OK, I see why this is not working. We've been changing some name conventions in our internal FreeSurfer repository after the public release of version 5.1, and somehow you managed to get an incompletely updated version.
It appears from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some versions for the Mac were updated *after* the release date (24 May 2011), so I'll check with the engineers what exactly happened. Do you remember which file you downloaded?
Thanks,
Koen
On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild ed.gronenschild@np.unimaas.nl wrote:
Hi Koen,
No worries. The result of grep is:
500 right_CA2_3 17 85 136 0 550 left_CA2_3 17 85 137 0
Ed
On 4 Apr 2012, at 12:41, Koen Van Leemput wrote:
Hi Ed,
Can you please do
"grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt"
and let me know what the result is?
Thanks, and sorry this seems so difficult to sort out.
Koen
On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild ed.gronenschild@np.unimaas.nl wrote:
Hi Koen,
As already mentioned, I'm using v5.1.0, Mac Intel Leopard version. The voxel values of posterior_left_CA2-3.mgz and posterior_right_CA2-3.mgz are between 0 and 255, if that is what you mean by "results". By the way: I always get the 8 lines with "invalid drawable" messages from freeview.
Ed
On 3 Apr 2012, at 21:29, Koen Van Leemput wrote:
Hi Ed,
What version of the FreeSurfer build are you using?
Also, could you please let me know what the result is of "ls posterior_left_CA2*"?
Thanks,
Koen
On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild ed.gronenschild@np.unimaas.nl wrote:
Hi,
I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory)
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
and got the following messages:
2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] 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)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name right_CA2-3 CTABrgbAtIndexi: index -1 was OOB
Nothing was shown on top of nu.mgz. All the left and righ posterior files are present.
(Mac OS X 10.6.8, FreeSurfer version 5.1.0)
Cheers, Ed _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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