Thank you both! Much appreciated.

Best,

Erin

--
Erin Walsh, Ph.D.
Postdoctoral Research Associate
University of Wisconsin-Madison
Department of Psychiatry: Abercrombie Lab
6001 Research Park Blvd.
Madison, WI 53719
edubwalsh@gmail.com

On Fri, Apr 26, 2013 at 3:07 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu> wrote:

The visualization Erin is shooting for actually weights the colors of
each subfield by their probabilities, generating a nice, smooth, soft
segmentation.
Erin, Zeke is looking into the problem and will get back to you
(hopefully) soon.
Cheers,
/Eugenio

On Fri, 2013-04-26 at 16:03 -0400, Louis Nicholas Vinke wrote:
> Hi Erin,
> Try this command after cd into the subject's mri dir, treating the hippo
> subfields as volumes.
>
> freeview nu.mgz posterior_Left-Hippocampus.mgz:colormap=heat
> posterior_Right-Hippocampus.mgz:colormap=heat
>
> The labels are probability maps (Eugenio correct me if wrong) so
> displaying with the FS look-up table makes them look like confetti.  As a
> heatmap makes more sense.
> -Louis
>
> On Fri, 26 Apr 2013, Erin Walsh wrote:
>
> > Hi Freesurfers,
> >
> > I have been experiencing issues with visualizing the hippocampal subfields.
> > I have attempted to try fixes I found in previous threads with no success.
> > Hopefully someone here may have a solution.
> >
> > Thanks for any help!
> >
> > Erin
> >
> >
> >
> > Freesurfer Info:
> >
> > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0
> > Kernel info: Darwin 12.2.0 x86_64
> >
> >
> > Error Message:
> >
> > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% freeview nu.mgz \
> >
> > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \
> >
> > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \
> >
> > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
> >
> > 2013-04-26 14:19:16.237 freeview.bin[42704:f07] invalid drawable
> >
> > 2013-04-26 14:19:16.238 freeview.bin[42704:f07] invalid drawable
> >
> > 2013-04-26 14:19:16.250 freeview.bin[42704:f07] invalid drawable
> >
> > 2013-04-26 14:19:16.251 freeview.bin[42704:f07] invalid drawable
> >
> > 2013-04-26 14:19:16.262 freeview.bin[42704:f07] invalid drawable
> >
> > 2013-04-26 14:19:16.263 freeview.bin[42704:f07] invalid drawable
> >
> > 2013-04-26 14:19:16.274 freeview.bin[42704:f07] invalid drawable
> >
> > 2013-04-26 14:19:16.275 freeview.bin[42704:f07] invalid drawable
> >
> > QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT
> > slot (QGroupBox::setShown(bool))
> >
> > QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT
> > slot (QGroupBox::setShown(bool))
> >
> > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels
> > posterior_left_* posterior_Left-Hippocampus.mgz \
> >
> > -p-labels: Command not found.
> >
> > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels
> > posterior_right_* posterior_Right-Hippocampus.mgz \
> >
> > -p-labels: Command not found.
> >
> > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-prefix posterior_
> > -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
> >
> > -p-prefix: Command not found.
> >
> >
> >
> > --
> > Erin Walsh, Ph.D.
> > Postdoctoral Research Associate
> > University of Wisconsin-Madison
> > Department of Psychiatry: Abercrombie Lab
> > 6001 Research Park Blvd.
> > Madison, WI 53719
> > edubwalsh@gmail.com
> >
> >

> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
-------------------------------------------------------------------------------------
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
iglesias@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
Department of Radiology, MGH, Harvard Medical School
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.

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