External Email - Use Caution
The graphics packages used in Freeview have changed since the Freesurfer
6 release, and also how they and the other Intel binaries are compiled for
current
versions of MacOS. So a run time error, e.g., segfault, could occur when
running under Ro
Use the patch
On 10/10/2019 11:07 AM, Daniel Westfall wrote:
External Email - Use Caution
Hi Everyone,
I just wanted to double check the current state of processing T3 submillimeter
data with Freesurfer 6. We have two studies: one with 0.9 mm isotropic and the
other with 0.8 mm isotro
External Email - Use Caution
Hi Everyone,
I just wanted to double check the current state of processing T3
submillimeter data with Freesurfer 6. We have two studies: one with 0.9 mm
isotropic and the other with 0.8 mm isotropic. After doing some
investigating, I found that there i
External Email - Use Caution
Hi Doug,
thanks a lot for the clarification!
Tim
> On August 16, 2019 at 6:19 PM "Greve, Douglas N.,Ph.D."
> wrote:
>
>
> The algorithm in v6 is not as you describe. The function below is based
> on Anderson Winkler's (cc'ed) work.
>
> /*!
>
The algorithm in v6 is not as you describe. The function below is based
on Anderson Winkler's (cc'ed) work.
/*!
\fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
\brief Compute vertex-wise volume based on dividing each obliquely
truncated
trilateral pyramid into three tetrahedra. Based on A
External Email - Use Caution
Dear FreeSurfer experts,
can anybody refer me to a publication that explains in detail how vertex-wise
cortical volume (the data in /surf/?h.volume) is computed in
FreeSurfer 6?
My understanding is the following:
* area is computed as 1/3 the area
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 17:52
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing
workflow question, more LH than RH files
External Em
: [Freesurfer] freesurfer 6 hippocampal longitudinal processing
workflow question, more LH than RH files
External Email - Use Caution
My apologies. Here is the long-hippocampal-subfields-T1.log
https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD
On Jun 12, 2018, at 10:45
.edu>>
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing
workflow question, more LH than RH files
External Email - Use Caution
Hi Eugenio,
Thank
Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of Nikita Nogovitsyn
Reply-To: Freesurfer support list
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal
External Email - Use Caution
Hi Eugenio,
Thank you very much for your prompt reply.
I was trying to support the tread titled Re: [Freesurfer] freesurfer 6
hippocampal longitudinal processing workflow question, more LH than RH files
We received results from the cross-sectional
urfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing
workflow question, more LH than RH files
External Email - Use Caution
HI
I would like to report to have the same issue. There were no errors in the log
yet the majority of results missing right
External Email - Use Caution
HI
I would like to report to have the same issue. There were no errors in the log
yet the majority of results missing right hemisphere.
Attaching here the log file, or you can also access it via googledrive here:
https://drive.google.com/open?id=13P
Hi Alan,
Can you please send me the log file for the longitudinal subfields?
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 3 May 2017, at 14:11, Martin Reuter
mail
Not sure what is going on, maybe Eugenio knows.
On 04/27/2017 10:29 PM, Salil Soman wrote:
Thank you for your email. Just to follow up, the rh and lh hippocampal
hippoSfVolumes-T1.v10.txt files are present, but for a large number of
cases, only the lh hippoSfVolumes-T1.long.v10.txt files are p
Thank you for your email. Just to follow up, the rh and lh hippocampal
hippoSfVolumes-T1.v10.txt files are present, but for a large number of
cases, only the lh hippoSfVolumes-T1.long.v10.txt files are present. I
reran the exact same recon-all -long command for all the cases, and I reran
them after
Hi,
I have run a number of cases through the FS6 hippocampal longitudinal
processing steps listed at
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields
and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
It seems that all steps completed, but when it came
Hi FLorian
the problem is that you have cortical labels from the aparc+aseg in your
.gca file, and these exceed the max label we are expecting in a .gca atlas.
Is there a reason you need them and not just left and right cortical gray
matter labels? I don't think labeling folds will be terribly
Hi FLorian
I think you are not running the release, but a slightly earlier version
(from the info at the top of your recon-all.log).
Can you try running with the standard atlases and see if that works? And if
it does, upload your rebuilt atlases so I can try to replicate the crash?
cheers
B
Hi Bruce,
It’s a custom atlas with minor changes that was build with the
rebuild_gca_atlas.csh script.
What is puzzling to me is the fact that if I omit the align-after flag the
mri_ca_register command works perfectly fine.
Many thanks & best wishes,
Florian
Am 24.01.17, 21:48 schrieb "Bruce
I think that should be enough, but your data doesn't segfault for me. I
also noticed the following in your recon-all.log file:
usr/local/freesurfer/bin/recon-all
-all -gca RB_all_2017-01-23.gca -gca-skull RB_all_withskull_2017-01-23.gca
-subjid vco1573test_mpr
are you using your own version
Hi Bruce,
it is a virtual machine with 8GB RAM dedicated to it. Any idea how much RAM
would be enough?
Thanks,
Florian
Am 24.01.17, 21:39 schrieb "Bruce Fischl"
:
Hi Florian
how much RAM do you have in that machine? I think it is not enough
cheers
Bruce
On
Hi Florian
how much RAM do you have in that machine? I think it is not enough
cheers
Bruce
On
Tue, 24 Jan 2017, Florian Krismer wrote:
Dear FreeSurfer Developers,
I'm attempting to run recon-all on a test subject (through recon-all –all
–subjid test001 in Freesurfer 6). Recon-all hangs
Hi Florian
can you tar and gzip that subject dir and we will take a look?
cheers
Bruce
On Tue, 24
Jan 2017, Florian Krismer wrote:
Dear FreeSurfer Developers,
I'm attempting to run recon-all on a test subject (through recon-all –all
–subjid test001 in Freesurfer 6). Recon-all hangs at the
Dear FreeSurfer Developers,
I'm attempting to run recon-all on a test subject (through recon-all –all
–subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register
command throwing a Segfault error.
This is the corresponding part of the recon-all.log:
---
Looks like the most up-to-date version of mri_surfcluster did not get
into the distribution. Try this one
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster
On 11/18/16 9:06 PM, Elijah Mak wrote:
Hi Freesurfer Team,
I came across the following error while running mri_glmfit-sim
Hi Freesurfer Team,
I came across the following error while running mri_glmfit-sim. What is
vwsigmax?
Thanks for your help again.
The full log is as follows:
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Sat Nov 19 02:00:45 GMT 2016
Darwin dhcp-10-240-201-24.cp.wireless.privat
Hi,
I downloaded the archive with Firefox instead of Safari and problem is solved.
Strangely, the archive downloaded with Safari was not full.
Damien
> On 10 Oct 2016, at 16:56, Damien MARIE wrote:
>
> Hi,
>
> I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El
> capit
Hi,
I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El
capitan 10.11.6, XQuartz 2.7.9 installed).
I allowed applications downloaded from Anywhere in privacy and settings, and
disabled csrutil (the System Integrity Protection, a security feature that
hobbles some of the ca
Hello James,
Is it only the mris_decimate binary that gives this error? What happens
if you try to perform a recon-all on the subjects bert under
$FREESURFER_HOME/subjects... Does it get far or does it spit out the
same error?
$>
$> export SUBJECTS_DIR=/Applications/subjects
$> recon
Dear Freesurfer developers
I've just tried out the beta version of Freesurfer 6.0 on my Mac, which I
downloaded from
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/, mainly
because I need to use the mris_decimate function. However, issuing
mris_decimate -d 0.25 inputfile outputfile
ret
On 01/28/2016 01:11 PM, Shady El Damaty wrote:
> Hi,
>
> I was curious to know what the tentative release date for FreeSurfer 6 is.
> I’m currently running FreeSurfer on multiple machines with El Capitan
> installed and I’m wondering whether it’s worth installing the beta
> distribution or rath
Hi,
I was curious to know what the tentative release date for FreeSurfer 6 is. I’m
currently running FreeSurfer on multiple machines with El Capitan installed and
I’m wondering whether it’s worth installing the beta distribution or rather
uninstalling SIP on each of these many machines.
Also
Hi,
I’m running freesurfer 6 on a cluster. I am having issues with the matlab
crashing during the hippocampal segmentation. I am allocating 10gb for each
job, however that hasn’t fixed the problem. Sometime the segmentation works
fine, however many segmentations fail due to matlab crash. I hav
Did you source the Freesurfer setup script?
$> export FREESURFER_HOME=/Applications/freesurfer6
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh
> Hello All,
>
> I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am
> getting the following error when I run recon-all from free
Hello All,
I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am getting
the following error when I run recon-all from freesurfer 6.
Can you please suggest how to fix it ?
Thank you,
Ri
ri@Magi [0] ~/ri/SampleDatasets$ export
FREESURFER_HOME=/Applications/freesurfer6;export
Hi Lauri
I think you forgot to attach the logs
Bruce
On Thu, 10 Dec 2015, Tuominen, Lauri Johannes wrote:
Dear Freesurfer experts,
I ran recon-all on launchpad using
/usr/local/freesurfer/stable6/bin/recon-all. This command worked nicely, but
part of the occipital cortex was missing and I t
Dear Freesurfer experts,
I ran recon-all on launchpad using /usr/local/freesurfer/stable6/bin/recon-all.
This command worked nicely, but part of the occipital cortex was missing and I
therefore ran the following command ( both in freesurfer6 ):
recon-all -skullstrip -wsthresh 35 -clean-bm -no
Hi Bruce,
I re-ran the -cortparc step with the current dev version
freesurfer-Linux-centos6_x86_64-dev-20151209
It took ~6 hours and the error is still the same. It seems to run through the
left hemisphere, but crashes on the right one.
Cheers!
Natalia
On 09 Dec 2015, at 14:37, Bruce Fischl
m
HI Natalia
can you try the dev version? I'm pretty sure I fixed this. You can just
rerun mris_ca_label. We'll hopefully be cutting a new stable 6 sometime
soon
cheers
Bruce
On Wed, 9 Dec 2015, Zaretskaya, Natalia wrote:
Dear all,
I am running recon-all with FreeSurfer 6 stable version on
You may need to download the Matlab Compiler Runtime (MCR) for Matlab 2012b.
To do so, please run the following commands (you might need root
permissions):
LINUX:
cd $FREESURFER_HOME
curl
"http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.t
Hi Scott,
hmmm, I know it says "exited with ERRORS", but I don't actually see any
errors. Did it appear to finish properly? Are the results visually ok?
ZBruce
On
Tue, 8 Dec 2015, Scott Quadrelli wrote:
Hi All,
I am trying to track down the source of an error on one of my first runs usi
Not sure. Can you run this command
cd /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/label
mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b
-a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab C02DL_t1 rh white
and send the terminal output. Does it not fail for th
Hey Guys,
Sorry if this is a frequently asked question.
Do we have an updated ETA for version 6 of Freesurfer? We are planning on
upgrading our 1024-node cluster and version 6 is a big deal for us.
Best
Pedro Paulo Jr.
-
Pedro
We are anticipating a beta release in about two weeks time followed by the
version 6 release about one week later.
-Zeke
> On May 2, 2015, at 9:35 AM, Elijah Mak wrote:
>
> Hello,
>
> I have just read Iglesias et al (2015) hippocampal subfields paper in
> Neuroimage with great interest.
>
Hello,
I have just read Iglesias et al (2015) hippocampal subfields paper in
Neuroimage with great interest.
Do you have an estimate on the release date of Freesurfer 6 for Mac OSX?
Apologies in advance if this has already been answered elsewhere on this
site.
Many thanks.
Best Wishes,
Elijah
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