Hi Duy

it is Unix permissions you need to check. It looks like the subject's label dir doesn't exist or couldn't be created. cheers Bruce

On Sat, 27 May 2017, Duy Nguyen wrote:

Dear Doug  Thank you for your quick response. I got the data from oasis website. How can I get the permission to continue my analysis?

Thanks Duy On Fri, May 26, 2017 at 8:46 PM Douglas Greve greve@nmr.mgh.harvard.edu wrote:

  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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Hi Duy

ls -l

Will show you permissions, but I think you will need to do a unix tutorial or get some local help

Cheers Bruce

On May 30, 2017, at 8:06 PM, Duy Nguyen duy.nguyenbme@gmail.com wrote:

Dear Bruce

Thanks for your response. Would you please showing me how to check the Unix permission? And further that when I tried with the tutorial subject data, it was fine. Please let me know if you have any more inquiries Thank you and warmest regards, Duy

...

On Sat, May 27, 2017 at 9:16 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Duy

it is Unix permissions you need to check. It looks like the subject's label dir doesn't exist or couldn't be created. cheers Bruce

On Sat, 27 May 2017, Duy Nguyen wrote:

...

Dear Doug Thank you for your quick response. I got the data from oasis website. How can I get the permission to continue my analysis?

Thanks Duy On Fri, May 26, 2017 at 8:46 PM Douglas Greve greve@nmr.mgh.harvard.edu wrote:

  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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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.

-- Sent from Iphone

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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.

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