Thanks all! Very helpful.
Happy Friday,
Erin
-- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Labhttp://www.psychiatry.wisc.edu/abercrombie/ 6001 Research Park Blvd. Madison, WI 53719 edubwalsh@gmail.com
On Fri, Apr 26, 2013 at 4:43 PM, Marcos Martins da Silva < marcosmds@terra.com.br> wrote:
** I guess during the copy/paste something not clearly visible was included and resulted in error. If you pay attention to freeview's info panel you will see each file loading along the time. Depending on the slices you are seeing at axial, sagital and coronal views you will see just a few colored points but after some time all the subfields will appear. I did not check the time but the process also takes about 5-10 minutes in my environment..
Em Sex, 2013-04-26 às 15:58 -0500, Erin Walsh escreveu:
Hi Eugenio and Zeke,
I attempted to enter the command line in again (re-copying/pasting) from the website. Perhaps I had entered in an error somewhere before because after 10+min, both volumes were able to load with the color maps. I will try replicating this to ensure it works.
Apologies for my previous premature email-- I had tried the command a few times with the same errors, clearly I made an error somewhere.
Just a few other questions:
The "invalid drawable" message: Is that standard or is something truly awry with the command? It continues to appear.
Does it normally take 10+min for the segmentation maps to appear?
Many thanks,
Erin
-- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Labhttp://www.psychiatry.wisc.edu/abercrombie/ 6001 Research Park Blvd. Madison, WI 53719 edubwalsh@gmail.com
On Fri, Apr 26, 2013 at 3:08 PM, Erin Walsh edubwalsh@gmail.com wrote:
Thank you both! Much appreciated.
Best,
Erin
-- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Labhttp://www.psychiatry.wisc.edu/abercrombie/ 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
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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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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 athttp://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.