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:
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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. <DGREVE@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:
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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.
<DGREVE@mgh.harvard.edu <mailto:DGREVE@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:
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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.
<DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
yes, that is fine
On 10/11/18 11:21 PM, Ting Li wrote:
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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.
<DGREVE@mgh.harvard.edu <mailto:DGREVE@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:
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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 <txli1@ualr.edu
<mailto:txli1@ualr.edu>
<mailto:txli1@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 <txli1@ualr.edu
<mailto:txli1@ualr.edu>
<mailto:txli1@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
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