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

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