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
_______________________________________________ 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.
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.
The "invalid drawable" are warning messages and are normal. No need to worry about them.
-Zeke
On 04/26/2013 04:58 PM, Erin Walsh wrote:
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 Lab http://www.psychiatry.wisc.edu/abercrombie/ 6001 Research Park Blvd. Madison, WI 53719 edubwalsh@gmail.com mailto:edubwalsh@gmail.com
On Fri, Apr 26, 2013 at 3:08 PM, Erin Walsh <edubwalsh@gmail.com mailto: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 Lab <http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwalsh@gmail.com <mailto:edubwalsh@gmail.com> On Fri, Apr 26, 2013 at 3:07 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu <mailto: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 <mailto:edubwalsh@gmail.com> > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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. 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.
freesurfer@nmr.mgh.harvard.edu
-
Erin Walsh -
zkaufman＠nmr.mgh.harvard.edu