Hi Tina,

(e.g. to compute a general cortical thickness average for the inferior frontal gyrus using the pars orbitalis, pars opercularis and pars triangularis data).

instead of "merging" existing thickness-data you could create a new label that constitutes your regions of interest. something like:

1. mri_annotation2label, gives you the labels. 2. mri_mergelabels, merge only the labels you are interested in. 3. mris_anatomical_stats, use the newly created label (e.g. inferior frontal gyrus) to compute thickness, surface area, volume etc.

Average cortical thickness= [(part 1 cortical thickness*part 1 surface area) + (part 2 cortical thickness*part 2 surface area) + …]/ >(part 1 surface area + part 2 surface area + …)

my 2 cents: 1. if you have an a priori hypothesis dealing with the mean thickness of certain region (e.g. inferior frontal gyrus, IFG) then your should calculate the mean thickness of IFG. if you have an a priori hypothesis about the mean thickness of a certain part of the IFG then you should calculate the mean thickness for that part. i think your approach doesn't follow this, you are going from subregions to IFG thereby weighing for surface area of the subregions, what's your a priori reason for doing this? why not measure the pars-regions directly and forget about IFG?

2. the linear relationship between thickness and surface area. e.g. if mean thickness is equal in all subregions that make up the IFG, you give more weight to the region with a larger surface area, why?

best, -joost

On Thu, Dec 23, 2010 at 4:00 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Tina,

I think weighting by surface area is a reasonable approach.

cheers Bruce On Wed, 22 Dec 2010, tina roostaei wrote:

...

Dear all,

I have access to a dataset of freesurfer segmentation  products (i.e. cortical volume, surface area, cortical thickness average  and standard deviation) for a number of patients. I wanted to merge the  data of some segmented parts (e.g. to compute a general cortical  thickness average for the inferior frontal gyrus using the pars orbitalis, pars opercularis and pars triangularis data). I wanted to know if it is right to compute the average cortical thickness using the following formula: Average cortical thickness= [(part 1 cortical thickness*part 1 surface area) + (part 2 cortical thickness*part 2 surface area) + ÿÿ]/ (part 1 surface area + part 2 surface area + ÿÿ) BTW,  I also checked whether the cortical volume equals ÿÿsurface area*average cortical thicknessÿÿ, to see if I could use the following formula  instead: Average cortical thickness= (part 1 cortical volume + part 2  cortical volume + ÿÿ)/ (part 1 surface area + part 2 surface area + ÿÿ) But it simply proved wrong.

Any suggestion is greatly appreciated.

Thanks in advance. Tina

---

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Dear all,

Thank you very much for all of the comments.

I do agree with creating a custom label, but for now I only have access to the parcellated products. I just wanted to reduce my data's dimensionality, because of the limitations imposed by the brain network analysis technique.

Best, Tina

________________________________ From: Michael Harms mharms@conte.wustl.edu To: j janssen joost.janssen76@gmail.com Cc: tina.roostaei@gmail.com; freesurfer@nmr.mgh.harvard.edu Sent: Thu, December 23, 2010 3:23:20 PM Subject: Re: [Freesurfer] merging average cortical thickness data

Creating a custom label and then using mris_anatomical_stats is probably the route I would go as well. But out of curiosity, if I was combining whole labels (and not splitting or subdividing any of them) I'd also compute an "average" thickness weighted by the mid-thickness surface area -- the two approaches should yield very similar results. (If not, please let the list know). You absolutely need to weight by surface area though if you go with this approach. (If a given label has 10x the surface area of another, then its contribution to the overall average thickness should be 10/11, and the contribution of the other area should be 1/11).

cheers, -MH

On Thu, 2010-12-23 at 10:00 +0100, j janssen wrote:

Hi Tina,

...

(e.g. to compute a general cortical thickness average for the inferior frontal gyrus using the pars orbitalis, pars opercularis and pars triangularis data).

instead of "merging" existing thickness-data you could create a new label that constitutes your regions of interest. something like:

1. mri_annotation2label, gives you the labels.
2. mri_mergelabels, merge only the labels you are interested in.
3. mris_anatomical_stats, use the newly created label (e.g. inferior

frontal gyrus) to compute thickness, surface area, volume etc.

...

Average cortical thickness= [(part 1 cortical thickness*part 1 surface area) +

(part 2 cortical thickness*part 2 surface area) + …]/ >(part 1 surface area + part 2 surface area + …)

my 2 cents:

1. if you have an a priori hypothesis dealing with the mean thickness

of certain region (e.g. inferior frontal gyrus, IFG) then your should calculate the mean thickness of IFG. if you have an a priori hypothesis about the mean thickness of a certain part of the IFG then you should calculate the mean thickness for that part. i think your approach doesn't follow this, you are going from subregions to IFG thereby weighing for surface area of the subregions, what's your a priori reason for doing this? why not measure the pars-regions directly and forget about IFG?

2. the linear relationship between thickness and surface area. e.g. if

mean thickness is equal in all subregions that make up the IFG, you give more weight to the region with a larger surface area, why?

best, -joost

On Thu, Dec 23, 2010 at 4:00 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Tina,

I think weighting by surface area is a reasonable approach.

cheers Bruce On Wed, 22 Dec 2010, tina roostaei wrote:

...

Dear all,

I have access to a dataset of freesurfer segmentation products (i.e. cortical volume, surface area, cortical thickness average and standard deviation) for a number of patients. I wanted to merge the data of some segmented parts (e.g. to compute a general cortical thickness average for the inferior frontal gyrus using the pars orbitalis, pars opercularis and pars triangularis data). I wanted to know if it is right to compute the average cortical thickness using the following formula: Average cortical thickness= [(part 1 cortical thickness*part 1 surface area) + (part 2 cortical thickness*part 2 surface area) + ÿÿ]/ (part 1 surface area + part 2 surface area + ÿÿ) BTW, I also checked whether the cortical volume equals ÿÿsurface area*average cortical thicknessÿÿ, to see if I could use the following formula instead: Average cortical thickness= (part 1 cortical volume + part 2 cortical volume + ÿÿ)/ (part 1 surface area + part 2 surface area + ÿÿ) But it simply proved wrong.

Any suggestion is greatly appreciated.

Thanks in advance. Tina

---

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---

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