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. DGREVE@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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Sure. Thank you.

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 Reading ctab /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt Number of ctab entries 1016 INFO: no labels specified, generating from ctab

$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 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 0 LabelThresh 0 0.000000 Loading /home/rachelsun/Software/freesurfer/subjects/p6/surf/rh.orig Mapping unhit to unknown Found 123407 unhit vertices Writing annot to /home/rachelsun/Software/freesurfer/subjects/p6/label/rh.t500.annot

Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年8月19日周一 下午10:14写道：

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. DGREVE@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

---

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 listFreesurfer@nmr.mgh.harvard.eduhttps://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