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 with the following three steps in the TRACULA processing stream (which is called by the command trac-all): * Pre-processing * FSL's bedpostX * Reconstructing white-matter (WM) pathways 2). Can I check the registration for individual subjects to see if it worked well or not on the MNI 152 template?
3) How can I see if there are clusters that survives to multiple comparison in group 1 (controls) versus group 2 (patients) without and covariant (not gender, not age). Can I get a txt file as output for this clusters?
Thank you. Antonella
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 you using tracula? Go through the tracula tutorial and read the tracula paper below to understand what tracula does: http://frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract
On Fri, 11 Nov 2011, Antonella Kis wrote:
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 with the following three steps in the TRACULA processing stream (which is called by the command trac-all):
- Pre-processing
- FSL's bedpostX
- Reconstructing white-matter (WM) pathways
2). Can I check the registration for individual subjects to see if it worked well or not on the MNI 152 template?
- How can I see if there are clusters that survives to multiple comparison
in group 1 (controls) versus group 2 (patients) without and covariant (not gender, not age). Can I get a txt file as output for this clusters?
Thank you. Antonella
Dear Anastasia,
Thank you very much for your help.
I have done a TBSS group analysis in FSL and I would like to do a similar study using Freesurfer. I understood I can use TRACULA for a similar TBSS study. Is this right? Or I should better use the dt_recon? I would like to compare my results from FSl with th eone from Freesurfer: TRACULA or dt_recon method.
Please advise.
Many thanks, Antonella
________________________________ From: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Friday, November 11, 2011 4:45 PM Subject: Re: [Freesurfer] DTI Group Analysis Study
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 you using tracula? Go through the tracula tutorial and read the tracula paper below to understand what tracula does: http://frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract
On Fri, 11 Nov 2011, Antonella Kis wrote:
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 with the following three steps in the TRACULA processing stream (which is called by the command trac-all): * Pre-processing * FSL's bedpostX * Reconstructing white-matter (WM) pathways 2). Can I check the registration for individual subjects to see if it worked well or not on the MNI 152 template?
- How can I see if there are clusters that survives to multiple comparison
in group 1 (controls) versus group 2 (patients) without and covariant (not gender, not age). Can I get a txt file as output for this clusters?
Thank you. Antonella
_______________________________________________ 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.
Dear Anastasia,
Thank you very much for your help.
I have done a TBSS group analysis in FSL and I would like to do a similar study using Freesurfer. I understood I can use TRACULA for a similar TBSS study. Is this right? Or I should better use the dt_recon? I would like to compare my results from FSl with th eone from Freesurfer: TRACULA or dt_recon method.
Please advise.
Many thanks, Antonella
________________________________ From: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Friday, November 11, 2011 4:45 PM Subject: Re: [Freesurfer] DTI Group Analysis Study
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 you using tracula? Go through the tracula tutorial and read the tracula paper below to understand what tracula does: http://frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract
On Fri, 11 Nov 2011, Antonella Kis wrote:
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 with the following three steps in the TRACULA processing stream (which is called by the command trac-all): * Pre-processing * FSL's bedpostX * Reconstructing white-matter (WM) pathways 2). Can I check the registration for individual subjects to see if it worked well or not on the MNI 152 template?
- How can I see if there are clusters that survives to multiple comparison
in group 1 (controls) versus group 2 (patients) without and covariant (not gender, not age). Can I get a txt file as output for this clusters?
Thank you. Antonella
_______________________________________________ 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
-
Anastasia Yendiki -
Antonella Kis