Hi
so I tried these steps. I tried taking a few subsets of subjects and
redoing the group level for these. I was getting the same results for
all the subsets I tried. So I redid the whole thing from scartch.
Bizarrely but serendipitiously it now worked perfectly! I am not sure
what happened
I am now trying to do a a beta extraction from the results and
wondering if it should be different in any way from the basic SPM beta
extraction?
Also, I ran a group level analysis (one sample t-test) with a
continuous reggressor and I was wondering if this also should follow
the same method as a non-PPI group level analysis with reggressor? I
want to see how the influence of the seed region varies with the
regressor (across the whole brain, across the whole group).
I have just done a one sample t-test and entered the regressor. I did
not demean as I was not sure if this is required in SPM. I also did
not change the defaults for the options (such as scaling). Does this
sound about right, for the PPI co-variate analysis?
I would be really grateful for any advice
Sincerely
Prerona
On Wed, Apr 9, 2014 at 11:39 AM, MCLAREN, Donald
<[log in to unmask]> wrote:
> This seems a bit odd.
>
> Can you do the following: (1) Add all the mask.img images together; (2)
> average the con_ images that you are using for inputs; (3) try a one-sample
> t-test of 5 subjects, then 10, then the full set.
>
> I am wondering if some of the images are corrupted for some reason and that
> you might need to re-run a few subjects.
>
> Best Regards, Donald McLaren
> =================
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General Hospital and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren
> Office: (773) 406-2464
> =====================
> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
> intended only for the use of the individual or entity named above. If the
> reader of the e-mail is not the intended recipient or the employee or agent
> responsible for delivering it to the intended recipient, you are hereby
> notified that you are in possession of confidential and privileged
> information. Any unauthorized use, disclosure, copying or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited and may be unlawful. If you have received this e-mail
> unintentionally, please immediately notify the sender via telephone at (773)
> 406-2464 or email.
>
>
> On Wed, Apr 2, 2014 at 10:31 PM, Prerona Mukherjee
> <[log in to unmask]> wrote:
>>
>> Hi Everyone
>>
>> I am having an issue with a between group PPI analysis using the gPPPI
>> toolbox and I was wondering if anyone could help me.
>>
>> I have run the analysis from one seed for a group of controls and a group
>> of patients. Now I want to run the second level analysis between these two
>> groups. However I am getting an error saying no inmask voxels.
>>
>> I know that this means there are no resulting voxels. But I was wondering
>> if anyone could help me figure out why I am getting this error and what I
>> can do about it
>>
>> I have tried looking at all the individual con files (by opening them
>> using check reg) and they seem okay (although there are a few very dark
>> spots on some of them). I was wondering if this is causing the problem
>>
>> To set up the second level design I have taken all the con files created
>> by the first level PPI and tried to do a 2 sample t test.
>>
>> I am not sure what is the correct masking option. I have tried both
>> explicit (with a mask) and implicit mask. I have also tried changing the spm
>> defaults (
>> defaults.mask.thresh = 0.8 to 0.2 and also to -Inf).
>>
>> I have also tried doing a within group analysis of each of the two groups
>> and ran into the same problem
>>
>> PS: The PPPI toolbox creates an SPM.mat file in the output directory and a
>> mask.img. This mask.img also looks okay and the SPM.mat looks like it is
>> including every subject together in one group
>>
>> Do you have any thoughts about this? I would really appreciate any help or
>> advice
>>
>>
>> Sincerely
>>
>> Prerona
>
>
------------------------------------------------------------------------------------------------------------
Prerona Mukherjee
Post Doctoral Research Associate
Stonybrook University
Department of Psychiatry
Putnam Building, Room 142 A
Work: 631 632-8894
Mobile: 773 916 7662
On Wed, Apr 9, 2014 at 2:39 PM, MCLAREN, Donald
<[log in to unmask]> wrote:
> This seems a bit odd.
>
> Can you do the following: (1) Add all the mask.img images together; (2)
> average the con_ images that you are using for inputs; (3) try a one-sample
> t-test of 5 subjects, then 10, then the full set.
>
> I am wondering if some of the images are corrupted for some reason and that
> you might need to re-run a few subjects.
>
> Best Regards, Donald McLaren
> =================
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General Hospital and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren
> Office: (773) 406-2464
> =====================
> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
> intended only for the use of the individual or entity named above. If the
> reader of the e-mail is not the intended recipient or the employee or agent
> responsible for delivering it to the intended recipient, you are hereby
> notified that you are in possession of confidential and privileged
> information. Any unauthorized use, disclosure, copying or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited and may be unlawful. If you have received this e-mail
> unintentionally, please immediately notify the sender via telephone at (773)
> 406-2464 or email.
>
>
> On Wed, Apr 2, 2014 at 10:31 PM, Prerona Mukherjee
> <[log in to unmask]> wrote:
>>
>> Hi Everyone
>>
>> I am having an issue with a between group PPI analysis using the gPPPI
>> toolbox and I was wondering if anyone could help me.
>>
>> I have run the analysis from one seed for a group of controls and a group
>> of patients. Now I want to run the second level analysis between these two
>> groups. However I am getting an error saying no inmask voxels.
>>
>> I know that this means there are no resulting voxels. But I was wondering
>> if anyone could help me figure out why I am getting this error and what I
>> can do about it
>>
>> I have tried looking at all the individual con files (by opening them
>> using check reg) and they seem okay (although there are a few very dark
>> spots on some of them). I was wondering if this is causing the problem
>>
>> To set up the second level design I have taken all the con files created
>> by the first level PPI and tried to do a 2 sample t test.
>>
>> I am not sure what is the correct masking option. I have tried both
>> explicit (with a mask) and implicit mask. I have also tried changing the spm
>> defaults (
>> defaults.mask.thresh = 0.8 to 0.2 and also to -Inf).
>>
>> I have also tried doing a within group analysis of each of the two groups
>> and ran into the same problem
>>
>> PS: The PPPI toolbox creates an SPM.mat file in the output directory and a
>> mask.img. This mask.img also looks okay and the SPM.mat looks like it is
>> including every subject together in one group
>>
>> Do you have any thoughts about this? I would really appreciate any help or
>> advice
>>
>>
>> Sincerely
>>
>> Prerona
>
>
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