Hi Faezeh, It is strange that the LUT file you sent doesn't seem to be named anything similar to the file you called. You are calling
new/002_S_0413/labels/aparc.annot.a2009s.ctab There also seem to be some basic issues with the command --s should just have the name of the subject not a separate directory as well. Why are you using the --nhits option? Here is an example, of what I think is closer to what you want: mris_label2annot --s 002_S_0413 --h lh --ctab faezeh_lut.ctab --a myaparc_test --l 002_S_0413/labels/lh.G_and_S_paracentral.label Work from there and see if that gets you the first one, then just add as you go. Also check that you are properly loading the data in freeview: freeview -f 002_S_0413/surf/lh.inflated:annot=lh.myaparc_test.annot hth d On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei <faezeved...@gmail.com> wrote: > Hi, > > > Here is the text format of those files. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei <faezeved...@gmail.com> wrote: >> >> Hi >> >> Thank you so much for your response. I attached here three files including >> the command lines, LUT file , and the list of names I want to get and what >> the result is actually. I'd appreciate if you look at them and let me know >> what is wrong with that. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei <faezeved...@gmail.com> >> wrote: >>> >>> Hi, >>> >>> I checked again to arrange the labels in the order of LUT file, but the >>> result has not changed. Can you help me more how I can fix this problem? >>> Thank you so much for your time and help. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei <faezeved...@gmail.com> >>> wrote: >>>> >>>> Hi, >>>> >>>> Thank you for your response. Yes, you are right. The names come from the >>>> color LUT file. But, the issue is that I chose the label files from that >>>> LUT >>>> file too. It meas the source that I chose the label files from and the >>>> source of the region's names in tksurfer are the same. The problem is just >>>> I >>>> do not have the label's names I merged to create annot file, in the >>>> tksurfer >>>> GUI. It shows another names of that list! So, what do you think about? What >>>> is the problem? >>>> >>>> Regards, >>>> Faezeh Vedaei >>>> >>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei <faezeved...@gmail.com> >>>> wrote: >>>>> >>>>> Hi Freesurfer experts, >>>>> >>>>> I have created an annotation file by several label files using >>>>> mris_label2annot command in Freesurfer. The problem is that when I open >>>>> this >>>>> annot file in tksurfer and click on colored regions which corresponded to >>>>> specific labels I had chosen them, I do not have their name on the vertex >>>>> information part at the bottom of tksurfer GUI. It shows very different >>>>> names for these regions. May you explains me what is the problem I could >>>>> not >>>>> see the exact region's name as I have them for label files? >>>>> >>>>> Thanks, >>>>> Faezeh Vedaei >>>> >>>> >>> >> > > > _______________________________________________ > 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. >
faezeh_lut.ctab
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