Dear FS list,
I have significant clusters from several QDEC analyses (each one for a different DV< i.e. thickness, area, etc). I would like to generate a picture of a standard brain (talairach or MNI) with several of these clusters superimposed on the same brain, to show where there are e.g. regions of increased thickness and of decreased volume.
I thought I could just load a standard brain in FreeView and then add the MGH files corresponding to all my contrasts of interest (after they've been MonteCarlo-corrected), in order to view all my clusters on the same brain. However, when I load any *mc-z.abs.th13.sig.cluster.mgh *in FreeView, the image seems to be blank, although in QDEC it shows a large blue cluster. I played around with the Min/Max/Level values in FreeView, but that didn't help.
Can anyone suggest how to accomplish this?
Thanks!
Tudor
That mgh file will have surface data in it. You need to convert it to volume data to show it on a volume. If you want to show it on the mni152, then use mri_surf2vol with --reg $FREESURFER_HOME/average/mni152.register.dat and specify the 2mm MNI152 brain as the target. Also tell it to fill the ribbon doug
On 10/02/2014 08:48 AM, Tudor Popescu wrote:
Dear FS list,
I have significant clusters from several QDEC analyses (each one for a different DV< i.e. thickness, area, etc). I would like to generate a picture of a standard brain (talairach or MNI) with several of these clusters superimposed on the same brain, to show where there are e.g. regions of increased thickness and of decreased volume.
I thought I could just load a standard brain in FreeView and then add the MGH files corresponding to all my contrasts of interest (after they've been MonteCarlo-corrected), in order to view all my clusters on the same brain. However, when I load any /mc-z.abs.th13.sig.cluster.mgh /in FreeView, the image seems to be blank, although in QDEC it shows a large blue cluster. I played around with the Min/Max/Level values in FreeView, but that didn't help.
Can anyone suggest how to accomplish this?
Thanks!
Tudor
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug. Is it not easier to use the *mc-z.abs.th13.sig.cluster.mgh *images to display the clusters as surfaces instead of volumes, superimposed on the standard FreeSurfer brain (MNI305) as opposed to on the MNI152? T
On 3 October 2014 18:23, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
That mgh file will have surface data in it. You need to convert it to volume data to show it on a volume. If you want to show it on the mni152, then use mri_surf2vol with --reg $FREESURFER_HOME/average/mni152.register.dat and specify the 2mm MNI152 brain as the target. Also tell it to fill the ribbon doug
On 10/02/2014 08:48 AM, Tudor Popescu wrote:
Dear FS list,
I have significant clusters from several QDEC analyses (each one for a different DV< i.e. thickness, area, etc). I would like to generate a picture of a standard brain (talairach or MNI) with several of these clusters superimposed on the same brain, to show where there are e.g. regions of increased thickness and of decreased volume.
I thought I could just load a standard brain in FreeView and then add the MGH files corresponding to all my contrasts of interest (after they've been MonteCarlo-corrected), in order to view all my clusters on the same brain. However, when I load any /mc-z.abs.th13.sig.cluster.mgh /in FreeView, the image seems to be blank, although in QDEC it shows a large blue cluster. I played around with the Min/Max/Level values in FreeView, but that didn't help.
Can anyone suggest how to accomplish this?
Thanks!
Tudor
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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yea, you can do it on the fsaverage/305, but if you want to see it as a volume, you'll have to run mri_surf2vol doug
On 10/03/2014 02:48 PM, Tudor Popescu wrote:
Thanks Doug. Is it not easier to use the /mc-z.abs.th13.sig.cluster.mgh /images to display the clusters as surfaces instead of volumes, superimposed on the standard FreeSurfer brain (MNI305) as opposed to on the MNI152? T
On 3 October 2014 18:23, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That mgh file will have surface data in it. You need to convert it to volume data to show it on a volume. If you want to show it on the mni152, then use mri_surf2vol with --reg $FREESURFER_HOME/average/mni152.register.dat and specify the 2mm MNI152 brain as the target. Also tell it to fill the ribbon doug On 10/02/2014 08:48 AM, Tudor Popescu wrote: > Dear FS list, > > I have significant clusters from several QDEC analyses (each one for a > different DV< i.e. thickness, area, etc). I would like to generate a > picture of a standard brain (talairach or MNI) with several of these > clusters superimposed on the same brain, to show where there are e.g. > regions of increased thickness and of decreased volume. > > I thought I could just load a standard brain in FreeView and then add > the MGH files corresponding to all my contrasts of interest (after > they've been MonteCarlo-corrected), in order to view all my clusters > on the same brain. However, when I load any > /mc-z.abs.th13.sig.cluster.mgh /in FreeView, the image seems to be > blank, although in QDEC it shows a large blue cluster. I played around > with the Min/Max/Level values in FreeView, but that didn't help. > > Can anyone suggest how to accomplish this? > > Thanks! > > Tudor > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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Tudor Popescu