Dear Freesurfer's experts,
I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.
The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006).
I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage ( https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no download link...
Where can I find this package and how to use it ?
Many thanks !
Best,
------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France
Thank you Michael for this link !
However, it seems that we have to install very precise versions of FSL and Freesurfer.
Once we get *fsl-5.0.6* package ( http://fsl.fmrib.ox.ac.uk/fsldownloads/oldversions/), how to install this one and which wiki to follow ?
Cheers,
------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France
2014-09-19 16:35 GMT+02:00 Harms, Michael mharms@wustl.edu:
Hi, I suggest you start with the documentation that accompanies the recently released HCP pipelines. see http://www.humanconnectome.org/documentation/HCP-pipelines/ and the link therein to the pipelines on GitHub.
cheers, -MH
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
From: Matthieu Vanhoutte matthieuvanhoutte@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, September 19, 2014 9:23 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion
Dear Freesurfer's experts,I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.
The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006).
I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage ( https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no download link...
Where can I find this package and how to use it ?
Many thanks !
Best,
-------------------------------------Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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More precisely how to install *fsl-5.0.6* on ubuntu 12.10 or 14.04 ?
Thanks !
------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France
2014-09-19 17:18 GMT+02:00 Matthieu Vanhoutte matthieuvanhoutte@gmail.com:
Thank you Michael for this link !
However, it seems that we have to install very precise versions of FSL and Freesurfer.
Once we get *fsl-5.0.6* package ( http://fsl.fmrib.ox.ac.uk/fsldownloads/oldversions/), how to install this one and which wiki to follow ?
Cheers,
Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France
2014-09-19 16:35 GMT+02:00 Harms, Michael mharms@wustl.edu:
Hi, I suggest you start with the documentation that accompanies the recently released HCP pipelines. see http://www.humanconnectome.org/documentation/HCP-pipelines/ and the link therein to the pipelines on GitHub.
cheers, -MH
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
From: Matthieu Vanhoutte matthieuvanhoutte@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, September 19, 2014 9:23 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion
Dear Freesurfer's experts,I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.
The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006).
I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage ( https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no download link...
Where can I find this package and how to use it ?
Many thanks !
Best,
-------------------------------------Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Harms, Michael -
Matthieu Vanhoutte