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Thank you, Bruce for your prompt reply. I used mris_anatomical_stats first but this only gave me an averaged thickness and std etc. I'd like to get absolute cortical thickness for each vertex within ROIs. I do not interested to compute vertex-wise volume using -th3. What option should I use to get a list of absolute cortical thickness for each vertex within ROI?

Thank you again, Hisako

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, April 27, 2018 2:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertex wise cortical thickness within ROIs

Hi Hisako

you can use mris_anatomical_stats for this purpose.

cheers Bruce

On Fri, 27 Apr 2018, Fujiwara, Hisako wrote:

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Hello FreeSurfer Developers,

I'm attempting to compute absolute cortical thickness for each vertices within anatomical ROIs using apac.annot. I have successfully output the whole brain vertex wise cortical thickness using:

mris_convert –c <subject>/surf/?h.thickness <subject>/surf/?h.org  <subject>/surf/?hthickenss.asc

Since this creates huge numbers (> e.g., 140,000) for each hemisphere for each participants, I would like to narrow out focus on the specific ROIs for relevant to our study? Is this achievable to add options to do?

Thank you for your help in advance.

Best regards,

Hisako

You can do it in matlab with read_curv.m (to read in the thickness) and read_annotation.m (to read in, eg, lh.aparc.annot), then pull out the vertices you want (make sure to account for the 1-based in matlab)

On 04/27/2018 02:35 PM, Bruce Fischl wrote:

oh sorry, I misunderstood. Hmm, that's a bit trickier. I think if you create the label with the thickness overlaid, then the label file will contain the thickness at each vertex, but that might only work in dev in freeview. Perhaps Ruopeng can comment?

cheers Bruce

On Fri, 27 Apr 2018, Fujiwara, Hisako wrote:

...

External Email - Use Caution

Thank you, Bruce for your prompt reply. I used mris_anatomical_stats first but this only gave me an averaged thickness and std etc. I'd like to get absolute cortical thickness for each vertex within ROIs. I do not interested to compute vertex-wise volume using -th3. What option should I use to get a list of absolute cortical thickness for each vertex within ROI?

Thank you again, Hisako

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, April 27, 2018 2:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertex wise cortical thickness within ROIs

Hi Hisako

you can use mris_anatomical_stats for this purpose.

cheers Bruce

On Fri, 27 Apr 2018, Fujiwara, Hisako wrote:

...

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compute absolute cortical thickness for each vertices within anatomical ROIs using apac.annot. I have successfully output the whole brain vertex wise cortical thickness using:

mris_convert –c <subject>/surf/?h.thickness <subject>/surf/?h.org <subject>/surf/?hthickenss.asc

Since this creates huge numbers (> e.g., 140,000) for each hemisphere for each participants, I would like to narrow out focus on the specific ROIs for relevant to our study? Is this achievable to add options to do?

Thank you for your help in advance.

Best regards,

Hisako

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