Dear Paul,
I have added a note to the "Quick Start Guide":
"Select threshold masking with an absolute value of 0.1. This threshold can ultimately be increased to 0.2 or even 0.25."
added: "if you still notice non-brain areas in your analysis."
Best,
Christian
On Mon, 17 May 2021 23:39:59 +0000, Paul, Jhelum <[log in to unmask]> wrote:
>Hello Christian,
>
>Thank you for this information. I strictly followed the manual absolute value but still was not getting it. Later saw the absolute value can go up to 0.2-0.25, so now I have a group analysis done with no non-GM areas in the significant cluster.
>Both 0.2 and 0.25 gave me only GM (no CSF/WM regions) areas in the significant cluster.
>
>Hope this helps anyone who might have been stuck in this situation like me.
>
>Thank you.
>
>Regards,
>Jhelum Paul
>
>-----Original Message-----
>From: Christian Gaser <[log in to unmask]>
>Sent: Thursday, April 29, 2021 4:10 PM
>To: [log in to unmask]; Paul, Jhelum <[log in to unmask]>
>Subject: Re: Regarding CAT12 and GM volume
>
>CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender.
>
>Dear Paul,
>
>I assume that you have not defined any absolute threshold in the stat. model to prevent that non-GM areas will show up. Please check the CAT12 manual for detailed instructions.
>
>Best,
>
>Christian
>
>iOn Thu, 29 Apr 2021 18:05:40 +0000, Paul, Jhelum <[log in to unmask]> wrote:
>
>>Hello,
>>
>>I am trying to find grey matter volume differences in two groups (control and patient) through CAT12 and I did segmentation of the T1 images with the following parameters:
>>
>>[cid:image001.jpg@01D73CE7.95F6CB50]
>>[cid:image002.jpg@01D73CE7.95F6CB50]
>>When I am doing a two sample t test, I am getting clusters in regions which is not the GM but CSF or WM. Even I changed some of the segmentation parameters and tried but I am getting the same result. Is it possible to help me out regarding why this is happening or what can I do to make this better? Attached is the screenshot of a significant cluster in non-GM region.
>>[cid:image003.png@01D73CE7.95F6CB50]
>>
>>Any suggestion is appreciated.
>>
>>Thank you.
>>
>>Regards,
>>Jhelum Paul
>>
>>
>>
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>>
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