Dear freesurfer exports,
As it is mentioned in the documentation that 'pediatric data violates the
fixed head size assumption' for the current longitudinal stream. Is there
any solution for the issue now?
Thanks
Dong
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Oh, sorry for that.
I pasted error message below;
#
#@# Curv .H and .K lh Mon Feb 13 20:27:14 KST 2017
/Applications/freesurfer/subjects/CUBEE0008/surf
\n mris_curvature -w lh.white.preaparc \n
total integrated curvature = 8.603*4pi (108.105) --> -8 han
On 13 February 2017 at 18:15, Francis Tyson Thomas
wrote:
> I'm trying to reduce the freesurfer runtime as much as possible and I was
> wondering if the GPU flags still work for recon-all in Freesurfer v6? If not
> is it possible to use the developer version to have it running? Also, if I
> follo
The Program for Translational Research on Adversity and Neurodevelopment
(P-TRAN) at The Pennsylvania State University is seeking a qualified
postdoctoral researcher with expertise in human brain imaging, specifically
magnetic resonance imaging (MRI)) with children and adolescents. This
position i
Hi,
I'm trying to reduce the freesurfer runtime as much as possible and I was
wondering if the GPU flags still work for recon-all in Freesurfer v6? If
not is it possible to use the developer version to have it running? Also,
if I follow the second approach would the results be the same as that
obt
What are your execution times? Can you send the recon-all files for your
parallel and non-parallel runs? If you run it with -time, then lots of
information will be printed to the log for each command. This can be
helpful for debugging these types of things.
On 02/13/2017 05:13 PM, Francis Tyso
I don't know that we have explicitly tested it on a mac, but it should.
On 02/13/2017 05:19 PM, Francesco Cardinale wrote:
> Dear Freesurfer experts,
> Does the parallelization work with Freesurfer 6.0 under MacOS?
> Best regards
>
> Francesco Cardinale, MD
>
> Neurosurgeon
> "Claudio Munari" Cen
Dear Freesurfer experts,
Does the parallelization work with Freesurfer 6.0 under MacOS?
Best regards
Francesco Cardinale, MD
Neurosurgeon
"Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda
"Ca' Granda"
Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia
phone
Hi,
I have run recon-all with both -parallel enabled (including different
openmp threads) and disabled and I'm not able to get processing times same
as the information provided in recon-all help. The CPU used is *Dual
Intel **Xeon
E5-2623 v3* paired with 32GB DDR4 RAM. Is the configuration present
we intensity normalize the entire volume, based on automatically detected
points within the white matter.
cheers
Bruce
On Mon, 13 Feb 2017, firet...@web.de wrote:
Hi
is there intensity normalisation in hippocampus or does freesurfer omit this
region?
Thanks
_
Hi
is there intensity normalisation in hippocampus or does freesurfer omit this region?
Thanks
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is
That's very strange, it sounds like nothing has changed. Can you please send
your trac-all.log file?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Abigail Waters
[awate...@suffolk.edu]
Sent: Monday, February 1
It's the same. These are all subjects from the same research protocol.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Sunday, February 12, 2017 9:39 PM
To: Free
Hi Katarina,
sorry, did not see your previous mail until now. In the future, if you put
"longitudinal” somewhere in the subject line, chances are higher that I find it
(but not guaranteed either :-)
I think using the real time vs using -generic time should give different
results in the SPC. S
Hi Eugenio,
Here are my outputs:
ls e009723_FS (one of my subject's freesurfer folder):
bem FS1.sh FS2.sh FS4.sh label mri scripts src stats surf tmp touch
trash
- you can ignore the FS#.sh files - these are matlab script files we run.
ls mri/lh.hippoSfVolumes*.txt:
mri/lh.hippoSf
That’s weird. What is the output of the following command?
ls /path/to/my/subjects/freesurferfolder
And of this one:
ls /path/to/my/subjects/freesurferfolder/SUBJECT/mri/lh.hippoSfVolumes*.txt
(where SUBJECT is a subject of your choice)
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Resea
glad it was something easy :)
On Mon, 13 Feb 2017, Gronenschild Ed (NP)
wrote:
Hi Bruce,
All output generated is redirected to a temporary log file by me.
Fortunately, it is still available
and when I look at it I see what happened: it doesn’t find Matlab runtime in
the FreeSurferv6
directory.
Hi Bruce,
All output generated is redirected to a temporary log file by me. Fortunately,
it is still available
and when I look at it I see what happened: it doesn’t find Matlab runtime in
the FreeSurferv6
directory. I’m sorry about this, I just have to copy the MCRv80 from
FreeSurferv6b to v6 a
Hi Eugenio,
That's actually the issue, it doesn't generate any file at all.. there's no
hippo.txt in the folder where I run it, or in the subject's directory that I
had specified.
Batool
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.ha
Hi Ed
was there any error message or anything? It just seems to end normally
but then gives a nonzero exit code causing recon-all to stop?
cheers
Bruce
On Mon, 13 Feb
2017, Gronenschild Ed (NP) wrote:
> Hi,
>
> All datasets that I've processed sofar with v6 resulted in exactly the same
> erro
Hi,
I'm having trouble getting any output from the hippocampal subfield analysis
command. I entered in:
quantifyHippocampalSubfields.sh T1 hippo.txt
/path/to/my/subjects/freesurferfolder
I tried both ways of having the environmental variable subjects directory
defined to the freesurfer folder
Hi Batool
What are the contents of hippo.txt? Just empty?
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 13 Feb 2017, at 16:41, Rizvi, Batool
mailto:br2...@cumc.col
Hi Juhyoung
First, can you please paste this kind of thing as text into your email
instead of taking snapshots? That makes things easier for us.
Second, why are you telling recon-all not to do the inflation with
-noinflate2? That is why it can't find the inflated surface.
cheers
Bruce
On
Dear all knowing list,
we are just playing around with the MSM code within FSL and noticed that
if we try to convert surface data to ascii like e.g. this
mri_convert --ascii funcdata.nii funcdata.asc
it produces an ascii file that looks good when opened in a text editor,
but doesn't seemt o be
Dear freesurfer experts,
I have some questions about the coordinates conversion, and the relationship
between several types of coordinates.
First of all, I’d like to confirm whether the coordinates reported in the
results summary are based on MNI305 space?
Second, I plan to combine multi-mod
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