can you send your command line and full terminal output?
On 8/19/2019 9:24 PM, Rachel S wrote:
External Email - Use Caution
Hi Greve,
Thank you for your prompt reply. I tried removing --l before. But it gave
Mapping unhit to unknown
Found 123407 unhit vertices
None of the vertices were labeled.
What could be the problem? Thank you.
Best regards,
Rachel
Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
于2019年8月19日周一 下午6:07写道：
You should remove the --l argument. That is incompatible with --ldir.
On 8/19/19 5:50 PM, Rachel S wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer community,
>
> I was trying to use mris_label2annot to generate annotation file, my
> commands are:
>
> mris_label2annot --s p6 --h rh --a t500 --ldir
> $SUBJECTS_DIR/p6/label/regenerated_rh_500 --nhits nhits.mgh --ctab
> /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt --l
> $SUBJECTS_DIR/p6/label/regenerated_rh_500/rh.pericalcarine_7.label
> --surf pial
>
> The output of the command is:
> Reading ctab /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt
> Number of ctab entries 1016
>
> $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
> cwd /home/rachelsun/Software/freesurfer/subjects/fsaverage5/mri
> cmdline mris_label2annot --s p6 --h rh --a t500 --ldir
> /home/rachelsun/Software/freesurfer/subjects/p6/label/regenerated_rh_500
> --nhits nhits.mgh --ctab
> /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt --l
> /home/rachelsun/Software/freesurfer/subjects/p6/label/regenerated_rh_500/rh.pericalcarine_7.label
> --surf pial
> sysname Linux
> hostname rachel-pc
> machine x86_64
> user rachelsun
>
> subject p6
> hemi rh
> SUBJECTS_DIR /home/rachelsun/Software/freesurfer/subjects
> ColorTable /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt
> AnnotName t500
> NHitsFile nhits.mgh
> nlables 1
> LabelThresh 0 0.000000
> Loading /home/rachelsun/Software/freesurfer/subjects/p6/surf/rh.pial
> 1 107939 rh.lateralorbitofrontal_9
> Mapping unhit to unknown
> Found 123130 unhit vertices
> Writing annot to
> /home/rachelsun/Software/freesurfer/subjects/p6/label/rh.t500.annot
>
> I am sure I have rh.pericalcarine_7 in the folder, but the code always
> generates rh.lateralorbitofrontal_9 region. And I also attached my
> colortable file for your reference.
>
> Thank you for your help.
>
> Best regards,
> Rachel
>
>
>
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