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Hi, 

I was wondering if you have any updates on this (getting the ctx-lh-primary-motor and ctx-lh-premotor labels or 9001 and 9002 from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT).

Thank you, 

Anja 

On Fri, Jul 10, 2020 at 10:46 AM Anja Samardzija <as2756@cornell.edu> wrote:

Sorry, I meant getting the labels 9001 (ctx-lh-primary-motor) and 9002 (ctx-lh-premotor) after running recon-all on a subject. Please disregard the mask aspect.

Thanks,
Anja

On Fri, Jul 10, 2020 at 10:31 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

I don't know what you mean by 9001 and 9002 masks

On 7/9/2020 3:16 PM, Anja Samardzija wrote:

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Hi, 

Thank you! That worked. 

I was also wondering if you can help me in getting the 9001 and 9002 masks. I tried to replicate the work from an archived post but had no luck. 

Thanks, 

Anja  

On Thu, Jul 9, 2020 at 2:51 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Sorry, gave you the wrong command line, try this

mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject lh ../surf/lh.sphere.reg  $FREESURFER_HOME/average/lh.atlas2005_simple.gcs ../label/lh.aparc.a2005s.annot

On 7/9/2020 2:12 PM, Anja Samardzija wrote:

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Hi, 

Thanks for the help! When I run the suggested commands I get redirected to the help output of the mris_ca_label. The command does not execute and looking at the mris_ca_label help page it seems as though the flags that you have suggested do not exist for mris_ca_label...Please let me know if you have any suggestions. 

Thanks, 

Anja

On Wed, Jul 8, 2020 at 11:08 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

That file is  no longer created by recon-all. But you can recreate it.

cd $SUBJECTS_DIR/subject/label
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject lh $FREESURFER_HOME/average/lh.atlas2005_simple.gcs ../label/lh.aparc.a2005s.annot

And the same for the rh

On 7/7/2020 6:17 PM, Anja Samardzija wrote:

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Hello,

I am trying to run mri_aparc2aseg with the flag --a2005s on a subject that I previously ran recon-all --all on. 

When trying to run mri_aparc2aseg with --a2005s I get the following error:
could not read annot file 010/label/lh.aparc.a2005s.annot
No such file or directory ERROR: MRISreadAnnotation() failed 010/label/lh.aparc.a2005s.annot.

How do I solve this issue (get the lh.aparc.a2005s.annot file)? 

Thank you, 

Anja 

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