Print

Print


[log in to unmask]> These 2D locations are created by projecting 3D locations represented in head coordinates so the differences you find are due to different head positions of your subjects in the helmet. This is by design, but you also can load a standard channel template file for all your subjects. Vladimir On Mon, Feb 28, 2011 at 10:55 PM, Erick Britis Ortiz <[log in to unmask]> wrote: > > Thank you as always for the prompt response! > > For you to know at least what I am talking about, a picture is attached > with the projected MEG sensors (colored by region) in my 22 subjects. > Left is greenish, right is reddish. > > The problem is that I see no reason for the MEG sensors not to have > simply a standard position. In the Fieldtrip plots, they have (for > example, in CTF151.lay). I will follow your advice, no matter. But this > is a bit dangerous in the general case, don't you think? As I said, I > just do not know if it is by design, else I could "fix" it. > > Best, > Erick > > On 2011-02-28 23:28, Vladimir Litvak wrote: >> Hi Erick, >> >> SPM uses the same algorithm as Fieldtrip to generate a layout from the >> sensor array so it should be quite similar, just the convention for >> representing it is slightly different. I don't know what exactly the >> problem is so it's hard for me to advise you. In principle you can use >> the GUI functionality in Prepare or your own script to generate any >> layout you like and then load it as a channel template file via >> Prepare  (this is a mat-file, there is an example for CTF in >> EEGTemplates). >> >> Best, >> >> Vladimir >> >> >> >> On Mon, Feb 28, 2011 at 10:22 PM, Erick Britis Ortiz >> <[log in to unmask]> wrote: >>> >>> Hi Vladimir, >>> >>> I have been using spm_eeg_convert2images to transform my MEG frequency >>> analysis results to image volumes and run statistics. The objective >>> being to determine lateralization in language (in children) by frequency. >>> >>> I assumed that spm_eeg_convert2scalp would use a standard 2D layout (ą >>> la Fieldtrip), and when I checked, this is not true. This makes >>> lateralization studies, for instance, much more difficult, and I could >>> think of others. What is the advantage? >>> >>> My guess was that setting D.channels.X_plot2D and Y_plot2D to empty >>> would generate a default arrangement, but this also did not work. Could >>> you shed some light at the issue? >>> >>> Best, >>> Erick >>> >>> >> > > ========================================================================Date: Mon, 28 Feb 2011 18:34:38 -0500 Reply-To: Pieter van de Vijver <[log in to unmask]> Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]> From: Pieter van de Vijver <[log in to unmask]> Subject: Re: question regarding flexible factorial model Comments: To: Jeffrey West <[log in to unmask]> In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary¼aec51a894a8f7f93049d601f97 Message-ID: <[log in to unmask]> --bcaec51a894a8f7f93049d601f97 Content-Type: text/plain; charset=ISO-8859-1 Hi Jeff, You should enter conditions for subjects in a nscans x factor matrix. The rows are your scans (4 in your case) and the columns indicate the factors (2, one for group and one for condition, subject is automatically modelled). So for a subject in group 2 with scans for all four conditions you would need: [2 1 2 2 2 3 2 4] Make sure your scans are entered in the right order! Also, main effect for subjects doesn't need to be specified, this is done automatically (this is because you chose 'Subjects' at the 'Specify Subjects or all Scans & Factors'). Good luck, Pieter On Mon, Feb 28, 2011 at 3:14 PM, Jeffrey West <[log in to unmask]>wrote: > Hello. > > I have question relating to setting up a flexible factorial model with 2 > groups, each group has 4 conditions. > > I have 3 factors: 1 = subject (independent, variance equal), 2 = group > (independent, variance not equal), 3 = condition (not independent, variance > equal) > > For the subject level, I entered in 20 subjects, for each subject, I > entered in the the 4 scans: con_image 1,2,3,4. For conditions, I entered 1 2 > 3 4. Once all 20 subjects were completed, I entered 3 main effects, and > interaction: main effect: 1, main effect: 2, main effect: 3, interaction: 2 > 3. > > The model did not run and I got the following error message: > > *Running job #2 > ----------------------------------------------------------------------- > Running 'Factorial design specification' > Failed 'Factorial design specification' > Index exceeds matrix dimensions. > In file "C:\Documents and > Settings\JWest\Desktop\spm8\config\spm_run_factorial_design.m" (v3067), > function "spm_run_factorial_design" at line 482.* > > *The following modules did not run: > Failed: Factorial design specification* > ** > I feel like the error is in the subject level: either the scan or the > conditions. I do not feel like the conditions step is correct. Can anyone > please explain what I did wrong setting up my model. > > Thank you for any suggestions. > > Jef > > > Jeffrey West, M.A. > Research Analyst > Maryland Psychiatric Research Center > Baltimore, Maryland 21228-0247 > Phone: 410-402-6018 > email: [log in to unmask] > > > --bcaec51a894a8f7f93049d601f97 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Jeff, 

You should enter conditions for subjects in a nscans x factor matrix. The rows are your scans (4 in your case) and the columns indicate the factors (2, one for group and one for condition, subject is automatically modelled). 
So for a subject in group 2 with scans for all four conditions you would need:
[2 1
2 2 
2 3
2 4]
Make sure your scans are entered in the right order!

Also, main effect for subjects doesn't need to be specified, this is done automatically (this is because you chose 'Subjects' at the 'Specify Subjects or all Scans & Factors').

Good luck, 

Pieter


On Mon, Feb 28, 2011 at 3:14 PM, Jeffrey West <[log in to unmask]> wrote:
Hello.
 
I have question relating to setting up a flexible factorial model with 2 groups, each group has 4 conditions.
 
I have 3 factors: 1 = subject (independent, variance equal), 2 = group (independent, variance not equal), 3 = condition (not independent, variance equal)
 
For the subject level, I entered in 20 subjects, for each subject, I entered in the the 4 scans: con_image 1,2,3,4. For conditions, I entered 1 2 3 4. Once all 20 subjects were completed, I entered 3 main effects, and interaction: main effect: 1, main effect: 2, main effect: 3, interaction: 2 3.
 
The model did not run and I got the following error message:
 
Running job #2
-----------------------------------------------------------------------
Running 'Factorial design specification'
Failed  'Factorial design specification'
Index exceeds matrix dimensions.
In file "C:\Documents and Settings\JWest\Desktop\spm8\config\spm_run_factorial_design.m" (v3067), function "spm_run_factorial_design" at line 482.
 
The following modules did not run:
Failed: Factorial design specification
 
I feel like the error is in the subject level: either the scan or the conditions. I do not feel like the conditions step is correct. Can anyone please explain what I did wrong setting up my model.
 
Thank you for any suggestions.
 
Jef
 
 
Jeffrey West, M.A.
Research Analyst
Maryland Psychiatric Research Center
Baltimore, Maryland 21228-0247
Phone: 410-402-6018
email: [log in to unmask]
 
 

--bcaec51a894a8f7f93049d601f97-- ========================================================================Date: Mon, 28 Feb 2011 18:38:06 -0500 Reply-To: Pieter van de Vijver <[log in to unmask]> Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]> From: Pieter van de Vijver <[log in to unmask]> Subject: Re: question regarding flexible factorial model Comments: To: Jeffrey West <[log in to unmask]> In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundarye6ba6e8996ee354c049d602b47 Message-ID: <[log in to unmask]> --90e6ba6e8996ee354c049d602b47 Content-Type: text/plain; charset=ISO-8859-1 Sorry, small correction. Main effect for subjects DOES need to be specified. Pieter On Mon, Feb 28, 2011 at 6:34 PM, Pieter van de Vijver <[log in to unmask]>wrote: > Hi Jeff, > > You should enter conditions for subjects in a nscans x factor matrix. The > rows are your scans (4 in your case) and the columns indicate the factors > (2, one for group and one for condition, subject is automatically > modelled). > So for a subject in group 2 with scans for all four conditions you would > need: > [2 1 > 2 2 > 2 3 > 2 4] > Make sure your scans are entered in the right order! > > Also, main effect for subjects doesn't need to be specified, this is done > automatically (this is because you chose 'Subjects' at the 'Specify Subjects > or all Scans & Factors'). > > Good luck, > > Pieter > > > On Mon, Feb 28, 2011 at 3:14 PM, Jeffrey West <[log in to unmask]>wrote: > >> Hello. >> >> I have question relating to setting up a flexible factorial model with 2 >> groups, each group has 4 conditions. >> >> I have 3 factors: 1 = subject (independent, variance equal), 2 = group >> (independent, variance not equal), 3 = condition (not independent, variance >> equal) >> >> For the subject level, I entered in 20 subjects, for each subject, I >> entered in the the 4 scans: con_image 1,2,3,4. For conditions, I entered 1 2 >> 3 4. Once all 20 subjects were completed, I entered 3 main effects, and >> interaction: main effect: 1, main effect: 2, main effect: 3, interaction: 2 >> 3. >> >> The model did not run and I got the following error message: >> >> *Running job #2 >> ----------------------------------------------------------------------- >> Running 'Factorial design specification' >> Failed 'Factorial design specification' >> Index exceeds matrix dimensions. >> In file "C:\Documents and >> Settings\JWest\Desktop\spm8\config\spm_run_factorial_design.m" (v3067), >> function "spm_run_factorial_design" at line 482.* >> >> *The following modules did not run: >> Failed: Factorial design specification* >> ** >> I feel like the error is in the subject level: either the scan or the >> conditions. I do not feel like the conditions step is correct. Can anyone >> please explain what I did wrong setting up my model. >> >> Thank you for any suggestions. >> >> Jef >> >> >> Jeffrey West, M.A. >> Research Analyst >> Maryland Psychiatric Research Center >> Baltimore, Maryland 21228-0247 >> Phone: <410-402-6018>410-402-6018 >> email: [log in to unmask] >> >> >> > > --90e6ba6e8996ee354c049d602b47 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Sorry, small correction. Main effect for subjects DOES need to be specified. 

Pieter

On Mon, Feb 28, 2011 at 6:34 PM, Pieter van de Vijver <[log in to unmask]> wrote:
Hi Jeff, 

You should enter conditions for subjects in a nscans x factor matrix. The rows are your scans (4 in your case) and the columns indicate the factors (2, one for group and one for condition, subject is automatically modelled). 
So for a subject in group 2 with scans for all four conditions you would need:
[2 1
2 2 
2 3
2 4]
Make sure your scans are entered in the right order!

Also, main effect for subjects doesn't need to be specified, this is done automatically (this is because you chose 'Subjects' at the 'Specify Subjects or all Scans & Factors').

Good luck, 

Pieter


On Mon, Feb 28, 2011 at 3:14 PM, Jeffrey West <[log in to unmask]> wrote:
Hello.
 
I have question relating to setting up a flexible factorial model with 2 groups, each group has 4 conditions.
 
I have 3 factors: 1 = subject (independent, variance equal), 2 = group (independent, variance not equal), 3 = condition (not independent, variance equal)
 
For the subject level, I entered in 20 subjects, for each subject, I entered in the the 4 scans: con_image 1,2,3,4. For conditions, I entered 1 2 3 4. Once all 20 subjects were completed, I entered 3 main effects, and interaction: main effect: 1, main effect: 2, main effect: 3, interaction: 2 3.
 
The model did not run and I got the following error message:
 
Running job #2
-----------------------------------------------------------------------
Running 'Factorial design specification'
Failed  'Factorial design specification'
Index exceeds matrix dimensions.
In file "C:\Documents and Settings\JWest\Desktop\spm8\config\spm_run_factorial_design.m" (v3067), function "spm_run_factorial_design" at line 482.
 
The following modules did not run:
Failed: Factorial design specification
 
I feel like the error is in the subject level: either the scan or the conditions. I do not feel like the conditions step is correct. Can anyone please explain what I did wrong setting up my model.
 
Thank you for any suggestions.
 
Jef
 
 
Jeffrey West, M.A.
Research Analyst
Maryland Psychiatric Research Center
Baltimore, Maryland 21228-0247
Phone: 410-402-6018
email: [log in to unmask]
 
 


--90e6ba6e8996ee354c049d602b47-- ========================================================================Date: Mon, 28 Feb 2011 18:44:34 -0500 Reply-To: John Fredy <[log in to unmask]> Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]> From: John Fredy <[log in to unmask]> Subject: sparse data analysis MIME-Version: 1.0 Content-Type: multipart/alternative; boundaryMessage-ID: <[log in to unmask]> --0016364991e7155337049d6043e2 Content-Type: text/plain; charset=ISO-8859-1 Hello all, I have recorded 80 volumes in a block design experiment with a TR of 6 seconds where 3 seconds are silence, the machine is silence, and the other 3 seconds are used for the adquisition. In the 3 seconds of machine silence I present a stimulus, 0.5 seconds later of the begins of the silence, with an aproximated duration of 1.5 seconds What is the best strategy for processing this data? Regards John Ochoa Universidad de Antioquia --0016364991e7155337049d6043e2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello all, I have recorded 80 volumes in a block design experiment with a TR of 6 seconds where 3 seconds are silence, the machine is silence, and the other 3 seconds are used for the adquisition. In the 3 seconds of machine silence I present a stimulus, 0.5 seconds later of the begins of the silence, with an aproximated duration of 1.5 seconds

What is the best strategy for processing this data?

Regards

John Ochoa
Universidad de Antioquia
--0016364991e7155337049d6043e2--