Thank you so much! I understand what's the problem and I will make my custom ctab file.
Last question, about the annot files, is it possible with freesurfer to create a mask with the annot or the label files in which the value 1 is assigned to the region and 0 to the rest of the brain? Thanks again! Best Francesca 2015-05-05 4:20 GMT+03:00 Nick Schmansky, MGH <ni...@nmr.mgh.harvard.edu>: > 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. > > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il
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