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 ās 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 Lab
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 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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