Hello Freesurfers - I just finished up with some group ROI analyses on thickness and surface area measures derived from Freesurfer. Basically ran the recon-all command, extracted individual ROI measures from the aparc and aseg files and did my between-group analyses in SPSS. Now, i'd like to display the significant ROIs on the brain with its corresponding p/F value. What would be the easiest and most straightforward way to do this?
Thanks, Shashwath
Hi,
I am trying to use this for the aparc+aseg-in-highres.mgz file instead of the default aparc
mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/labels this works
But how do I specify aparc+aseg-in-highres.mgz
I tried --aparc+aseg-in-highres but it was not recognised..
Thank you, S
What is aparc+aseg-in-highres.mgz?
On Jun 15, 2011, at 5:16 PM, "Sudhin A. Shah" sut2006@med.cornell.edu wrote:
aparc+aseg-in-highres.mgz
If you're trying to create a label from a volume then use mri_cor2label. doug
Sudhin A. Shah wrote:
Hi,
I am trying to use this for the aparc+aseg-in-highres.mgz file instead of the default aparc
mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/labels this works
But how do I specify aparc+aseg-in-highres.mgz
I tried --aparc+aseg-in-highres but it was not recognised..
Thank you, S
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Actually, its the opposite. I'm trying to get a volume from the label aka http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-fr...
On 06/16/11, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
If you're trying to create a label from a volume then use mri_cor2label. doug
Sudhin A. Shah wrote:
Hi,
I am trying to use this for the aparc+aseg-in-highres.mgz file instead of the default aparc
mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/labels this works
But how do I specify aparc+aseg-in-highres.mgz
I tried --aparc+aseg-in-highres but it was not recognised..
Thank you, S
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
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Hi Shashwath:
The QDEC model in FS will allow you to do this. The website has all the details.
best,
Alan
On Wed, Jun 15, 2011 at 5:02 PM, Shashwath Meda shashwath123@gmail.comwrote:
Hello Freesurfers - I just finished up with some group ROI analyses on thickness and surface area measures derived from Freesurfer. Basically ran the recon-all command, extracted individual ROI measures from the aparc and aseg files and did my between-group analyses in SPSS. Now, i'd like to display the significant ROIs on the brain with its corresponding p/F value. What would be the easiest and most straightforward way to do this?
Thanks, Shashwath
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Alan - I dont see the instructions on how QDEC handles this? Could you point me out to the wiki page that has this info. Again I dont want to draw manual ROIs instead i want to assign my own value to the color tables corresponding to the aparc labels in FS.
On Wed, Jun 15, 2011 at 4:28 PM, Alan Francis alandarkenergy@gmail.comwrote:
Hi Shashwath:
The QDEC model in FS will allow you to do this. The website has all the details.
best,
Alan
On Wed, Jun 15, 2011 at 5:02 PM, Shashwath Meda shashwath123@gmail.comwrote:
Hello Freesurfers - I just finished up with some group ROI analyses on thickness and surface area measures derived from Freesurfer. Basically ran the recon-all command, extracted individual ROI measures from the aparc and aseg files and did my between-group analyses in SPSS. Now, i'd like to display the significant ROIs on the brain with its corresponding p/F value. What would be the easiest and most straightforward way to do this?
Thanks, Shashwath
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.
Hi Shashwath
you can load a color table from the file menu in tksurfer. We almost never do this, so I'm not positive it works. The other thing you could do is read the annotation into matlab and change the color table that is stored in it, then write it back out.
cheers Bruce On Thu, 16 Jun 2011, Shashwath Meda wrote:
Hi Alan - I dont see the instructions on how QDEC handles this? Could you point me out to the wiki page that has this info. Again I dont want to draw manual ROIs instead i want to assign my own value to the color tables corresponding to the aparc labels in FS.
On Wed, Jun 15, 2011 at 4:28 PM, Alan Francis alandarkenergy@gmail.comwrote:
Hi Shashwath:
The QDEC model in FS will allow you to do this. The website has all the details.
best,
Alan
On Wed, Jun 15, 2011 at 5:02 PM, Shashwath Meda shashwath123@gmail.comwrote:
Hello Freesurfers - I just finished up with some group ROI analyses on thickness and surface area measures derived from Freesurfer. Basically ran the recon-all command, extracted individual ROI measures from the aparc and aseg files and did my between-group analyses in SPSS. Now, i'd like to display the significant ROIs on the brain with its corresponding p/F value. What would be the easiest and most straightforward way to do this?
Thanks, Shashwath
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