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> > 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 <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 >> <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 > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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