I would segment the T2s, but using the longitudinally processed T1s/subjects.
Unless the T1s are high-res. Then, segment the T1s ;-)
--
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: Frees
Dear Daniel,
Is this Linux or MAC? It looks like a mix to me.
Cheers,
/Eugenio
--
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: Sunday, 4 August 2019 at 15:
Dear Jessica,
There is no intensity image associated with the atlases, so this is not trivial.
I guess you could register your subjects to the atlas, and propagate the hard
segmentations?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http:/
Dear Jessica,
You can register your image to the atlas, and then apply the same transform to
the segmentations (“propagate”). That will bring the segmentations to atlas
(Brainnetome) space.
I hope this helps,
/E
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT
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
Ouch. Is the aseg also like that?
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: Thursday, 8 August 2019 at 08:20
To: Freesurfer support list
Please try using the 1mm version of the segmentation in FreeSurfer space.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Jessica Bourgin
Reply-To: Freesurfer support list
Date: Thursday, 8 Au
directories didn't include
l(r)h.hippoSfLabels-T1.v10.mgz file.
Sincerely,
Zheng
At 2019-08-08 09:49:30, "Iglesias Gonzalez, Juan E."
wrote:
Dear Zheng,
Can you please send us the log files?
Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL)
Dear Jamie,
Sorry for the late response; I was on vacation.
If I’m understanding correctly, the file without “surnames” is what you need:
[lr]h.hippoAmygLabels-T1.v2x.mgz.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.
Dear Chris,
Can you please send us the output txt file?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Krzysztof Gbyl
Reply-To: Freesurfer support list
Date: Wednesday, 18 September 2019 at 08:4
Dear Liwen,
We rebuilt the atlas and there were also minor changes in the code, so the
volume won’t be exactly the same.
Having said that, if you plot 6 vs dev volumes, they should be highly
correlated.
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
Dear Zhiyong,
We currently do not provide such metrics.
Kind regards,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of ZZY
<799057...@qq.com>
Reply-To: Freesurfer support list
Date: Thursday, 26 September
Dear CC,
Did you source FreeSurfer at
/g5/dcn/freesurfer_testing/HippoSegment_Test/freesurfer/ ?
setenv FREESURFER_HOME
/g5/dcn/freesurfer_testing/HippoSegment_Test/freesurfer/
source $FREESURFER_HOME/SetUpFreeSurfer.csh
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (U
Dear Frederic,
I’ll defer to Jean Augustinack (CCed) for a more granular answer (pun
intended), but here are my initial thoughts.
1. You can find the definition in Table 2 of the paper, which is open
access: https://www.sciencedirect.com/science/article/pii/S1053811915003420
2. Yes.
3.
Dear Ola,
This looks like a very ugly error but someone experienced something similar in
the past and it turned out to be a permissions problem.
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+FS6.0%5C-dev+%5C%28Jun27%2C+2018%5C%29
deployrc," or "matlabrc," and I don't know where to begin to look. Please let
me know if you have any suggestions!
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez, Juan
E.
Sent: Thursday, October 10, 2019 3:0
Dear Larissa,
What do you mean by " anatomical ROI Analysis "?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On 08/11/2019, 22:21, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Larissa Bechtle" wrote:
Dear Isabella,
You need to download the development version to run segmentHA_T1.sh. However,
you do not need to rerun your subjects through the development recon-all (in
fact, you should *never* do that).
If/when you write a paper, you would state that you used FS 6.0 to recon the
cases, and the
Dear Daniel,
I’ll defer to Jean Augustinack (CCed) on this one.
Cheers,
/Eugenio
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: Thursday, 14 November 2019 at
Forwarding Jean’s response:
Hi Daniel,
We used specific anatomical landmarks, visually inspecting the hippocampal
head and body in an anterior-posterior direction. Once the uncus (the
medial most region in the hippocampus) ends posteriorly, it is considered
hippocampal body. The hippocampal body
Dear Dalton,
Did you install the Matlab 8.4 runtime as explained in the wiki?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Dalton Bermudez
Reply-To: Freesurfer support list
Date: Thursday, 21
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
Dear Naveed,
You need the development version; these files are not given by FreeSurfer 6.0.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Muhammad Naveed
Iqbal Qureshi
Reply-To: Freesurfer suppo
Please try:
segmentThalamicNuclei.sh 4001
/Applications/freesurfer_dev/freesurfer/subjects/
/Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii
T2_THALAMUSt2
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://
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
Yes, you should be following the instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
rather than the wiki page for 6.0 here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
Dear Meena,
Running the dev version of recon-all is a really bad idea, as your results will
not be reliable or reproducible.
I would use dev for the hippo/amygdala substructures and then switch back to
6.0.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and
Dear Wisteria,
Did you run the command segmentHA_T1.sh on those subjects using the development
version?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Deng, Yushan
Wisteria"
Reply-To: Freesurfe
other ideas what the possible cause might be?
Best,
Wisteria
Date: Tue, 7 Jan 2020 09:05:32 +0000
From: "Iglesias Gonzalez, Juan E."
mailto:jiglesiasgonza...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Amygdala Segmentation T1.v20 Command
To: Freesurfer support list
mailto:freesur
n T1.v20 Command
Hi Eugenio,
Please see attached for the list of files. Thank you so much for your kind help!
Best,
Wisteria
Date: Wed, 8 Jan 2020 08:12:04 +0000
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Amygdala Segmentation T1.v20 Command
To: Freesurfer support li
Dear Gabor,
It’s all about the physical coordinates, so (b) is the right answer!
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Gabor Perlaki
Reply-To: Freesurfer support list
Date: Saturday, 11 January
Yes!
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of sara ponticorvo
Reply-To: Freesurfer support list
Date: Tuesday, 14 January 2020 at 17:45
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Thalamus
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
Dear Dawn,
Thank you very much for your interest in the tool, but we do not have such a
dataset, sorry! Having said that, I don’t think the alveus should make a big
difference in Dice scores…
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www
the amygdala
in the first place? Or is it mandatory to have both structures fully covered
within the additional scan when I want to run it in isolation?
Thank you very much,
René
<http://www.meduniwien.ac.at/neuroimaging/>
<http://www.meduniwien.ac.at/neuroimaging/>
Am 23.01.2020 um
That is correct, Tegan! And welcome to FreeSurfer ;-)
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Tegan Hargreaves
Reply-To: Freesurfer support list
Date: Tuesday, February 11, 2020 at 14:55
To: "'freesurfe
Kaixo, Teresa.
Yes, you would simply sum CA1-body + C1-head to get what used to be CA1 in
FreeSurfer 6.0.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On 2/18/20, 05:57, "freesurfer-boun...@nmr.mgh.harvard.e
Dear Victor,
That’s a good question!
We inform the estimation of the gray matter intensities with the median of the
voxels segmented as GM in the main stream. Because the median is a robust
statistic, the thalamic nucleia and hippocampal subfields should be fine. But
yes, you’re definitely bette
Hi Flavia,
Did the hippo subfield routine complete successfully? Are the outputs in the
mri directories of the subjects? Did you look at the log files of the subfield
routine?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.co
Please try:
sudo curl
"https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2014bMAC.tar.gz";
-o "runtime.tar.gz"
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: o
Dear Alex,
Can you please try this?
https://uk.mathworks.com/matlabcentral/answers/196961-why-do-i-receive-fatal-error-on-startup-unable-to-start-the-jvm-because-of-a-bad-java-option-or-un
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jei
Dear Casey,
We don’t really have an easy way to work with meshes, so please understand that
the support we can provide is limited.
But if you’re feeling very adventurous: before running segmentHA_T1.sh, set the
environment variable WRITE_MESHES to 1, and you’ll get three new files per
hemisphe
Hi Pascale,
This is a weird one, particularly since it run the first part, apparently
without errors.
Can you please send us:
1. The recon and hippocampal log files.
2. The exact dev version, and information on your system (MAC/Linux,
version, etc)
Cheers,
/E
Juan Eugenio Iglesias
Senior
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
Same as in 2018, I’ll resort to Andrew here :-)
Andrew, any ideas?
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Chester Kang
Reply-To: Freesurfer support list
Date: Sunday, March 29, 2020 at 18:54
To: "frees
e Mar 24 15:09:46 EDT 2020
#@#%# recon-all-run-time-hours 0.001
recon-all -s Sub_42 finished without error at Tue Mar 24 15:09:46 EDT 2020
Hopefully someone has an idea of what could be done next. Thanks!
All the best,
Alex
On Sun, Mar 22, 2020 at 10:57 AM Iglesias Gonzalez, Juan E.
mailto:jiglesi
sn't pointed to
downloading a version of Java. I do have Java on the MAC I'm using, but the
error "unable to start JVM because of a bad java option" still appears. Any
other ideas on how to fix this?
Thanks,
Alex
On Mon, Mar 30, 2020 at 10:12 AM Iglesias Gonzalez, Juan E.
mailt
Dear Devika,
The command is longHippoSubfieldsT1.sh. You can find the instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From
It should be fine but please make sure you correct by scanner in subsequent
analyses.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Kate Marvel
Reply-To: Freesurfer support list
Date: Tuesda
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
Hi Veronica
Did you source FreeSurfer?
After that, the command would be:
segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Parisi Veroni
Hi Steve,
It looks good except for using the mean eTIV of the subgroup. Please use the
global average or don’t multiply by anything at all.
Multiplying by the global average has the cosmetic effect of giving you a
volume that is the range of subiculum volumes (rather than fractions <<< 1),
but
No no sorry for the misunderstanding. Either you correct by division with
subic_vol = average_eTIV_allsample * subic_vol / eTIV_subject
OR y0ou correct by regression. Only if you do regression, I’d use (eTIV_subject
- average_eTIV_allsample) rather than eTIV_subject directly (and the same for
all
Dear Qi,
The correct syntax is that of your First try, but I’m very surprised you got
that error, as we fixed this a while ago… Can you please send me the complete
output?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.
ng.v21_left
SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1
Best,
Qi
On Wed, Apr 29, 2020 at 3:23 PM Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza...@mgh.harvard.edu>>
wrote:
Dear Qi,
The correct syntax is that of your First try, but I’m very surprised you got
that error, as we f
individual from the control group. Here
attached the error script I described. Sorry for the confusion.
Best,
Qi
On Wed, Apr 29, 2020 at 5:47 PM Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza...@mgh.harvard.edu>>
wrote:
Wait but this isn’t the error your first described…?
Juan Eugenio
ith errors
External Email - Use Caution
Hi Eugenio:
recon -all --version
freesurfer-linux-centos6_x86_64-dev-20180509-5a99f28
operating system: Linux
Best,
Qi
On Thu, Apr 30, 2020 at 12:06 PM Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza...@mgh.harvard.edu>>
wrote:
This
.
Thank you so much!
Best,
Qi
On Thu, Apr 30, 2020 at 1:38 PM Zeng, Qi
mailto:qi.z...@icahn.mssm.edu>> wrote:
Thank you so much. I will upgrade the dev and run it again, fingers crossed.
Best,
Qi
On Thu, Apr 30, 2020 at 1:25 PM Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza...@mgh.h
Dear Soichi,
Can you please double check that you’ve got writing permissions on your subject
directory?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Soichi Hayashi
Reply-To: Freesurfer support lis
ala
subfields again. Error message indicates:
"Error in SegmentSubfieldsT1Longitudinal (line 1795)". I have attached the log
file.
Can you help figure this out?
Thank you so much !
Best,
Qi
On Fri, May 1, 2020 at 1:35 PM Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza...@
s. Missing right
hemispheres for all.
Best,
Qi
On Mon, May 4, 2020 at 12:44 PM Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza...@mgh.harvard.edu>>
wrote:
Dear Qi,
I’m really sorry you’re running into all these problem.
We’ll look into it and get back to you asap
Cheers,
/Eugenio
Juan
Dear Sneha,
We use cortical and white matter parcels in the hippocampal subfields, which is
more reliable than using the whole white / gray matter to compute parameters.
But it could be hacked, albeit it would be a bit less reliable. I’ll add this
to the wishlist / to-do list (unfortunately it i
Uuummm this is funny. A directory “hippoSF_T1_v21_left” should have been
created under tmp, but it isn’t there. Are you sure you have writing
permissions for the subject directory?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesia
Dera Elisabetta,
Can you please give us some more detail on what you mean by “I am trying to
translate the same subdivision to MRI acquisition for spectroscopy purposes.”?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
F
Dear Vanessa,
1. No changes were made in the hippocampal module between 7.0 and 7.1, so
you don’t need to rerun (as the subjects were reconned-all with 6.0, which
doesn’t have any problems).
2. Yeah it may not be as easy to reproduce as running everything with the
same version, but it’s p
Dear Baris,
It’s hard to tell without seeing images… Would you mind sharing a scan?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of barış genç
Reply-To: Freesurfer support list
Date: Sunday, May 24,
Hi Elizabeth,
segment_T1.sh uses a bunch of files in native space for initialization that
you’d also have to deform, if you wanted to run it in MNI space.
I think the easiest would be to run it in native space, and then warp the
segmentation to MNI, using e.g., the registration given by CVS.
Chee
Dear all,
The Laboratory for Computational Neuroimaging (LCN) is seeking to fill a
postdoctoral position in image analysis as part of an exciting NIH project
titled: “Open-source software for multi-scale mapping of the human brain”,
awarded to Drs. J. Eugenio Iglesias and Bruce Fischl as part o
Dear Qi,
You can try:
mri_threshold -U [lr]h.hippoAmygLabels-T1.v21.mgz 300
[lr]h.hippoLabelsNoAmyg-T1.v21.mgz
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Zeng, Qi"
Reply-To: Freesurfer support list
Da
ugh?
Best,
Qi
On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza...@mgh.harvard.edu>>
wrote:
Dear Qi,
You can try:
mri_threshold -U [lr]h.hippoAmygLabels-T1.v21.mgz 300
[lr]h.hippoLabelsNoAmyg-T1.v21.mgz
Juan Eugenio Iglesias
Senior research fellow
CMIC
urfer] Get hippocampus segmention from
[lr]h.hippoAmygLabels-T1.v21.mgz
External Email - Use Caution
Thanks. I was wondering If there is another way around to get the amygdala mgz.
Best,
Qi
On Fri, Jun 5, 2020 at 2:44 PM Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza...@mgh.harvard.ed
It totally looks like you don’t 😉
Did you rn the command as superuser (with sudo)?
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Yann Quidé
Reply-To: Freesurfer support list
Date: Thursday, June 11, 2020 at 0
Dear Julien,
Thanks for your very interesting email! One thing at the time:
At each voxel, the discrete segmentation is given by the label with the highest
probability. Therefore, there is no fixed threshold. One voxel my require a
probability of 0.51 to "win" (if another class has probability
ilto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of "Iglesias Gonzalez, Juan E."
<mailto:jiglesiasgonza...@mgh.harvard.edu>
Reply to: Freesurfer support list
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 28 May 2020 at 10:20 pm
To: Freesurfer support li
Dear Victor,
Sorry for the slow response.
1.5 T is not a problem.
Do you have a companion 1mm T1?
If no: then the main problem is the main recon stream.
If yes: what is the in-plane resolution and orientation? If it’s a high-res
coronal, it may help with the subfields. For the thalamus, I’d just u
I'm assuming
the thickness is 1.5). I am told that the fov is 240, but I'm not sure how I
can confirm.
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez, Juan
Dear Jenna,
1.Manually editing aseg.mgz fixes the initialization (super important).
2.Manually editing wmparc.mgz fixes the intensity priors (less important, but
still important)
If it’s only 1 subject in a bigger study, I’d probably call it a QC fail and
leave it out.
If it’s a single case you’r
opy the HC from
aseg.mgz to wmparc.mgz? Can you clarify what you mean by "you still need to fix
the surrounding labels"?
Thank you,
Jenna
Message: 3
Date: Tue, 7 Jul 2020 20:53:12 +0000
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfie
y what you mean by "you still need to fix
the surrounding labels"?
Thank you,
Jenna
Message: 3
Date: Tue, 7 Jul 2020 20:53:12 +0000
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: Freesurfer support list
Messag
Dear GZ,
The atlas lives in its own space, and it is hard to register to MNI because it
only describes probabilities, and not image intensities. But you could try
registering your subjects to MNI, propagating the thalamic segmentations, and
analyzing the data in that coordinate frame.
Cheers,
/E
I had no idea they had added the FreeSurfer thalamic nuclei; thanks a lot for
the pointer!
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Zeng, Victor
(BIDMC - Keshavan - Psychiatry)"
Reply-To: Freesurfer sup
This has happened to a number of my subjects but I have
finished editing the HC label in their aseg files. How would I copy the HC from
aseg.mgz to wmparc.mgz? Can you clarify what you mean by "you still need to fix
the surrounding labels"?
Thank you,
Jenna
Message: 3
Date: Tue
ail%2ffreesurfer%2fattachments%2f20200703%2f7658d9da%2fattachment%2d0001.html&umid=EF661599-A989-D805-85ED-26495DA1044B&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-81a2656a4617dc3904e9b2831c302cc681ec2133>
--
Message: 3
Date: Fri, 3 Jul 2020 13:52:38 +
Fr
rounding labels"?
Thank you,
Jenna
Message: 3
Date: Tue, 7 Jul 2020 20:53:12 +
From: "Iglesias Gonzalez, Juan E."
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: Freesurfer support list
Message-ID: <85489126-5dc1-4464-810b-01a7e8258...@mgh.harvard
Hi Jenna,
Would it be posible for you to share the subject? This is very weird.
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Jenna Katherine
Blujus
Reply-To: Freesurfer support list
Date: Monday,
Hard to tell, Jenna!
Please do upload a sample subject using the instructions in the wiki, and I’ll
take a look.
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Jenna Katherine
Blujus
Reply to: Freesur
Dear HR,
You can run the FS7 substructures on data reconned with 6.0. It's not ideal in
the sense that the results are a bit harder to reproduce, but definitely doable
(as long as you report it in the papers your write!). The results will indeed
be slightly different than if you ran the whole th
Dear Angel,
It’s hard to tell without seeing the segmentation in 3D. Would you mind
sharing, please?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Angel Hammond
Reply-To: Freesurfer support l
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 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 HW,
What was the exact command you ran?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Haewon Roh
Reply-To: Freesurfer support list
Date: Wednesday, August 19, 2020 at 03:26
To: "freesurf
ny file was not made after this command.
On Aug 19, 2020, at 10:18 PM, Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza...@mgh.harvard.edu>>
wrote:
Dear HW,
What was the exact command you ran?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH
Dear all,
Haewon Roh has discovered a small bug in quantifyThalamicNuclei.sh. We’ll fix
it in the development version as soon as possible.
In the meantime, we will post an amended version in the wiki; please see:
https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei
Thanks Haewon for picking u
Hi Molly,
Can you please send me the listing of files in the mri directories of one of
the subjects? (i.e., /media/ubuntu/cxy/FreesT1/output.long/[SOME_SUBJECT]/mri
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From:
rh.ribbon.mgz
ribbon.mgz
segment.dat
T1.mgz
talairach.invalid.mgz
talairach.label_intensities.txt
talairach.status.mgz
transforms
wm.asegedit.mgz
wm.mgz
wmparc.mgz
wm.seg.mgz
Please also see the screenshot of mri directory in the attachment.
Iglesias Gonzalez, Juan E.
mailto:jiglesiasgonza
Dear Liz,
Other than killing the fissure, the rest should be the same. Could you please
send us un example?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On 8/26/20, 11:30, "freesurfer-boun...@nmr.mgh.harvard
Hi Lou,
Can you please send us your exact command line?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Blanpain, Lou"
Reply-To: Freesurfer support list
Date: Wednesday, August 26, 2020 at 20:
Engineering, GATech
lou.blanp...@emory.edu<mailto:lou.blanp...@emory.edu>
443 676 9804
From: on behalf of "Iglesias Gonzalez,
Juan E."
Reply-To: Freesurfer support list
Date: Wednesday, August 26, 2020 at 9:48 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Error us
Hi Kelsey,
The volumes are derived from the probabilistic segmentation at the finest level
of detail, so there’s no direct mapping to the different hierarchical
segmentations. Your safest bet is probably to count the number of voxels in the
hard segmentation and multiply by the volume of the vox
They’re different modules with different algorithms, which give different yet
very highly correlated results. So, whatever you use the volumes for further
down the stream, the results should be very similar with either version.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC
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