ded. In extracting the timecourse
> should I adjust using an F-contrast spaning the first 6 columns only ([1 1 1
> 1 1 1]->right-padded with zeros)?? Is it problematic if I have not done
> this? What are the consequences?
>
> What about if I were only interested in the parametric modulations of the
> first condition in the PPI analysis? Should I adjust for the first 3 columns
> only ([1 1 1 0 0 0])?
>
> All your comments will be greatly appreciated.
>
> Richard
>
--20cf3054a4b5dbb06a049d5a5beb
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<div>Richard,</div><div><br></div>I'd use an F-contrast that is one row=
per condition/modulator. In your case:<div>1 0 0 0 0 0 ...</div><div>0 1 0=
0 0 0 ...</div><div>0 0 1 0 0 0 ...</div><div>0 0 0 1 0 0 ...</div><div>
0 0 0 0 1 0 ...</div><div>0 0 0 0 0 1 ...</div><div><br></div><div>The goal=
of the adjustment is to extract only the BOLD signal related to neural act=
ivity and eliminate the activity due to motion.=A0<br clear=3D"all"><br>Bes=
t Regards, Donald McLaren<br>
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<br>D.G. McLaren, Ph.D.<=
br>Postdoctoral Research Fellow, GRECC, Bedford VA<br>Research Fellow, Depa=
rtment of Neurology, Massachusetts General Hospital and Harvard Medical Sch=
ool<br>Office: (773) 406-2464<br>
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<br>This e-m=
ail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCAR=
E 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 f=
or delivering it to the intended recipient, you are hereby notified that yo=
u are in possession of confidential and privileged information. Any unautho=
rized use, disclosure, copying or the taking of any action in reliance on t=
he contents of this information is strictly prohibited and may be unlawful.=
If you have received this e-mail unintentionally, please immediately notif=
y the sender via telephone at (773) 406-2464 or email.<br>
<br><br><div class=3D"gmail_quote">On Mon, Feb 28, 2011 at 11:35 AM, Richar=
d Binney <span dir=3D"ltr"><<a href=3D"mailto:[log in to unmask]
om">[log in to unmask]</a>></span> wrote:<br><blockquote class=
=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padd=
ing-left:1ex;">
<div>Hi Darren G/ Karl F/other PPI-ers,</div>
<div>=A0</div>
<div>I can't find any posts on this and wondered if you can clear it up=
for me.</div>
<div>=A0</div>
<div>In extracting the principal eigenvariate from your VOI, you are asked =
if you want to adjust the extracted timecourse. When should you adjust and =
when should you not worry? what is the impact of adjusting?</div>
<div>=A0</div>
<div>My impression was that the raw timecourse would be extracted always. T=
he option to adjust suggests this is not always true. Do you use this optio=
n (only?)=A0when you have time or dispersion derivatives and/or motion regr=
essors?</div>
<div>=A0</div>
<div>I have a parametric design with two conditions (tasks)=A0and two param=
etric modulations per condition. The design matrix therefore has 6 regresso=
rs of interest. Motion regressors are also included. In extracting the time=
course should I adjust using an F-contrast spaning the first 6 columns only=
([1 1 1 1 1 1]->right-padded with zeros)?? Is it problematic if I have =
not done this? What are the consequences?</div>
<div>=A0</div>
<div>What about if I were only interested in the parametric modulations of =
the first condition in the PPI analysis? Should I adjust for the first 3 co=
lumns only ([1 1 1 0 0 0])?</div>
<div>=A0</div>
<div>All your comments will be greatly appreciated.</div>
<div>=A0</div><font color=3D"#888888">
<div>Richard</div>
</font></blockquote></div><br></div>
--20cf3054a4b5dbb06a049d5a5beb--
=========================================================================
Date: Mon, 28 Feb 2011 11:31:33 -0600
Reply-To: Pilar Archila-Suerte <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Pilar Archila-Suerte <[log in to unmask]>
Subject: Art repair - mean signal change
MIME-Version: 1.0
Content-Type: multipart/alternative; boundary=0015177fcec43a8612049d5b0ea2
Message-ID: <[log in to unmask]>
--0015177fcec43a8612049d5b0ea2
Content-Type: text/plain; charset=UTF-8
SPM Users,
When using the "scaling to percent signal change" option in ArtRepair,
sometimes I get what I want from the files selected and sometimes I don't
(depending on which files I select).
Why would ArtRepair give this answer:
*Direct calls to spm_defauts are deprecated.*
*Please use spm('Defaults',modality) or spm_get_defaults instead.*
*Automatically estimated peak and contrast scaling.*
* Normalizing by beta_0008.img*
*Peak value = 4.97*
*Contrast sum = 0.996*
*Mean value = NaN*
*(peak/contrast_sum)*100/bmean = **NaN*
*
*
*ans =*
*
*
* 4.9700 0.9960 ** NaN*
All files follow the same path so I don't think that's the problem. Does
anybody know why this is happening and how I can fix this?
Thank you,
Pilar A.
--0015177fcec43a8612049d5b0ea2
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<div><div><div><div>SPM Users,</div></div></div></div><div>When using the &=
quot;scaling to percent signal change" option in ArtRepair, sometimes =
I get what I want from the files selected and sometimes I don't (depend=
ing on which files I select).</div>
<div><br></div><div>Why would ArtRepair give this answer:</div><div><br></d=
iv><div><div><i>Direct calls to spm_defauts are deprecated.</i></div><div><=
i>Please use spm('Defaults',modality) or spm_get_defaults instead.<=
/i></div>
<div><i>Automatically estimated peak and contrast scaling.</i></div><div><i=
>=C2=A0Normalizing by beta_0008.img</i></div><div><i>Peak value =C2=A0 =C2=
=A0=3D 4.97</i></div><div><i>Contrast sum =C2=A0=3D 0.996</i></div><div><i>=
Mean value =C2=A0 =C2=A0=3D NaN</i></div>
<div><i>(peak/contrast_sum)*100/bmean =C2=A0=3D </i><font class=3D"Apple-st=
yle-span" color=3D"#CC0000"><b><i>NaN</i></b></font></div><div><i><br></i><=
/div><div><i>ans =3D</i></div><div><i><br></i></div><div><i>=C2=A0=C2=A0 =
=C2=A04.9700 =C2=A0 =C2=A00.9960 =C2=A0 =C2=A0</i><b><font class=3D"Apple-s=
tyle-span" color=3D"#FF0000"><i> =C2=A0 NaN</i></font></b></div>
</div><br><div>=C2=A0All files follow the same path so I don't think th=
at's the problem.=C2=A0Does anybody know why this is happening and how =
I can fix this?</div><div><br></div><div>Thank you,</div><div>Pilar A.=C2=
=A0</div>
--0015177fcec43a8612049d5b0ea2--
=========================================================================
Date: Mon, 28 Feb 2011 12:36:59 -0500
Reply-To: Chris Watson <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Chris Watson <[log in to unmask]>
Subject: Re: Art repair - mean signal change
Comments: To: Pilar Archila-Suerte <[log in to unmask]>
In-Reply-To: <[log in to unmask]>
MIME-Version: 1.0
Content-Type: text/plain; charset="UTF-8"; format=flowed
Content-Transfer-Encoding: 7bit
Message-ID: <[log in to unmask]>
I think that was a bug in an older version of ArtRepair. Do you have the
latest version?
Pilar Archila-Suerte wrote:
> SPM Users,
> When using the "scaling to percent signal change" option in ArtRepair,
> sometimes I get what I want from the files selected and sometimes I
> don't (depending on which files I select).
>
> Why would ArtRepair give this answer:
>
> /Direct calls to spm_defauts are deprecated./
> /Please use spm('Defaults',modality) or spm_get_defaults instead./
> /Automatically estimated peak and contrast scaling./
> / Normalizing by beta_0008.img/
> /Peak value = 4.97/
> /Contrast sum = 0.996/
> /Mean value = NaN/
> /(peak/contrast_sum)*100/bmean = /*/NaN/*
> /
> /
> /ans =/
> /
> /
> / 4.9700 0.9960 /*/ NaN/*
>
> All files follow the same path so I don't think that's the
> problem. Does anybody know why this is happening and how I can fix this?
>
> Thank you,
> Pilar A.
=========================================================================
Date: Mon, 28 Feb 2011 11:38:50 -0600
Reply-To: Pilar Archila-Suerte <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Pilar Archila-Suerte <[log in to unmask]>
Subject: Re: Art repair - mean signal change
Comments: To: Chris Watson <[log in to unmask]>
In-Reply-To: <[log in to unmask]>
MIME-Version: 1.0
Content-Type: multipart/alternative; boundary=00163683195045f1c4049d5b2847
Message-ID: <[log in to unmask]>
--00163683195045f1c4049d5b2847
Content-Type: text/plain; charset=UTF-8
I have ArtRepair v4. Isn't this the latest version?
On Mon, Feb 28, 2011 at 11:36 AM, Chris Watson <
[log in to unmask]> wrote:
> I think that was a bug in an older version of ArtRepair. Do you have the
> latest version?
>
>
> Pilar Archila-Suerte wrote:
>
>> SPM Users,
>> When using the "scaling to percent signal change" option in ArtRepair,
>> sometimes I get what I want from the files selected and sometimes I don't
>> (depending on which files I select).
>>
>> Why would ArtRepair give this answer:
>>
>> /Direct calls to spm_defauts are deprecated./
>> /Please use spm('Defaults',modality) or spm_get_defaults instead./
>> /Automatically estimated peak and contrast scaling./
>> / Normalizing by beta_0008.img/
>> /Peak value = 4.97/
>> /Contrast sum = 0.996/
>> /Mean value = NaN/
>> /(peak/contrast_sum)*100/bmean = /*/NaN/*
>> /
>> /
>> /ans =/
>> /
>> /
>> / 4.9700 0.9960 /*/ NaN/*
>>
>> All files follow the same path so I don't think that's the problem. Does
>> anybody know why this is happening and how I can fix this?
>>
>> Thank you,
>> Pilar A.
>>
>
--00163683195045f1c4049d5b2847
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Content-Transfer-Encoding: quoted-printable
I have ArtRepair v4. Isn't this the latest version?<br><br><div class=
=3D"gmail_quote">On Mon, Feb 28, 2011 at 11:36 AM, Chris Watson <span dir=
=3D"ltr"><<a href=3D"mailto:[log in to unmask]">Ch=
[log in to unmask]</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;">I think that was a bug in an older version =
of ArtRepair. Do you have the latest version?<div><div></div><div class=3D"=
h5">
<br>
<br>
Pilar Archila-Suerte wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
SPM Users,<br>
When using the "scaling to percent signal change" option in ArtRe=
pair, sometimes I get what I want from the files selected and sometimes I d=
on't (depending on which files I select).<br>
<br>
Why would ArtRepair give this answer:<br>
<br>
/Direct calls to spm_defauts are deprecated./<br>
/Please use spm('Defaults',modality) or spm_get_defaults instead./<=
br>
/Automatically estimated peak and contrast scaling./<br>
/ Normalizing by beta_0008.img/<br>
/Peak value =C2=A0 =C2=A0=3D 4.97/<br>
/Contrast sum =C2=A0=3D 0.996/<br>
/Mean value =C2=A0 =C2=A0=3D NaN/<br>
/(peak/contrast_sum)*100/bmean =C2=A0=3D /*/NaN/*<br>
/<br>
/<br>
/ans =3D/<br>
/<br>
/<br>
/ =C2=A0 =C2=A04.9700 =C2=A0 =C2=A00.9960 =C2=A0 =C2=A0/*/ =C2=A0 NaN/*<br>
<br>
=C2=A0All files follow the same path so I don't think that's the pr=
oblem. Does anybody know why this is happening and how I can fix this?<br>
<br>
Thank you,<br>
Pilar A. <br>
</blockquote>
</div></div></blockquote></div><br><br clear=3D"all"><div><div><br><div><di=
v><br></div></div></div></div><br>
--00163683195045f1c4049d5b2847--
=========================================================================
Date: Mon, 28 Feb 2011 12:47:00 -0500
Reply-To: Jason Steffener <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Jason Steffener <[log in to unmask]>
Subject: matlabbatch "decode dependencies"
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Message-ID: <[log in to unmask]>
Dear All,
Hello all.
I am trying to create some provenance info from an SPM batch file. So
I would like to take an SPM job file and read through it to pull out
the different steps, the data and the parameters. I have no problem
doing this EXCEPT where I have specified some dependencies. I am
having trouble decoding what the dependencies refer to.
Essentially if I have the following steps:
Realign << Input data
Reslice >> Output data
smooth << Output data from reslice
I would like the following:
Step1 Realign
input data: FILENAME
parameters :XX
Step2 Reslice
input data: output from Step 1
output data: rFILENAME
parameters: XX
Step3 Smooth
input data: rFILENAME
output data: srFILENAME
parameters: XX
And ideas? Or if someone can point me to the code that translates the
dependencies in the job file into something I can figure out, that
would also be great.
Thank you,
Jason
--
Jason Steffener, Ph.D.
Department of Neurology
Columbia University
http://www.cogneurosci.org/steffener.html
=========================================================================
Date: Mon, 28 Feb 2011 14:08:11 +0100
Reply-To: Alexander Hammers <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Alexander Hammers <[log in to unmask]>
Subject: Re: question on VOI analysis
Comments: To: sarika cherodath <[log in to unmask]>
In-Reply-To: <[log in to unmask]>
Mime-Version: 1.0 (Apple Message framework v1082)
Content-Type: multipart/mixed; boundary=Apple-Mail-79-616227633
Message-ID: <[log in to unmask]>
--Apple-Mail-79-616227633
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
charset=us-ascii
Dear Sarika,
How did you define the VOI(s)? If they are in MNI space as your second =
level implies, then you're applying one VOI to all the subjects... and =
this will unsurprisingly have the same volume in all.
I don't know what kind of data you have - it sounds like fMRI. An =
approximation of individual volumetrics would be to backtransform your =
standard space VOIs into individual space - if you've used Unified =
Segmentation for your MRI spatial normalisation, then the =
*inv_seg_sn.mat file can accomplish this.
Such a procedure's accuracy will be limited by 1) the quality and =
provenience of your standard space VOI (see our recent thread on =
single-subject vs multi-subject atlases) and 2) the low-ish number of =
degrees of freedom of the transformation for standard normalisation and =
Unified Segmentation. Point #2 should be improve-able if you use DARTEL.
The gold standard for just one particular area would be to devise a =
protocol, check the reliability of results and ideally their veracity, =
and then outline those areas by hand in your subjects.
Hope this helps,
Best wishes,
Alexander
-----------------------------
Alexander Hammers, MD PhD
--Apple-Mail-79-616227633
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--Apple-Mail-79-616227633
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Chair in Functional Neuroimaging
Neurodis Foundation
http://www.fondation-neurodis.org/
Postal Address:
CERMEP =96 Imagerie du Vivant
H=F4pital Neurologique Pierre Wertheimer
59 Boulevard Pinel, 69003 Lyon, France
Telephone +33-(0)4-72 68 86 34
Fax +33-(0)4-72 68 86 10
Email =
[log in to unmask];[log in to unmask]
---------------------------------
Other affiliations:
Visiting Reader; Honorary Consultant Neurologist
Division of Neuroscience and Mental Health, Faculty of Medicine
Imperial College London, UK
---------------------------------
Honorary Reader in Neurology; Honorary Consultant Neurologist
Department of Clinical and Experimental Epilepsy
National Hospital for Neurology and Neurosurgery/ Institute of =
Neurology, University College London, UK
On 28 Feb 2011, at 10:11, sarika cherodath wrote:
>=20
> Hi SPMers,
>=20
> I have been trying to perform VOI analysis to obtain signal =
changes at a particular area for individual subjects in the dataset, so =
as to make correlations with behavioral scores. When i tried to =
calculate the values, SPM returns the same value for all subjects! Can =
anybody explain why this might be? The dataset has been analysed at =
second level and then moved to another directory (along with first level =
data). Is it possible that SPM is not able to access the data because of =
the path change??
>=20
> Thanks in advance,
> --=20
> Sarika Cherodath
> Graduate Student
> National Brain Research Centre
> Manesar, Gurgaon -122050
> India
>=20
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=========================================================================
Date: Mon, 28 Feb 2011 15:14:22 -0500
Reply-To: Jeffrey West <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Jeffrey West <[log in to unmask]>
Subject: question regarding flexible factorial model
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Hello.
=20
I have question relating to setting up a flexible factorial model with 2 =
groups, each group has 4 conditions.
=20
I have 3 factors: 1 =3D subject (independent, variance equal), 2 =3D group =
(independent, variance not equal), 3 =3D condition (not independent, =
variance equal)
=20
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.=20
=20
The model did not run and I got the following error message:
=20
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_factor=
ial_design.m" (v3067), function "spm_run_factorial_design" at line 482.
=20
The following modules did not run:
Failed: Factorial design specification
=20
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.=20
=20
Thank you for any suggestions.
=20
Jef
=20
=20
Jeffrey West, M.A.
Research Analyst
Maryland Psychiatric Research Center
Baltimore, Maryland 21228-0247
Phone: 410-402-6018
email: [log in to unmask]
=20
=20
--=__Part4569690E.0__=
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Description: HTML
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; charset=3Diso-8859-1"=
>
<META content=3D"MSHTML 6.00.6000.17095" name=3DGENERATOR></HEAD>
<BODY style=3D"MARGIN: 4px 4px 1px; FONT: 10pt Tahoma">
<DIV>Hello.</DIV>
<DIV> </DIV>
<DIV>I have question relating to setting up a flexible factorial model =
with 2 groups, each group has 4 conditions.</DIV>
<DIV> </DIV>
<DIV>I have 3 factors: 1 =3D subject (independent, variance equal), 2 =3D =
group (independent, variance not equal), 3 =3D condition (not independent, =
variance equal)</DIV>
<DIV> </DIV>
<DIV>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. </DIV>
<DIV> </DIV>
<DIV>The model did not run and I got the following error message:</DIV>
<DIV> </DIV>
<DIV><STRONG>Running job #2<BR>--------------------------------------------=
---------------------------<BR>Running 'Factorial design specification'<BR>=
Failed 'Factorial design specification'<BR>Index exceeds matrix =
dimensions.<BR>In file "C:\Documents and Settings\JWest\Desktop\spm8\config=
\spm_run_factorial_design.m" (v3067), function "spm_run_factorial_design" =
at line 482.</STRONG></DIV>
<DIV> </DIV>
<DIV><STRONG>The following modules did not run:<BR>Failed: Factorial =
design specification</STRONG></DIV>
<DIV><STRONG></STRONG> </DIV>
<DIV>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. </DIV>
<DIV> </DIV>
<DIV>Thank you for any suggestions.</DIV>
<DIV> </DIV>
<DIV>Jef</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Jeffrey West, M.A.<BR>Research Analyst<BR>Maryland Psychiatric =
Research Center<BR>Baltimore, Maryland 21228-0247<BR>Phone: 410-402-6018<BR=
>email: <A href=3D"mailto:[log in to unmask]">[log in to unmask]
u</A> </DIV>
<DIV> </DIV>
<DIV> </DIV></BODY></HTML>
--=__Part4569690E.0__=--
=========================================================================
Date: Tue, 1 Mar 2011 09:17:07 +1300
Reply-To: Ehsan Negahbani <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Ehsan Negahbani <[log in to unmask]>
Subject: Unsubscribe me please
MIME-Version: 1.0
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--
Ehsan
--0022150475f729946e049d5d5d2c
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<br clear=3D"all"><br>-- <br><span style=3D"color:rgb(102, 102, 102)">Ehsan=
=A0</span><br>
--0022150475f729946e049d5d5d2c--
=========================================================================
Date: Mon, 28 Feb 2011 22:28:55 +0000
Reply-To: Vladimir Litvak <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Vladimir Litvak <[log in to unmask]>
Subject: Re: spm_eeg_convert2scalp
Comments: To: Erick Britis Ortiz <[log in to unmask]>
In-Reply-To: <[log in to unmask]>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
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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 (=E0
> 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 23:08:58 +0000
Reply-To: Vladimir Litvak <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Vladimir Litvak <[log in to unmask]>
Subject: Re: spm_eeg_convert2scalp
Comments: To: Erick Britis Ortiz <[log in to unmask]>
In-Reply-To: <[log in to unmask]>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Message-ID: <[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 =A0(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 frequenc=
y.
>>>
>>> I assumed that spm_eeg_convert2scalp would use a standard 2D layout (=
=E0
>>> 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; boundary=bcaec51a894a8f7f93049d601f97
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,=A0<div><br></div><div>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, subje=
ct is automatically modelled).=A0</div>
<div>So for a subject in group 2 with scans for all four conditions you wou=
ld need:</div><div>[2 1<br>2 2=A0<br>2 3</div><div>2 4]</div><div>Make sure=
your scans are entered in the right order!</div><div><br></div><div>Also, =
main effect for subjects doesn't need to be specified, this is done aut=
omatically (this is because you chose 'Subjects' at the 'Specif=
y Subjects or all Scans & Factors').</div>
<div><br></div><div>Good luck,=A0</div><div><br></div><div>Pieter</div><div=
><br></div><div><br><div class=3D"gmail_quote">On Mon, Feb 28, 2011 at 3:14=
PM, Jeffrey West <span dir=3D"ltr"><<a href=3D"mailto:[log in to unmask]
and.edu">[log in to unmask]</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;">
<div style=3D"margin:4px 4px 1px;font:10pt Tahoma">
<div>Hello.</div>
<div>=A0</div>
<div>I have question relating to setting up a flexible factorial model with=
2 groups, each group has=A04 conditions.</div>
<div>=A0</div>
<div>I have 3 factors: 1 =3D subject (independent, variance equal), 2 =3D g=
roup (independent, variance not equal), 3 =3D condition (not independent, v=
ariance equal)</div>
<div>=A0</div>
<div>For the subject level, I entered in 20 subjects, for each subject, I e=
ntered 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 in=
teraction: main effect: 1, main effect: 2, main effect: 3, interaction: 2 3=
. </div>
<div>=A0</div>
<div>The model did not run and I got the following error message:</div>
<div>=A0</div>
<div><strong>Running job #2<br>--------------------------------------------=
---------------------------<br>Running 'Factorial design specification&=
#39;<br>Failed=A0 'Factorial design specification'<br>Index exceeds=
matrix dimensions.<br>
In file "C:\Documents and Settings\JWest\Desktop\spm8\config\spm_run_f=
actorial_design.m" (v3067), function "spm_run_factorial_design&qu=
ot; at line 482.</strong></div>
<div>=A0</div>
<div><strong>The following modules did not run:<br>Failed: Factorial design=
specification</strong></div>
<div><strong></strong>=A0</div>
<div>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 p=
lease explain what I did wrong setting up my model. </div>
<div>=A0</div>
<div>Thank you for any suggestions.</div>
<div>=A0</div>
<div>Jef</div>
<div>=A0</div>
<div>=A0</div>
<div>Jeffrey West, M.A.<br>Research Analyst<br>Maryland Psychiatric Researc=
h Center<br>Baltimore, Maryland 21228-0247<br>Phone: <a href=3D"tel:410-402=
-6018" target=3D"_blank">410-402-6018</a><br>email: <a href=3D"mailto:jwest=
@mprc.umaryland.edu" target=3D"_blank">[log in to unmask]</a> </div>
<div>=A0</div>
<div>=A0</div></div>
</blockquote></div><br></div>
--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=90e6ba6e8996ee354c049d602b47
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=
.=A0<div><br></div><div>Pieter<br><br><div class=3D"gmail_quote">On Mon, Fe=
b 28, 2011 at 6:34 PM, Pieter van de Vijver <span dir=3D"ltr"><<a href=
=3D"mailto:[log in to unmask]">[log in to unmask]</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;">Hi Jeff,=A0<div><br></div><div>You should e=
nter 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 gr=
oup and one for condition, subject is automatically modelled).=A0</div>
<div>So for a subject in group 2 with scans for all four conditions you wou=
ld need:</div><div>[2 1<br>2 2=A0<br>2 3</div><div>2 4]</div><div>Make sure=
your scans are entered in the right order!</div><div><br></div><div>Also, =
main effect for subjects doesn't need to be specified, this is done aut=
omatically (this is because you chose 'Subjects' at the 'Specif=
y Subjects or all Scans & Factors').</div>
<div><br></div><div>Good luck,=A0</div><div><br></div><font color=3D"#88888=
8"><div>Pieter</div></font><div><div></div><div class=3D"h5"><div><br></div=
><div><br><div class=3D"gmail_quote">On Mon, Feb 28, 2011 at 3:14 PM, Jeffr=
ey West <span dir=3D"ltr"><<a href=3D"mailto:[log in to unmask]" t=
arget=3D"_blank">[log in to unmask]</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
<div style=3D"margin:4px 4px 1px;font:10pt Tahoma">
<div>Hello.</div>
<div>=A0</div>
<div>I have question relating to setting up a flexible factorial model with=
2 groups, each group has=A04 conditions.</div>
<div>=A0</div>
<div>I have 3 factors: 1 =3D subject (independent, variance equal), 2 =3D g=
roup (independent, variance not equal), 3 =3D condition (not independent, v=
ariance equal)</div>
<div>=A0</div>
<div>For the subject level, I entered in 20 subjects, for each subject, I e=
ntered 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 in=
teraction: main effect: 1, main effect: 2, main effect: 3, interaction: 2 3=
. </div>
<div>=A0</div>
<div>The model did not run and I got the following error message:</div>
<div>=A0</div>
<div><strong>Running job #2<br>--------------------------------------------=
---------------------------<br>Running 'Factorial design specification&=
#39;<br>Failed=A0 'Factorial design specification'<br>Index exceeds=
matrix dimensions.<br>
In file "C:\Documents and Settings\JWest\Desktop\spm8\config\spm_run_f=
actorial_design.m" (v3067), function "spm_run_factorial_design&qu=
ot; at line 482.</strong></div>
<div>=A0</div>
<div><strong>The following modules did not run:<br>Failed: Factorial design=
specification</strong></div>
<div><strong></strong>=A0</div>
<div>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 p=
lease explain what I did wrong setting up my model. </div>
<div>=A0</div>
<div>Thank you for any suggestions.</div>
<div>=A0</div>
<div>Jef</div>
<div>=A0</div>
<div>=A0</div>
<div>Jeffrey West, M.A.<br>Research Analyst<br>Maryland Psychiatric Researc=
h Center<br>Baltimore, Maryland 21228-0247<br>Phone: <a href=3D"tel:410-402=
-6018" target=3D"_blank"></a><a href=3D"tel:410-402-6018" target=3D"_blank"=
>410-402-6018</a><br>
email: <a href=3D"mailto:[log in to unmask]" target=3D"_blank">jwest@=
mprc.umaryland.edu</a> </div>
<div>=A0</div>
<div>=A0</div></div>
</blockquote></div><br></div>
</div></div></blockquote></div><br></div>
--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; boundary=0016364991e7155337049d6043e2
Message-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 T=
R 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 silenc=
e, with an aproximated duration of 1.5 seconds<div>
<br></div><div>What is the best strategy for processing this data?</div><di=
v><br></div><div>Regards</div><div><br></div><div>John Ochoa</div><div>Univ=
ersidad de Antioquia</div>
--0016364991e7155337049d6043e2--
