Can't you just average the lh and rh values? You can weight by the surface area or number of vertices

On 9/10/2020 12:53 PM, vittal korann wrote:

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Sorry, Douglas, I might have confused you.

Freesurfer will provide mean thickness for the whole-brain. similarly, can I have mean gyrification for the whole brain (not individual values for left and right hemisphere)?

Finally, it worked. Thank you, Douglas.

So far I was able to get mean gyrification values for each hemisphere separately. 

What?

I want to club the left and right hemisphere values into a single value.

On Thu, Sep 10, 2020 at 9:50 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

On 9/10/2020 12:08 PM, vittal korann wrote:

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Finally, it worked. Thank you, Douglas.

My question is regarding the mean gyrification similar to what we get for thickness as a whole-brain mean thickness.

I'm not sure what you are asking here. gyrification and thickness are different

If there is a way to calculate, please let me know.

What?

Here is a command that I executed and got the mean gyrification value for the left/right hemisphere.

mri_segstats --slabel CSRI004  rh  $SUBJECTS_DIR/CSRI004/label/rh.cortex --i $SUBJECTS_DIR/CSRI004/surf/rh.pial_lgi  --sum h.aparc.pial_lgi-csri004.stats

On Thu, Sep 10, 2020 at 7:22 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Can you send the actual command you ran and all the terminal output?

On 9/10/2020 12:58 AM, vittal korann wrote:

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Yes, I did replace question marks with left and right.

Thank you so much, Douglas.

With regards

Vittal

On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Are you using actual question marks or are you replacing them with l or r? (you have to replace)

On 9/9/2020 2:26 PM, vittal korann wrote:

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I did that, but the error remains the same.

mri_segstats --slabel CSRI001 ?h  $SUBJECTS_DIR/CSRI001/label/?h.cortex --i $SUBJECTS_DIR/CSRI001/surf/?h.pial_lgi --sum h.aparc.pial_lgi-csri001.stats

On Wed, Sep 9, 2020 at 11:32 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

You need to include the hemisphere in the --slabel arguments (maybe the 2nd one)

On 9/9/2020 2:10 PM, vittal korann wrote:

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Dear Douglas

Thank you for your help! 

I got an error while executing the mris_segstats command.

Command:
mri_segstats --slabel CSRI001?h  $SUBJECTS_DIR/CSRI001/label/?h.cortex.label --i $SUBJECTS_DIR/CSRI001/surf/?h.pial_lgi --sum h.aparc.pial_lgi-csri001.stats

ERROR: Option /usr/local/freesurfer//subjects/CSRI001/surf/rh.pial_lgi unknown

Please correct me if something wrong in the command line.

Sorry for troubling you again.

With regards

Vittal

On Wed, Sep 9, 2020 at 10:23 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

You can use mri_segstats with the --slabel option, specifying the ?h.cortex.label and using the gyrification as input

On 9/9/2020 12:54 PM, vittal korann wrote:

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Thank you so much, Douglas.

Could you please guide me to obtain the global mean gyrification index for each subject?

With regards

korann

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