Re: [Freesurfer] About Mean LGI value

Thu, 09 Nov 2023 07:38:32 -0800

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Dear. Dr. Greve,

Thank you for your response.
I attached both “*h.aparc.pial_lgi.stats” and “*h.aparc.mean_pial_lgi.stats” files.
For example, in left hemisphere, mean LGI value is 3.0761 (SegId 1, Seg0001, is it correct as mean LGI value?), while the average of the LGI values is about 3.0327 (the sum of the LGI values of the 34 DK atlas ROIs divided by 34: value calculated here).
Are these values acceptable?

Daiki Sasabayashi

Attachment: lh.aparc.pial_lgi.stats
Description: Binary data

Attachment: lh.aparc.mean_pial_lgi.stats
Description: Binary data

Attachment: rh.aparc.pial_lgi.stats
Description: Binary data

Attachment: rh.aparc.mean_pial_lgi.stats
Description: Binary data


2023/11/09 9:33、Douglas N. Greve <dgr...@mgh.harvard.edu>のメール:

How different are the values? Those two stats files are created with different programs, so there could be some small differences. But if you're seeing large differences, then that is something else. If the latter, then send both stats files.

On 11/3/2023 9:14 AM, 笹林大樹 wrote:

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Dear Freesurfer experts,

I have calculated the mean LGI value for each hemisphere by referring to previous archives below. 
However, this mean LGI value differs from the average of the LGI values listed in *h/aparc.pial_lgi.stats (i.e., the sum of the LGI values of the 34 DK atlas ROIs divided by 34). 
Are these values originally subject to discrepancy?

Best,

Daiki Sasabayashi

Re: [Freesurfer] Mean Gyrification index

 Wed, 09 Sep 2020 08:26:32 -0700

It is giving you values for two segmentations: inside the label and outside the label. Use --id 1 to get only values inside the cortex label 
On 9/9/2020 11:27 AM, vittal korann wrote:

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Dear FreeSurfer experts
I am working on the gyrification index of schizophrenia patients. I had collated global brain values such as thickness, GM, and WM volumes. In addition, I wanted to tabulate gyrification values. Using the below link I was able to extract the hemispheric mean gyrification values. 
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But it is giving me 2 rows of output that are adding more ambiguity to the existing problem. Below is the command which I used to get mean gyrification for the left hemisphere and also the corresponding output. 
    *Command Line: *

    mri_segstats --slabel CSRI104 lh
    /usr/local/freesurfer//subjects/CSRI104/label/lh.cortex --i
    /usr/local/freesurfer//subjects/CSRI104/surf/lh.pial_lgi --sum
lh.aparc.pial_lgi.stats  
    *Output: *

    # NRows 2
    # NTableCols 10
    # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
    StdDev Min Max Range
      1   0      6879     4687.8  Seg0000     2.4509     0.2838  
    1.8067     2.8873     1.0806
      2   1    128054    84259.7  Seg0001     3.0148     0.6366  
1.9369     4.7611     2.8242 My confusion is that which row I should take it as a mean gyrification value for the left hemisphere (seg0000 or seg0001)?Please guide me if there is a way to combine two hemispheric values and make it as mean gyrification alike mean thickness. 
With regards
Korann
On Wed, Sep 9, 2020 at 4:51 PM vittal korann <vittalkor...@MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be gmail.com <mailto:vittalkor...@gmail.com>> wrote: 
    FreeSurfer experts

    I am trying to extract the mean gyrification values for the whole
    brain alike cortical thickness.
    We have all the whole-brain parameters in 'aparc.stats' file. But
    we do not have one for the gyrification index. Is there a way to
    do it?

    Would be grateful for your help.

    Best
    Korann
    */
    /*


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