Francesca, I looked at the files you sent and replicated the problem. It is due to creating your lh.EKppa.annot file using FreeSurferColorLUT.txt as the colortable file. You should create your own colortable file, which is simple to do, and create a new .annot file using that colortable (ie, the --ctab option in mris_label2annot).
Here is a simple colortable.txt file (just a text file) with four entries, which in this example, means that you have three annotations. The first entry must be as it is shown, ie, 'unknown', as this is used to automatically 'label' all the vertices which do not have a .label file. 0 unknown 25 5 25 0 1 mylabel1 0 92 23 0 2 mylabel2 131 148 255 0 3 mylabel3 0 0 255 0 I fixed the code locally so that it doesn't segfault, and you can get the new mris_convert here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0/bin/ but note this does not fix your core problem, it only allows mris_convert to run to completion and create a valid .annot.gii file. It will still have strange label names for your annotations (like "Left_Hippocampus") taken from the embedded FreeSurferColorLUT. Nick On Thu, 2015-04-30 at 14:17 +0300, Francesca Strappini wrote: > Hi, sorry to bother, I'm re-posting this question just in case it got > lost. Thanks. > > Hi, > > I have a question about mris_convert. I've created some regions on the > surface and now I would like to make them directly readable into SUMA. I > ran this command but it ended with an error message. > mris_convert --annot lh.EKppa.annot > /usr/local/freesurfer/subjects/EK/surf/lh.white lh.EKppa.annot.gii > > reading colortable from annotation file... > colortable with 14176 entries read (originally > /usr/local/freesurfer/FreeSurferColorLUT.txt) > Segmentation fault (core dumped) > > I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 running on > Ubuntu 14.04.2 LTS. > > Thanks in advance for the help! > > Best > Francesca > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
