I've put together the basic tutorial on getting started using Amazon AWS
system:
It's in the same place Nick pointed out:
https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud
-
Pedro Paulo de Magalhães Oliveira Junior
I had previously worked on a script which, given Amazon EC2 credentials,
would spin up the instance, upload freesurfer data and run it, then send an
email when done - if this would be helpful to anyone I'll bother to finish
it, we use local compute resources so I never quite bothered. Now that
Hi Freesurfers,
Is there a tool to flip the orientation of surface data to the opposite
hemisphere? We are working with stroke patients, and I would like to do
analysis of the contralesional hemisphere of all the patients. However,
this requires putting them on the same hemisphere for ttests,
thanks Pedro Paulo!
Thomas, yes that script would be useful. A handy 'use case' for a
contributor to add to that wiki page would be to show how to use your
script to process the 40 tutorial subjects we supply on our site.
n.
On Fri, 2011-11-11 at 09:11 -0500, Thomas Ballinger wrote:
I had
FYI
-- Forwarded message --
Date: Fri, 11 Nov 2011 11:58:19 -0500
From: Thomas Talavage t...@purdue.edu
Subject: Job posting for Purdue BME
Hi all ---
Purdue has posted a job announcement for our BME department, including
(substantial) potential to hire someone into medical
Hi all,
I am conducting a contrast of z (r) maps from 3 seed-based resting-state
networks (e.g., 1 2 and 3). To eliminate the influence of
anticorrelations on the contrast results, I thresholded the z (r) maps at 0
before running mri_glmfit, thereby eliminating voxels with negative z (r)
values.
Hi Kevin, the problem is that once you threshold for 0, there are no
voxels that have non-zero values in all of the input subjects. Such
voxels are pruned because there is not a good model for them. The GLM
code does not do a different design at each voxels. In general, doing
such thresholding
Hi guys,
There is an issue with recon-all abending if you use the -expert option
on the very first call to recon-all, because recon-all attempts to copy
to $subjid/scripts/expert-options before the scripts directory has been
created.
As an attempted workaround I manually created an empty
Hi,
I am trying to do a DTI Group Analysis study using a MNI152 standard space for
registration.
1). I wonder in case I want to use MNI 152 and not CVS space using TRACULA if I
have to follow all the steps
starting Setting Up a Configuration File to run Tracula and then to
continue
thanks, i've fixed recon-all locally for the next release.
i added this line:
mkdir -p $subjdir/scripts
before this line:
set XOptsPreExist = $subjdir/scripts/expert-options
n.
On Fri, 2011-11-11 at 14:52 -0600, Michael Harms wrote:
Hi guys,
There is an issue with recon-all abending if
Hi Mike
that's just our way of ensuring that people using the expert opts are
actually experts :)
Bruce
On Fri, 11 Nov 2011, Michael Harms wrote:
Hi guys,
There is an issue with recon-all abending if you use the -expert option
on the very first call to recon-all, because recon-all
Ok, so a successful work-around strategy currently would be a two
command approach:
recon-all -s $subjid -i input.nii
recon-all -s $subjid -all -expert expert.opts
But it would be nice if
recon-all -s $subjid -i input.nii -expert expert.opts
worked as well :)
cheers,
-MH
On Fri, 2011-11-11
1. Currently trac-all uses only the MNI template, not CVS. So yes, all
steps apply.
2. See the tracula tutorial, section outputs from tracula, to see where
to find the MNI-space outputs.
3. What clusters are you talking about? Do you want to do a voxel-based
analysis? If so, why are
Hello,
I am having a similar problem to one described on the freesurfer mail
archive, where I receive the following error when trying to identify V1
using the Hinds method (i.e. recon-all -s subject -label_v1):
processing subject V1_average...
MRISreadVertexPosition(white): could not open file
I've posted two scripts -- one for starting an instance and one for running
freesurfer -- using Pedro's AMI. They're in Python, and require two
additional Python packages which are easily installable. If people find
this a good starting point, please send me suggestions or code (including
Thanks, Pedro!
I am glad to see that you posted a public AMI for freesurfer. And
thanks to Thomas for producin documentation on how to use it.
This thread inspired me share a StarCluster AMI (ami-27f1384e in the
us-east-1 region) that I built for batch FS jobs, which includes the
initial setup
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