Does SUMA support GIFTI and provide a utility to convert between its formats and GIFTI? I was also wondering what a .dset was and how to get it into GIFTI so it could be easily used across software platforms.
Thanks, Matt. On 5/5/15, 5:30 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >sorry, I think this may be a question for the SUMA people - I don't know >what .dset format is. Are you going to do the masking within SUMA? I'll >cc >Ziad so he can chime in. > >cheers >Bruce > >On Tue, 5 May 2015, Francesca Strappini wrote: > >> 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-L >>in >> >> >> >> 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 >> >>_______________________________________________ >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
