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.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
