I'm trying to mask a time series dataset that I mapped to the surface in SUMA (surface created with freesurfer and imported into SUMA). I think the input should be in the .dset fomat (region mapped to the surface). The problem is that when I save my label the annotation file has only a list of vertexes related to the region and not all the surface vertexes.
Thanks for the help! Francesca 2015-05-05 23:04 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > you can just create a label file I guess. What input does SUMA take? > > On Tue, 5 May 2015, Francesca Strappini wrote: > > 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 >> >> > _______________________________________________ > 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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