Hi Kiyotaka,

Thank you so much for looking into my model so carefully. I sincerely appreciate that!

I changed "Implicit Mask" to "Yes", but the error remains. So I guess I will need to look into my data, as suggested by you. In fact, I have run the analysis once with no mask at all. It runs OK, but I am not sure what are the potential pitfalls for not using the mask.

As for the centering issue, indeed, I overlooked the suggestions in the tutorial. So I should NOT center age, gender, and group (indicating Alzheimer's, MCI, or normal). May I check why? To me, it is definitely not necessary, but it doesn' hurt, either.

Thank you so much again for your kindness and advice! 

Warmest gratitude,

Marris

On Tue, May 5, 2015 at 1:11 PM, Kiyotaka Nemoto <[log in to unmask]> wrote:

Hi Marris,

I saw your settings and noticed that Implicit Mask is set to 'No'.
I think this should be set to 'Yes.'

If you still see errors, something must be wrong in one or more files
in your dataset.

I will go through each one of them.

Guillaume and Donald gave a good advice on checking data a few days ago.

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;501709e8.1504

<quote>
>> load SPM.mat
>> spm_check_registration(SPM.xY.P)

and scroll through your entire dataset. Plotting the globals can also
give you a hint about suspicious scans:

>> figure, plot(SPM.xGX.rg)
</quote>

note that spm_check_registration can load up to 24 files.
Since your dataset is quite large, I think

>> load SPM.mat
>> figure, plot(SPM.xGX.rg)

will give you some hint.

If you prefer GUI, I recommend using "Check sample homogeneity using
covariance" function implemented in VBM8 toolbox. It's easy to use and
quite useful to detect the poor quality data.



Another concern: I see you set centering on Gender. Basically you
don't want to center dummy variables such as gender. It's also
described in VBM tutorial. I would set "No centering" on gender. (and
probably group if the order of group doesn't mean anything.)

Best regards,

Kiyotaka

2015-05-05 13:30 GMT+09:00 Marris Atwood <[log in to unmask]>:
> Hi Kiyotaka and Indrajeet,
>
> Sincere thanks to both of you! Now I understand what I edit should be a setting file instead of SPM.mat.
>
> Your pointers on global normalization are very enlightening. Yet, the strange thing is, I am not using "proportional" for global normalization. Instead, I am treating it as a covariate by using "ANCOVA".
>
> I have attached my saved settings here. Any guess is very much welcomed and appreciated!
>
> Thanks a lot,
> MA
>
>

--
Kiyotaka Nemoto, M.D., Ph.D.
Assistant Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: [log in to unmask]