Hi,
I am doing source reconstruction and would like to do statistical analysis on top of this.
Is there a way to record the result of inversion as a 'mesh by time'?
And apply RFT on this 3D output?
Many thanks,
Adrien
________________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of SPM automatic digest system [[log in to unmask]]
Sent: Thursday, July 23, 2015 12:00 AM
To: [log in to unmask]
Subject: SPM Digest - 21 Jul 2015 to 22 Jul 2015 (#2015-25)
There are 9 messages totaling 2954 lines in this issue.
Topics of the day:
1. Regarding creating an anatomical ROI of Hypothalamus
2. Fwd: New Subscription
3. Segmentation changes from SPM8 to SPM12
4. Postmortem scans
5. Specifying eigenvariates for PPI (2)
6. GIFT toolbox - urgent
7. confine analysis in Gary mater
8. Significance statistics for marsbar
----------------------------------------------------------------------
Date: Wed, 22 Jul 2015 11:35:11 +0530
From: avantika mathur <[log in to unmask]>
Subject: Regarding creating an anatomical ROI of Hypothalamus
Hello,
I would like to create an anatomical* ROI of Hypothalamus*. However, I
found that * Hypothalamus is* not labelled in the current version (v 2.1)
of Anatomy toolbox.
At the same time, I have found studies where they have used Anatomy Toolbox
to label Hypothalamus, for instance (Koelsch, S., & Skouras, S. (2014).
Functional centrality of amygdala, striatum and hypothalamus in a
“small-world” network underlying joy: An fMRI study with music. Human Brain
Mapping, 35(7), 3485–3498. doi:10.1002/hbm.22416).
I am not able to figure out labeling of hypothalamus through anatomy
toolbox.
It would be of great help if you could help me regarding the same.
Thanks in advance.
--
Avantika Mathur
Int.Phd student
National Brain Research Centre
Manesar,Gurgaon
------------------------------
Date: Wed, 22 Jul 2015 14:11:08 +0530
From: Samyak Raj Mehta <[log in to unmask]>
Subject: Fwd: New Subscription
I am subscribe for SPM.
--
Regards
Samyak Raj
--
Regards
Samyak Raj
------------------------------
Date: Wed, 22 Jul 2015 11:02:23 +0100
From: John Ashburner <[log in to unmask]>
Subject: Re: Segmentation changes from SPM8 to SPM12
In the computations of deformations, bias fields and cluster parameters,
the code will ignore any voxels with value of zero. When it comes to
writing out the segmented images though, the behaviour with these zeroed
voxels is a bit unpredictable, so you may need to do something with your
mask.
Best regards,
-John
On 21 July 2015 at 19:11, Cristina Roman <[log in to unmask]> wrote:
> Dr. Ashburner,
>
> Thank you sincerely for your response! I am still learning how to use SPM,
> so might you be able to elaborate on your response a bit more? Also, might
> you also be able to shed light on why the mask option was removed from the
> SPM12 segmentation module?
>
> Thank you so much for your help and time!
>
> - C
>
> On Tue, Jul 21, 2015 at 1:27 PM, John Ashburner <[log in to unmask]>
> wrote:
>
>> Set the parts of the image that you want to mask out to have a value of
>> zero.
>>
>> Best regards,
>> -John
>>
>>
>> On 21 July 2015 at 17:20, C. Roman <[log in to unmask]> wrote:
>>
>>> SPM Experts,
>>>
>>> I noticed that in the new version of SPM (SPM12), the segmentation
>>> module no longer allows for one to enter a mask image (as in SPM8). May I
>>> ask why this change was made and how the process is different now? My
>>> question stems from the fact that I work with data that has lesions
>>> (multiple sclerosis), which significantly affect segmentation. Therefore,
>>> it is important that I account for lesions during segmentation, which I had
>>> hoped to do by including a binary lesion map as a "mask image" in the
>>> segmentation step. However, since this option is no longer available, how
>>> might I account for the lesions during segmentation, or does the new
>>> segmentation process in SPM12 take issues like this into account? Any
>>> information you can provide about the background/rationale of this change
>>> and how it may account damage in brains would be greatly appreciated!
>>>
>>> Thank you!
>>> Cristina
>>>
>>
>>
>
>
> --
> *Cristina A. F. Roman*
> Graduate Student, Adult Clinical Psychology
> The Pennsylvania State University
> 419 Bruce V. Moore Building
> University Park, Pennsylvania 16802
> ________________________________
>
> *Confidentiality Notice*
>
> The information in this email is intended *only for the individual or
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> to please notify us immediately by telephone or email, and destroy the
> original message.
>
------------------------------
Date: Wed, 22 Jul 2015 11:17:04 +0100
From: Mario <[log in to unmask]>
Subject: Postmortem scans
Dear Experts
I started to work with postmortem scans of different neurological populations and I am interested to explore the structural aspects. To start, I tried to use an affine coregistration and the result seems very good. I would like to know if someone has already used SPM8 to perform analysis (i.e. VBM) on postmortem scans and what is your opinion about the more correct procedure .
Many thanks
All best
Mario
------------------------------
Date: Wed, 22 Jul 2015 13:41:25 +0100
From: "D. Hewitt" <[log in to unmask]>
Subject: Specifying eigenvariates for PPI
Hi all,
I have completed GLM analysis on fMRI data. I am currently trying to specify eigenvariates for VOIs to use for PPI. My VOIs are amygdala and bilateral ventral striatum. I have loaded the contrast for my condition of interest where I expect to find these areas activated, and have inputted MRI coordinates for each region one at a time. When I press eigenvariate, it asks me if I want to adjust for the effects of interest, and then to name my VOI, but then I get this error message:
"Error using uicontrol
While setting the 'Max' property of UIControl:
Value must be numeric or logical.
Error in spm_input (line 1286)
h = uicontrol(Finter,'Style','Pushbutton',...
Error in spm_regions (line 138)
s = spm_input('which session','!+1','n1',s,Inf);
Error using waitfor
Error while evaluating UIControl Callback
Error using spm_input (line 843)
Input window cleared whilst waiting for response: Bailing out!
Error in spm_regions (line 112)
xY.name = spm_input('name of region','!+1','s','VOI');
Error while evaluating UIControl Callback"
Has anyone come across this? I get the same message regardless of the subject, of whether I adjust for effects of interest and whatever the name is for the region. I have had the error for all regions so it doesn't seem related to the region itself.
Any help would be appreciated!
- D
------------------------------
Date: Wed, 22 Jul 2015 16:00:18 +0200
From: Joana Braga Pereira <[log in to unmask]>
Subject: Re: GIFT toolbox - urgent
Thanks Vince!
joana
2015-07-21 20:20 GMT+02:00 Vince Calhoun <[log in to unmask]>:
> Try now (http://mialab.mrn.org/software), have updated the links to
> bypass sourceforge.
>
>
>
> VDC
>
>
>
>
>
> *From:* SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] *On
> Behalf Of *Joana Braga Pereira
> *Sent:* Tuesday, July 21, 2015 1:38 AM
> *To:* [log in to unmask]
> *Subject:* [SPM] GIFT toolbox - urgent
>
>
>
> Dear all,
>
> I need the GIFT toolbox to perform some urgent analyses for a revision.
>
> Unfortunately, the website for downloading it is not working at the moment.
>
> Could any of you kindly provide me with the compressed file of the toolbox?
>
> Many thanks!!
>
> Best wishes,
>
>
>
> Joana
>
------------------------------
Date: Wed, 22 Jul 2015 15:26:15 +0100
From: Guillaume Flandin <[log in to unmask]>
Subject: Re: Specifying eigenvariates for PPI
Dear Danielle,
the error you get is due to an incompatibility between SPM and recent
MATLAB versions (R2014b onwards), which I hope to have fixed in the
attached version of spm_input.m.
Many thanks,
Guillaume.
On 22/07/15 13:41, D. Hewitt wrote:
> Hi all,
>
> I have completed GLM analysis on fMRI data. I am currently trying to specify eigenvariates for VOIs to use for PPI. My VOIs are amygdala and bilateral ventral striatum. I have loaded the contrast for my condition of interest where I expect to find these areas activated, and have inputted MRI coordinates for each region one at a time. When I press eigenvariate, it asks me if I want to adjust for the effects of interest, and then to name my VOI, but then I get this error message:
>
> "Error using uicontrol
> While setting the 'Max' property of UIControl:
> Value must be numeric or logical.
>
> Error in spm_input (line 1286)
> h = uicontrol(Finter,'Style','Pushbutton',...
>
> Error in spm_regions (line 138)
> s = spm_input('which session','!+1','n1',s,Inf);
>
> Error using waitfor
> Error while evaluating UIControl Callback
>
> Error using spm_input (line 843)
> Input window cleared whilst waiting for response: Bailing out!
>
> Error in spm_regions (line 112)
> xY.name = spm_input('name of region','!+1','s','VOI');
>
> Error while evaluating UIControl Callback"
>
> Has anyone come across this? I get the same message regardless of the subject, of whether I adjust for effects of interest and whatever the name is for the region. I have had the error for all regions so it doesn't seem related to the region itself.
>
> Any help would be appreciated!
>
> - D
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
------------------------------
Date: Wed, 22 Jul 2015 19:01:30 +0100
From: Mike <[log in to unmask]>
Subject: confine analysis in Gary mater
Hi,
My group analysis of fMRI showed subthreshold activations in my hypothetical regions. To reduce the effect of global multiple comparisons, I want to confine my contrast results in gray mater (GM) only, i.e., excluding voxels in white mater and CSF. Two questions:
(1) Can any one give me a hint about how to get the GM mask? My idea is to do segmentation for each subject's T1-weighted image , normalised their T1 to standard space, and then average all normalised T1 images.
(2) How to confine multiple comparisons in this GM mask? Is it just an ROI process (i.e., first use uncorrected p< 0.005 or 0.001, select SVC button, and then select this GM mask) ? Or, after selecting Results, use this GM mask as inclusive mask, and then select FWE?
Thanks.
Mike
------------------------------
Date: Wed, 22 Jul 2015 16:56:29 -0500
From: Victoria Klimaj <[log in to unmask]>
Subject: Significance statistics for marsbar
Dear neuroimagers,
I'm doing ROI analyses in marsbar and I was wondering where I could find
significance values corresponding to the extracted betas. Any help would be
most appreciated!
Thanks in advance,
Victoria
------------------------------
End of SPM Digest - 21 Jul 2015 to 22 Jul 2015 (#2015-25)
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