right/
Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Researc
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Hi Jamie,
It’s a message from mri_robust_register in the initialization of the atlas
position. If the finaloutput looks reasonable (which it mostly likely will),
don’t worry too much.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fell
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Dear FreeSurfer users,
It is my pleasure to announce that our new tool to segment the thalamic nuclei
from structural MR scans is available in the development version of FreeSurfer.
The tool relies on an atlas derived from manual annotations made on
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Hi Sophie. No output is better than the other. If you have run all your
subjects with both, I'd say to take the average!
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
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Dear Vasudev,
It is expected that you get different volume estimates with different atlases
(FreeSurfer vs CobraLab), as the manual delineation protocols that were used to
create them are very different (e.g., see Yushkevich et al., NeuroImage, 2015).
+09:00 Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>>:
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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 Iglesia
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
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Dear KT,
They range from 8100 to 8300.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of
egmentHA_T1.sh
subject003", it's well done! When run
Thanks,
Fiona
-- ???? ------
??: "Iglesias Gonzalez, Eugenio";
: 2018??7??18??(??) 8:35
??: "Freesurfer support
list";"Freesurfersupport
list";
:
ys. No error reported here.
Thanks ,
Fiona Ding.
-- --
??????: "Iglesias Gonzalez, Eugenio";
: 2018??7??18??(??) 7:29
??: "Freesurfer support list";
: Re: [Freesurfer] Re??segmentHA_T2.sh
External Email -
External Email - Use Caution
Thanks, Fiona.
Is the error reproducible? Does it always die at the same step? Do you get the
same problem with other subjects?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University C
External Email - Use Caution
Weird! Maybe you ran out of RAM memory?
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of 墨初
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