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Nikolas Borrel-Jensen souhaite se connecter à vous sur LinkedIn :
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Freesurfer,
Je vous invite à faire partie de mon réseau professionnel en ligne sur le site
LinkedIn.
Accepter l'invitation de Nikolas Borrel-Jensen
As requested I removed the AMI image because that image contains a .license
file.
I can republish the image when we find a solution for the licensing issue.
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Pedro Paulo de Magalhães Oliveira Junior
Netfilter SpeedComm Telecom
Hi PPJ,
I would rather people use FS without licenses than find themselves unable
to use it, so why not leave it for now. Can you put a request that they
first download a license or register on your website? Alternatively, can
you just remove the .license file from the AMI forcing the users
I have restored the image: 060244368407/FREESURFER51
I'll create a web service that can log the number of instances spawned. Is
that ok with you?
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Pedro Paulo de Magalhães Oliveira Junior
Netfilter SpeedComm Telecom
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To whom it may concern,
When running the hippocamapal subfield segmentation routine on the left
hippocampus for a normal subject (early Parkinson) I get the following
segmentation fault error:
kvlSegmentHippocampalSubfields.sh: line 18: 29522 Segmentation
fault kvlSegmentWithoutGUI
When I used the AMI, (maybe not Pedro's), so I sftp'd a license file to
each instance prior to running an analysis. Not a big deal. I didn't get a
new license for each instance, but copied the same one to multiple
instances.
Joshua
2011/11/18 Pedro Paulo de Magalhães Oliveira Junior
Hi,
I'd like to follow the fsfast tutorial but I can't find the data for it:
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz
ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz
Were they renamed or displaced?
Thanks, Verena
Dear Freesurfers,
I've previoiusly run reg-feat2anat on some fsl feat data, but now my
advisor things i should re-preprocess my fsl data with a larger kernel size.
Since it's the same dataset , do I have to re-run reg-feat2anat on this or
can I just copy the registration folder from the old
Hi Peter - Each of the volumes in your DWI series was acquired with a
certain b-value and a certain diffusion gradient direction. These have to
be in the bvals and bvecs files, respectively, in the same order. This
means for every volume in the DWI series, there'll be 1 number in bvals
and 3
We've been manually editing brainmask.mgz to remove voxels that are included in
the pial surface that shouldn't be, and recently found on the wiki that to
remove cerebellum voxels we should be editing brain.finalsurfs.manedit.mgz
instead. What is the reason for this difference? Do we need to
You can copy your edited brainmask.mgz to brain.finalsurfs.manedit.mgz
then rerun the case from the beginning using:
recon-all -all -clean-bm -s subjid
This will recreate the brainmask.mgz so no chunks of cerebellum are
missing (and therefore cerebellum volume estimates won't be off). If you
Hi Jordan,
I just had a similar discussion (off-list) with Nick recently.
The distinction only matters if you end up trimming cerebellum voxels
out of the aseg, and want your aseg for cerebellum to be correct.
Quoting Nick:
it [brain.finalsurfs.manedit.mgz] is used only in the instance (which
Long term, after we put together an 'official' instance of the AMI with
scripts (which might well be an instance that Pedro Paulo created) I
think sftp'ing the .license file to each instance is the way to go.
The .license file need only apply to the user (not each instance or
run).
N.
On Fri,
hi nick,
i really like pedro's idea of tracking through instance tracking as opposed
to licenses. on a separate project we are setting up the ability to pull up
as many instances as necessary and install whatever software environment
that's needed to run your analysis. we'll try to ensure that
Hi Satra
we did originally consider tracking usage in that way, but it seemed
invasive and a bit creepy to have FreeSurfer keeping track of what you
were up to and reporting back to us, so ultimately we decided not to
Bruce
On Fri,
18 Nov 2011, Satrajit Ghosh wrote:
hi nick,
i really
Hi Bruce et al,
Thanks for the stimulating discussion on the Hippocampal subfields. I have
a question. How exactly does FS segment and parcellate the Corpus Callosum
volume ?
thanks again,
Alan
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Freesurfer mailing list
Hi Alan
we divide it into equal length sections along it's primary eigen-axis,
and identify it as the region of maximal left/right wm adjacency.
cheers
Bruce
On Fri, 18
Nov 2011, Alan Francis wrote:
Hi Bruce et al,
Thanks for the stimulating discussion on the Hippocampal subfields. I
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