Hi Sam,

It seems that you should change the permission of "Users/Sampada/Desktop/AD/fsaverage/label/“ as 755:

chmod $DIR 755

If you cannot do this because you are not the owner of the directory, then just copy fsaverage directory into your working directory:

cp -r ${SUBJECTS_DIR}/fsaverage ${YOUR_DIR}/fsaverage

Best,

-- 

Seung-Goo KIM

On 2017-02-04, at 03:07, Dr Sampada Sinha <drsampadasinha@gmail.com> wrote:

Dear Freesurfer experts,

I am trying to create medial temporal lobe and for that I ran the command mri_annotation2label to create ?h.entorhinal.label, ?h.temporalpole.label and ?h.parahippocampal.label from fsaverage and stored these labels in labels.?h directory. After this I ran mris_label2annot, taking cue from page https://surfer.nmr.mgh.harvard.edu/fswiki/mris_label2annot.

My command line is the following (fsaverage has been linked to my subject directory:

rmbp:AD Sampada$ mris_label2annot  --s fsaverage --h lh --ctab /Applications/freesurfer/subjects/bert/label/aparc.annot.ctab --a myaparc --l ./labels_lh/lh.temporalpole.label --l ./labels_lh/lh.parahippocampal.label --l ./labels_lh/lh.entorhinal.label --nhits nhits.mgh 

However, it comes with following error

Writing annot to /Users/Sampada/Desktop/AD/fsaverage/label/lh.myaparc.annot

could not write annot file /Users/Sampada/Desktop/AD/fsaverage/label/lh.myaparc.annot

Permission denied

Will you please let me know how to fix this problem . I can see its a permission error but don't know how to overcome it. 

Thanks for your help

Kind regards,

--

Sampada

​Research medical scientist (B)​

Department of Geriatric Mental Health (DGMH)

King George Medical University

Lucknow-226003

​, Uttar Pradesh​

India

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.