Dear ladies and gentlemen,
for a research project I need to measure the volume of the different
hippocampus subregions. I want to use FreeSurfer 6.0 for that but I can
only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet released and if
so, when will it be released? If it is already released
Hi there
Do we have a potential date for the Freesurfer 6.0 release? I was told I
would want to re-run all my subjects to create better surfaces using
Freesurfer 6.0 and I am wondering if it really will improve surface
extraction that much.
Many thanks!
Trisanna
--
Ph.D. Candidate
McGill Unive
Hi all,
I can see a link for Freesurfer 6.0 on the website, but when I click on it to
download, it just blinks at me. I also tried to ftp to your ftp site, and
unfortunately, I got the message
421 Proxy is closed (unknown user location).
Could you please tell me how I could get the new version
> >> - Original Message -
> >> From: "Bruce Fischl"
> >> To: "Freesurfer support list"
> >> Sent: Wednesday, March 16, 2016 3:49:31 PM
> >> Subject: Re: [Freesurfer] FreeSurfer 6.0
> >>
> >> yes, although the
actually there is no beta yet, but hopefully within a week or so
On Wed, 16
Mar 2016, Alan Francis wrote:
Hi Elizabeth:
I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
Beta is available for download. Here is the URL:
https://surfer.nmr.mgh.harvard.edu/fswiki/Downlo
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> - Original Message -
>> From: "Bruce Fischl"
>> To: "Freesurfer support list"
>> Sent: Wednesday, March 16, 2016 3:49
Hi Elizabeth:
I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
Beta is available for download. Here is the URL:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
best,
Alan
On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul <
elisabeth.p...@student.uva.nl> wrote:
> Dea
Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
ran the HSF method successfully. Have they retracted that version?
best,
Alan
On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl
wrote:
> actually there is no beta yet, but hopefully within a week or so
>
> On Wed, 16 Mar 20
ischl"
To: "Freesurfer support list"
Sent: Wednesday, March 16, 2016 3:49:31 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0
yes, although the hippocampal stuff hasn't changed I don't think
(Eugenio: is that correct)?
On Wed, 16 Mar 2016, Alan Francis wrote:
> Bruce, with
e -
> From: "Bruce Fischl"
> To: "Freesurfer support list"
> Sent: Wednesday, March 16, 2016 3:49:31 PM
> Subject: Re: [Freesurfer] FreeSurfer 6.0
>
> yes, although the hippocampal stuff hasn't changed I don't think
> (Eugenio: is that correc
Hi Elisabeth
we don't have an exact date yet, but have finished our code modifications
(hopefully!) and are in the process of freezing a version after which we
will run a set of tests and hopefully release it
cheers
Bruce
On Wed, 16 Mar
2016, Elisabeth Paul wrote:
> Dear ladies and gentleme
yes, although the hippocampal stuff hasn't changed I don't think
(Eugenio: is that correct)?
On Wed, 16 Mar 2016, Alan Francis wrote:
Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
ran the HSF method successfully. Have they retracted that version?
best,
Alan
On W
We are working pretty hard to get it out but we are still reluctant to
set a hard date. I think we'll have a beta version in two weeks, but
that's just a guess.
doug
On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote:
Hi there
Do we have a potential date for the Freesurfer 6.0 release? I was
thanks, Doug!
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Mon, Jul 25, 2016 at 11:57 PM, Douglas Greve
wrote:
> We are working pretty hard to get it out but we are still reluctant to set
> a hard date. I think we'll have a beta version in two weeks, bu
>
> Dear FreeSurfer team,
> we are trying to find a downloadable version of FS6.0 to use on our data.
> We can not find it on the web.
> Could you help us with that?
> Thank you,
> best regards,
> Elisabetta
>
> --
> *Elisabetta C. del Re, Ph.D.*
>
> *Instructor,*
> *Department of Psychiatry*
> *
Hi Elisabetta
FS 6 is not available yet. We are hoping to have a beta in a couple of
weeks and are actively working on getting it out
cheers
Bruce
On Thu, 28 Jul 2016,
elisabetta_de...@hms.harvard.edu wrote:
Dear FreeSurfer team,
we are trying to find a downloadable version of FS6.0 to
behalf of Bruce Fischl
Sent: Thursday, July 28, 2016 4:31 PM
To: Freesurfer support list
Cc: Anastasia Haidar
Subject: Re: [Freesurfer] FreeSurfer 6.0
Hi Elisabetta
FS 6 is not available yet. We are hoping to have a beta in a couple of
weeks and are actively working on getting it out
cheers
Bruce
On
Did you receive a reply/
Any news update for 6.0 release?
On Mon, Jul 25, 2016 at 1:01 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> Hi there
>
> Do we have a potential date for the Freesurfer 6.0 release? I was told I
> would want to re-run all my subjects to create
Hi Matt
this would be a beta - the new version isn't ready to be distributed yet
(although we are getting closer)
Bruce
On Tue, 3 Nov 2015, Hoptman, Matthew wrote:
Hi all,
I can see a link for Freesurfer 6.0 on the website, but when I click on it
to download, it just blinks at me. I also tri
It must be an issue with your browser. Try using either of the following
commands (depending on your platform) in a terminal window.
Linux:
wget
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015.tar.gz
Mac OSX:
curl -O
ftp:/
Hi experts,
How can I download Freesurfer version 6.0? Is there an available URL link?
Thank you,
Aziz
--
Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campu
Please do not forget windows people
John
On Jan 25, 2017 12:45 PM, "Aziz Nanthaamornphong"
wrote:
> Hi experts,
>
> How can I download Freesurfer version 6.0? Is there an available URL link?
>
> Thank you,
> Aziz
> --
>
> Aziz Nanthaamornphong, Ph.D.,
> Chair of Master of Science Program in
Hi fs developers,
I am wondering if you have any estimation when fs 6.0 will come out. The
reason that I ask this is because we are running some analysis using fs 5.1
and planning to switch to a more recent version of fs. If fs 6.0 will come
out soon, we will probably hold and wait for it. If not
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote:
> Hi experts,
>
> How can I download Freesurfer version 6.0? Is there an available URL link?
>
> Thank you,
> Aziz
> --
>
> Aziz Nanthaamornphong, Ph.D.,
> Chair of Master of Science P
Thank a lot.
Aziz.
On Wed, Jan 25, 2017 at 9:38 PM, Z K wrote:
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
> On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote:
> > Hi experts,
> >
> > How can I download Freesurfer version 6.0? Is there an available URL
> link?
> >
> > Tha
External Email - Use Caution
I noticed that you guys released a fix to improve the -hires option. I
have been processing some of our data using the hires flag. if i use this
fix do i need to run recon-all from the beginning or can I run over the old
folders?
__
Hello Freesurfer Experts,
I am having a bit of trouble with the hippocampal subfield analysis
using the Freesurfer 6.0 program.
My data is organized as /AnalysisFolder/Group/Subject/Anatomical/SUB_FS ..
where SUBJECTS_DIR=/AnalysisFolder/Group/Subject/Anatomical/ and my subject
specific folder
Hi Freesurfer Experts,
I am trying to understand the difference between qcache option and
mris_fwhm and which is appropriate for a cortical thickness analysis. I
processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii
(converted) files. I used an afni tool SurfFWHM to estima
Hi Fengji
we have frozen the code and are going through various tests now so are
hoping sometime in the next few weeks, but of course it's impossible to say
as it depends on how well the tests turn out.
cheers
Bruce
On Mon, 1
Aug 2016, Fengji Geng wrote:
Hi fs developers,
I am wonderin
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v
Dear Eugenio,
I am writing because I am getting a mkdir error when I try to run the
FreeSurfer 6.0 hippocampal subfields segmentation. I tried moving my
installation of freesurfer to a local directory where I have write
permission and I also made sure I had write permission in my subject's
direct
Me again,
Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in MNI305
space or have they been updated to the MNI152 space?
many thanks!
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
___
Free
You have to rerun from the beginning. (sorry)
On 9/9/19 3:12 PM, Aaron Tanenbaum wrote:
>
> External Email - Use Caution
>
> I noticed that you guys released a fix to improve the -hires option.
> I have been processing some of our data using the hires flag. if i use
> this fix do i need
Hi Freesurfer Experts,
Just as a followup through my reading i've come across posts which use
qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my
cortical thickness analysis I would like to smooth all of my
rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
Underneath, they both use the same code, so they should give the same
results. Are you saying they are different? I don't know what SurfFWHM
is doing so I can't comment on what those results mean. Measuring the
FWHM on the surface is quite tricky.
doug
On 5/4/16 6:41 PM, Ajay Kurani wrote:
H
Hi Doug,
Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and
mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness
analysis?
Thanks,
Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani
wrote:
> Hi Freesurfer Experts,
>Just as
There is not a difference between mris_fwhm and mri_surf2surf.
mris_smooth smoothes the xyz coordinates of the vertices of a surface
(the others smooth an overlay).
On 05/05/2016 03:53 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference from qcache/mris_
Hi Doug,
Thanks for the clarification. So in the case of cortical thickness,
qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
should be getting similar results if everything is entered in the same
fashion. This would be the approriate choice compared to mri_smooth.
For
Hi Doug,
I wanted to figure out what is the minimum cluster extent for a given
monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the
following tutorial :
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I
wanted to know if freesurfer estimates the smoothness
It estimates the FWHM from the data (glmdir/fwhm.dat). It does this by
computing the pearson correation coefficient of the residual error
between adjacent vertices. This is then averaged over all vertices to
compute a mean cor coef. A transform is then applied to compute the
FWHM. This is consi
Hi Doug,
Thanks for the explanation. In using p=0.05 with my thickness files
(smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
file.
In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alp
Hi Doug,
Thanks for the explanation. In using p=0.05 with my thickness files
(smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
file.
In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alp
On 05/09/2016 04:11 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness files
> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/
> cdf file.
>
> In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean
> the ov
Hi Doug,
Ok this makes more sense now. In my case if I choose abs I would look
at the max cdf < 0.05 for the corresponding cluster extent in the TH13
folder.
In terms of the |a-b|<0,05 does this mean that if I got results in blue it
just means significant but with no directionality as to if A
The color still indicates the direction. If you have a signed
hypothesis, then you can run it with pos or neg instead of abs, however,
in this case it will change the voxel-wise cluster-forming threshold
(make it more liberal) because the voxel-wise p-value is computed
assuming an unsigned test
disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Priyanka"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need
iso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Priyanka"
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Wednesday, July 29, 2015 7:59:37 AM
> Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
>
> Hi,
>
> I
: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Priyanka Mehta"
To: "Freesurfer support list"
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how
ot;Priyanka Mehta"
> To: "Freesurfer support list"
> Sent: Wednesday, July 29, 2015 11:26:04 AM
> Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
>
>
>
>
>
>
>
> Thanks Eugenio! Thats worked!
> One more question- how would I convert the lh
rt list"
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted the le
Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Priyanka Mehta"
> To: "Freesurfer support list"
> Sent: Wednesday,
quot;Priyanka Mehta"
To: "Freesurfer support list"
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${s
enio
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> - Original Message -
&g
on will be 1
> mm, rather than the 0.333 mm that you'd
> >> get in option 1.
> >> Cheers,
> >> Eugenio
> >>
> >> Juan Eugenio Iglesias
> >> Postdoctoral researcher BCBL
> >> www.jeiglesias.com
> >
toral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
>>
>> - Original Message -
>> From: "
ves in the same voxel
>> space as T1.nii, and should be properly overlayed
>> >> by MriCron. However, the resolution of the segmentation
>> will be 1 mm, rather than the 0.333 mm that you'd
>> >> get in option 1.
>>
volume lives in the same voxel
>>> space as T1.nii, and should be properly overlayed
>>> >> by MriCron. However, the resolution of the segmentation
>>> will be 1 mm, rather than the 0.333 mm that you'd
>>> >> get
>> 1. Use FreeSurfer's Freeview rather than MriCron to
> >>> visualize the output. FreeView will correctly overlay
> >>> >> the segmentation.
> >>> >> 2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
>
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Priyanka Mehta"
To: "Freesurfer support list"
Sent: Sunday, September 13, 2015 10:14:34 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version
Hello Freesurfer experts,
I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu
14.04 with a high resolution image (0.5mm isotropic). I set
OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags
in my autorecon 2 line command. Autorecon1 and the beginning
Hi there
I am wondering if the Freesurfer 6.0 version is more flexible with the
parameters used for ex-vivo scans other than what 5.3 required, as listed
here
https://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo.
We acquired some ex-vivo scans at 0.4mm iso but not with those above
parameters.
many
Still in 305
On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote:
> Me again,
>
> Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in
> MNI305 space or have they been updated to the MNI152 space?
>
> many thanks!
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrat
thanks Doug!
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Wed, Jan 25, 2017 at 6:27 PM, Douglas N Greve
wrote:
> Still in 305
>
>
> On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote:
> > Me again,
> >
> > Are the fsaverage volumetric coordinates in Fre
urfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
External Email - Use Caution
I ran standard recon-all on a single subject and then trac-all -prep.
The process ran for approximately 1 hour and exited with errors: Segmenta
] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700
Hi Matt – It looks like some sort of registration issue. When you display
the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there
Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
External Email - Use Caution
Yes, a part of the brain appears missing. See attached screenshot.
I did not use a configuration file, I simply accepted
hough some appear more noisy and
pixelated than others.
This is a mTBI subject with no other anatomical brain anomalies scanned
with a Siemens 3T.
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:
like that?
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Matthew Grecsek
Sent: Thursday, September 20, 2018 2:00:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
External
t: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
External Email - Use Caution
Hi Anastasia,
Please see attached screenshots from dwi.nii.gz. The first 4 are rotated 90
degrees around y axis and the last 2 are top and bottom.
Thanks,
-Matt
On Thu, Sep 20, 2018 at 7:19 PM Ye
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <
> m...@grecsek.com>
> *Sent:* Friday, September 21, 2018 10:27:37 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesur
recsek mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, September 25, 2018 at 9:57 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Trac
External Email - Use Caution
Hi:
Where can I find the FreeSurfer 6.0 disk image for VirtualBox?
Sincerely,
Gonzalo Rojas Costa
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/li
Hi Ajay
it's kind of dicey to use an arbitrary nightly build as we have no idea
what was in that that might have been fixed the next day. I would wait
for a beta, or at the very least try a new version as I don't think our
current version exhibits the behavior you are experiencing.
cheers
Br
Hi Trisanna
it is better about handling highres data, but the ex vivo recon stream is
still a work in progress
cheers
Bruce
On Tue, 24 Jan 2017, Trisanna Sprung-Much wrote:
Hi there
I am wondering if the Freesurfer 6.0 version is more flexible with the
parameters used for ex-vivo scans other
thanks for the quick response Bruce!
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Tue, Jan 24, 2017 at 1:18 PM, Bruce Fischl
wrote:
> Hi Trisanna
>
> it is better about handling highres data, but the ex vivo recon stream is
> still a work in progress
>
Hi,
I'm wondering if it's okay to run some of the analyses within one study on
v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us
starting over for the analyses we've already done in 5.3 for that study?
Thank you!
Batool
___
Freesu
External Email - Use Caution
Hello Gonzola,
I use a CentOS7 VM image (on virtualbox) originally downloaded from
osboxes.org. After downloading and bringing up the image, I installed
various packages for freesurfer. But apart from my image being CentOS7
(and not CentOS6), I t
Dear experts,
I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for
hippocampal subfield features extraction (always on Ubuntu 14.01 environment).
After several trial I realized that before pipeline ends I've got the following
error:
/opt/FreeSurfer-6-Beta/bin//mri_
Hi,
Can anyone comment on my question below?
I think the FAQ page mentions that the same version should be used to process
all cases within a dataset, but my question is whether I can have the same
dataset used for two different versions for separate analyses? This is
considering that I've alrea
I believe Dr. Iglesias previous responses on this exact question have been,
"yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time
having to download 2 different versions of freesurfer to achieve comparable
results
Dear Batool,
Sorry for missing your message.
And dear Adam:
Thanks for covering me! That’s exactly my standard answer to that question ;-)
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
ucl.ac.uk]
Sent: Thursday, January 26, 2017 11:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer 6.0 with some of the analyses
Dear Batool,
Sorry for missing your message.
And dear Adam:
Thanks for covering me! That’s exactly my standard answer to that question ;-)
Juan Eugen
mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez,
> Eugenio [e.igles...@ucl.ac.uk]
>
>
> *Sent:* Thursday, January 26, 2017 11:01 AM
>
>
> *To:* Freesurfer support list
>
>
> *Subject:* Re: [Freesurfer] freesur
mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez,
> Eugenio [e.igles...@ucl.ac.uk]
>
>
> *Sent:* Thursday, January 26, 2017 11:01 AM
>
>
> *To:* Freesurfer support list
>
>
> *Subject:* Re: [Freesurfer] freesur
Ciao Daniele,
This is weird. Would you mind verifying that file T1resampled.mgz actually
exists in the temporary directory of the subject? You can do that by CDing to
$SUBJECT_DIR/[SUBJECT_NAME]/tmp and running the command:
find . -name “T1resampled.mgz”
Cheers,
/Eugenio
Juan Eugenio Iglesias
ER
Hi all,
I am using Freesurfer 6.0 for hippocampal subfield segmentation (Mode B:
-hippocampal-subfields-T1T2).
For each subject, I have a 3T-T1 MRI (whole brain) and a 7T-T2 MRI (partial
brain).
Segmentation works in most subjects, but in some subjects the co-registration
of the 7T-T2 MRI sca
Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of Patricia Linortner
Reply-To: Freesurfer support list
Date: Tuesday, 31 October 2017 at 22:54
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Freesurfer 6.0 - Hippocampal
Hello Freesurfer experts,
I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version)
with the -hires flag to process an MNI template image which is 0.5mm
isotropic. Stage 1 ran well and on stage 2 there is an error during
pocessing:
Command run:
recon-all -s ICBM -autorecon2 -openmp
he fixing stage the
>> surfaces got damaged somehow, therefore you have
>> to
>> recreate it them. I’m
>> not entirely sure about the qsphere. Probably you
>> have to run the -
Hello all
FYI
I have found non-negligeable differences in eTIV for 5.3 versus 6.0 in my
healthy young sample
It is probably due to the cerebellum computation changes (presented in released
notes for 6.0)
Unsurprisingly the supratentorial volumes 5.3 versus 6.0 are very similar
(all was chec
Hi Ajay
are you sure you didn't run out of disk space? That error is a sanity
check on the surfaces that should never occur
cheers
Bruce
On Sun, 29 Nov 2015, Ajay
Kurani wrote:
Hello Freesurfer experts,
I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version)
with the -hires
-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Sonntag, 29. November 2015 22:48
An: Freesurfer support list
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
(mris_euler_number) using high res (
endet: Sonntag, 29. November 2015 22:48
An: Freesurfer support list
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
(mris_euler_number) using high res (0.5mm isotropic) T1 image
Hi Ajay
are you sure you didn't run out of disk space? That error is a sanity check on
the surfaces t
:48
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
> (mris_euler_number) using high res (0.5mm isotropic) T1 image
>
> Hi Ajay
>
> are you sure you didn't run out of disk space? That error is a sanity
> check on the surfaces that shou
etreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
(mris_euler_number) using high res (0.5mm isotropic) T1 image
Hi Ajay
are you sure you didn't run out of disk space? That error is a
sanity check on the surfaces that should never occur
cheers
gh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
> Gesendet: Sonntag, 29. November 2015 22:48
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
> (mris_euler_number) using high res (0.5mm isotropic) T1 image
-qsphere stage
again also.
Best,
Falk
Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
Gesendet: Montag, 30. November 2015 21:50
An: Falk Lüsebrink
Cc: Freesurfer support list; Bruce Fischl
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
(mris_euler_number) using high res (0.5mm
Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
Gesendet: Montag, 30. November 2015 21:50
An: Falk Lüsebrink
Cc: Freesurfer support list; Bruce Fischl
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
(mris_euler_number) using high res (0.5mm isotropic) T1 image
Hi Falk,
entirely sure about the qsphere. Probably you have to run the -qsphere
>> stage again also.
>>
>>
>>
>> Best,
>>
>> Falk
>>
>>
>>
>>
>>
>> Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
>> Gesendet: Montag, 30. November
Best,
Falk
Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
Gesendet: Montag, 30. November 2015 21:50
An: Falk Lüsebrink
Cc: Freesurfer support list; Bruce Fischl
Betreff: Re:
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