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
