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
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
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.
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
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.
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
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.
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
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.
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
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.
I have downloaded the file freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, date 26/05/2011.
Ed
On 4 Apr 2012, at 13:09, Koen Van Leemput wrote:
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
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.
Hi Ed,
It seems that the 5.1.0 release for the Mac was composed two days after the one for Linux, and during exactly those two days one of us made a change to the file $FREESURFER_HOME/FreeSurferColorLUT.txt.
To correct this issue, please make a back-up copy of your FreeSurferColorLUT.txt file, and execute the following commands:
cd $FREESURFER_HOME sed -i "s/CA2_3/CA2/3/g" FreeSurferColorLUT.txt sed -i "s/CA4_DG/CA4/DG/g" FreeSurferColorLUT.txt
Thanks,
Koen
On Wed, Apr 4, 2012 at 9:32 AM, Ed Gronenschild ed.gronenschild@np.unimaas.nl wrote:
I have downloaded the file freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, date 26/05/2011.
Ed
On 4 Apr 2012, at 13:09, Koen Van Leemput wrote:
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 > > > 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. >
Hi Koen,
Thanks, this solved the problem.
Ed
On 4 Apr 2012, at 19:21, Koen Van Leemput wrote:
Hi Ed,
It seems that the 5.1.0 release for the Mac was composed two days after the one for Linux, and during exactly those two days one of us made a change to the file $FREESURFER_HOME/FreeSurferColorLUT.txt.
To correct this issue, please make a back-up copy of your FreeSurferColorLUT.txt file, and execute the following commands:
cd $FREESURFER_HOME sed -i "s/CA2_3/CA2/3/g" FreeSurferColorLUT.txt sed -i "s/CA4_DG/CA4/DG/g" FreeSurferColorLUT.txt
Thanks,
Koen
On Wed, Apr 4, 2012 at 9:32 AM, Ed Gronenschild ed.gronenschild@np.unimaas.nl wrote:
I have downloaded the file freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, date 26/05/2011.
Ed
On 4 Apr 2012, at 13:09, Koen Van Leemput wrote:
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 >> >> >> 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
-
Ed Gronenschild -
Koen Van Leemput