Thanks Dr Kim, the cp -r command worked beautifully and I got the annotation file now. However, the permission error I tried to fix earlier too but, I still get the same permission denied error. Thanks much for your help.

Kind regards,

Sampada

On Sat, Feb 4, 2017 at 3:39 PM, Seung-Goo KIM solleo@gmail.com wrote:

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

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Thanks Dr Greve.

Kind regards,

Sam

On Monday, February 6, 2017, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

You need to give yourself write permission into that directory (using chmod). This is tricky because you may have to give everyone write permission. You can also save the annot to another folder (something like --a ./myaparc to save in the current directory)

On 02/03/2017 03:21 AM, Dr Sampada Sinha 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

-- Sampada ​Research medical scientist (B)​ Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 ​, Uttar Pradesh​ India

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