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.gronensch...@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.gronensch...@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.gronensch...@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.gronensch...@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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
