Hmm, not sure what to tell you. The label is derived directly from the annot. If you click on a vertex in the branch, does it appear to be in the label based on what displays in the control panel? If you load it on the inflated surface, do you still see the branch?
On 10/15/2018 08:42 PM, Ting Li wrote: > External Email - Use Caution > > The annot file loaded successfully and without any branches. Thanks a lot. > > Ting >> On Oct 15, 2018, at 2:22 PM, Greve, Douglas N.,Ph.D. >> <dgr...@mgh.harvard.edu> wrote: >> >> Click on the surface file name in the upper left corner of FreeView, >> then load the Annotation from the panel just below it. It does not make >> sense that you would see the branches on the folded surface but not on >> the inflated. >> >> On 10/15/2018 03:06 PM, Ting Li wrote: >>> External Email - Use Caution >>> >>> I didn't load the annot file. I just use the annot file to create the >>> label. if I check the clusters in a inflated brain, they are looks >>> fine. If I need to load annot file for checking, how can I do it? >>> Thanks a lot. >>> >>> Ting >>> >>> On Mon, Oct 15, 2018 at 9:25 AM Greve, Douglas N.,Ph.D. >>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: >>> >>> does the same thing happen when you load the annot file? >>> >>> On 10/13/18 10:03 PM, Ting Li wrote: >>>> External Email - Use Caution >>>> >>>> Dear Dr. Douglas, >>>> >>>> I can load the label, but some clusters have branches. Some of >>>> them are just looks fine. Do you know the reason? Thanks a lot. >>>> >>>> Regards, >>>> Ting >>>> >>>> >>>> >>>> >>>>> On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D. >>>>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: >>>>> >>>>> yes, that is fine >>>>> >>>>> On 10/11/18 11:21 PM, Ting Li wrote: >>>>>> External Email - Use Caution >>>>>> >>>>>> Dear Dr. Douglas, >>>>>> >>>>>> Thank you so much for your response. With your instruction, it >>>>>> works. This is how I did. >>>>>> >>>>>> First, copy the significant cluster annot file from the >>>>>> simulation fold to one of subject label folder. >>>>>> Secondly, use the mir_annotation2label command to make this >>>>>> cluster into a label file >>>>>> Thirdly, copy this label file to fsaverage label folder >>>>>> Finally, I can load the label to the fsaverage surf. >>>>>> >>>>>> Is this the right procedure? Thanks a lot! >>>>>> >>>>>> Regards, >>>>>> Ting >>>>>>> On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D. >>>>>>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: >>>>>>> >>>>>>> Which subject did you load it on? It must be fsaverage. Can >>>>>>> you send the >>>>>>> terminal output and command line? >>>>>>> >>>>>>> On 10/03/2018 11:31 PM, Ting Li wrote: >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Dear Freesurfer Expert, >>>>>>>> >>>>>>>> I have figured out the problem is that I didn’t specify lh >>>>>>>> before the >>>>>>>> annot file. However, in this method, I didn’t get the right >>>>>>>> label for >>>>>>>> I have loaded the label into the subject file. It is the >>>>>>>> scatter points. >>>>>>>> >>>>>>>> I want to create label through mri_glm-fit-sim clusters. What >>>>>>>> command >>>>>>>> I should use? Please specify it for me. Thanks a lot! >>>>>>>> >>>>>>>> Your help means a lot. >>>>>>>> >>>>>>>> Regards, >>>>>>>> Ting >>>>>>>>> On Oct 3, 2018, at 9:38 PM, Ting Li <tx...@ualr.edu >>>>>>>>> <mailto:tx...@ualr.edu> >>>>>>>>> <mailto:tx...@ualr.edu>> wrote: >>>>>>>>> >>>>>>>>> I have also tried the command without annot in specifying the >>>>>>>>> annotation file. Thanks a lot. >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> >>>>>>>>> Ting >>>>>>>>>> On Oct 3, 2018, at 9:36 PM, Ting Li <tx...@ualr.edu >>>>>>>>>> <mailto:tx...@ualr.edu> >>>>>>>>>> <mailto:tx...@ualr.edu>> wrote: >>>>>>>>>> >>>>>>>>>> Dear Freesurfer Experts, >>>>>>>>>> >>>>>>>>>> I really need your attention and help. Thanks a lot. >>>>>>>>>> >>>>>>>>>> We want to create label through the mri_glm-fit-sim cluster >>>>>>>>>> results. >>>>>>>>>> >>>>>>>>>> We have found the same topic in 2013 and tried the method >>>>>>>>>> you have >>>>>>>>>> provided. However, it doesn’t work. If you think it is not >>>>>>>>>> the right >>>>>>>>>> way, could you give me an example to do it right. I really >>>>>>>>>> appreciate your great help. Thanks a lot. >>>>>>>>>> >>>>>>>>>> Here is my code: >>>>>>>>>> >>>>>>>>>> mri_annotation2label --subject F999 --hemi lh --annotation >>>>>>>>>> cache.th20.neg.sig.ocn.annot --labelbase lh.test_label >>>>>>>>>> >>>>>>>>>> Here is my error information: >>>>>>>>>> subject = F999 >>>>>>>>>> annotation = cache.th20.neg.sig.ocn.annot >>>>>>>>>> hemi = lh >>>>>>>>>> labelbase = lh.test_label >>>>>>>>>> surface = white >>>>>>>>>> >>>>>>>>>> Reading surface >>>>>>>>>> /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white >>>>>>>>>> Loading annotations from >>>>>>>>>> >>>>>>>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot >>>>>>>>>> could not read annot file >>>>>>>>>> >>>>>>>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot >>>>>>>>>> No such file or directory >>>>>>>>>> INFO: could not load from >>>>>>>>>> >>>>>>>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot, >>>>>>>>>> trying >>>>>>>>>> >>>>>>>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot >>>>>>>>>> could not read annot file >>>>>>>>>> >>>>>>>>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot >>>>>>>>>> No such file or directory >>>>>>>>>> ERROR: MRISreadAnnotation() failed >>>>>>>>>> >>>>>>>>>> This is the annot files in my directory F999: >>>>>>>>>> ls F999/label/*.annot >>>>>>>>>> F999/label/cache.th20.neg.sig.ocn.annot >>>>>>>>>> F999/label/lh.BA_exvivo.annot >>>>>>>>>> F999/label/rh.aparc.DKTatlas.annot >>>>>>>>>> F999/label/lh.aparc.a2009s.annot >>>>>>>>>> F999/label/lh.BA_exvivo.thresh.annot >>>>>>>>>> F999/label/rh.BA_exvivo.annot >>>>>>>>>> F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot >>>>>>>>>> F999/label/rh.BA_exvivo.thresh.annot >>>>>>>>>> F999/label/lh.aparc.DKTatlas.annot >>>>>>>>>> F999/label/rh.aparc.annot >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto: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 >> >> _______________________________________________ >> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
