External Email - Use Caution If I loaded the label to the inflated surface, it also gives me the cluster with branches. As you can see in the below.
If I loaded the annot file to the inflated surface, it works well. Thanks for your help. Ting > On Oct 16, 2018, at 1:51 PM, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> > wrote: > > 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
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