Hi Ziad, yes, it's related to that. Thank you for the help! Best Francesca
2015-05-06 16:25 GMT+03:00 Ziad Saad <sa...@mail.nih.gov>: > Hello folks, > > I am ccing all those on the thread because I am not sure my reply to the > support list will get through. > > GIFTI is the way to go as Matt suggested and all of AFNI and SUMA programs > support that format for datasets. The .dset itself is not a format, merely > a convenient way to indicate that a file is a dataset (as opposed to a > surface, tracts, etc.). The format of .dset can be .gii, .niml, or .1D > which is the simple ascii table of numbers. > > Francesca: I suspect this is related to the AFNI message board posting > from a couple of days ago. I have not gotten around to it yet but I hope to > do so later today. > > cheers > Ziad > > On May 5, 2015, at 18:30 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-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 > > -- 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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