Do you have write permission into that folder?

The surface is just the surface that the annotation is on. Once you have your label, you can use it for thickness

On 5/26/17 3:54 AM, Duy Nguyen wrote:

Dear FreeSurfer experts

I am trying to extract the label using standard aparc.annot and will be using mri_mergelabels to create my own lobes to do GLM fit later on for ROI analysis.

However, it shows me the error like this when I check there are the files aparc.annot and the file from surf folder.

[toibigi2007@localhost OASIS_Data]$ mri_annotation2label --subject OASIS_0002_MR1 --hemi lh --outdir $SUBJECTS_DIR/OASIS_0002_MR1/label

subject = OASIS_0002_MR1

annotation = aparc

hemi = lh

outdir = /media/3B110EAE3B9DE8E0/OASIS_Data/OASIS_0002_MR1/label

surface   = white

ERROR: creating directory /media/3B110EAE3B9DE8E0/OASIS_Data/OASIS_0002_MR1/label

No such file or directory

One more question is that it says default is "white" surface, but I want to measure the cortical thickness.  Can I leave white in like this or do I change into --surf to gray for this?

Thank you and best regards,

--v-- Peace --v--

Duy Nguyễn 

Biomedical Engineering Department- IU HCMC

Cell: (+84)909999056

Email: duy.nguyenbme@gmail.com

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