Sorry, just to be clear, I meant how can I create a mask on the surface in which at each vertex is assigned a value, 0 or 1. I need to create this mask for exporting the freesurfer labels into SUMA and ultimately to extract the time series from each vertex.
Thanks Francesca 2015-05-05 16:06 GMT+03:00 Francesca Strappini <francescastrapp...@gmail.com >: > Thank you! Do you know which function should I use? > > Best > Francesca > > 2015-05-05 15:30 GMT+03:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > >> yes, you can use a label for this (we use the ?h.cortex.label for this >> purpose routinely to remove non-cortical stuff) >> >> On Tue, 5 May 2015, Francesca Strappini wrote: >> >> 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-Lin >>> ux-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 >>> >>> >> _______________________________________________ >> 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 > -- 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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