[log in to unmask]>
--20cf3054a2f72ca08e049d4f4d70
Content-Type: text/plain; charset=ISO-8859-1
Set the interpolation option to nearest neighbor. That should make it exact.
Also, you might want to think about other transforms since the data is
likely not to be normally distributed.
Best Regards, Donald McLaren
================D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
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 Sun, Feb 27, 2011 at 10:13 AM, Nynke L
<[log in to unmask]>wrote:
> Hello all,
>
> I have a particular group level analysis for which I want to use spm.
> However, till now I don't manage to so I hope you have suggestions for me.
>
> I use fMRI for the prediction of a certain binary outcome. Therefore, I use
> a different classification software package that computes
> prediction-accuracies for all voxels. For each subject, I have a .nii file
> with as values the accuracies (range between 0 and 1). So, this is a brain
> map just like you usually feed to the second level.
>
> What I want to test in the second level analysis is which brain areas have
> accuracies significantly higher than 0.5. So I want to test against the
> null-hypothesis that accuracies are 0.5 or lower. Now the problem is that
> the 1 sample t-test in spm on default tests against the null-hypothesis that
> the values are zero or higher.... So my first question is whether it is
> possible to set a custum value for the t-test to test against a manually set
> value?
>
> I already tried a different approach, namely subtracting 0.5 from the
> values in my input images (to put them in the default spm t-test). However,
> when I trie to do this with the image calculator of spm (with as expression
> i1 - 0.5) I do not get correct results: I do not get a map with exactly 0.5
> subtracted from each value but a range between 0.4-0.6. It seems that
> spm-image-calc is also doing something else with the image... So my second
> question is: how can I make image-calc subtract exactly 0.5 from all values
> in the image?
>
> Thanks in advance!
>
> Best regards,
> Nynke van der Laan
>
--20cf3054a2f72ca08e049d4f4d70
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Set the interpolation option to nearest neighbor. That should make it exact.
Also, you might want to think about other transforms since the data is likely not to be normally distributed.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School
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 Sun, Feb 27, 2011 at 10:13 AM, Nynke L
<[log in to unmask]> wrote:
Hello all,
I have a particular group level analysis for which I want to use spm. However, till now I don't manage to so I hope you have suggestions for me.
I use fMRI for the prediction of a certain binary outcome. Therefore, I use a different classification software package that computes prediction-accuracies for all voxels. For each subject, I have a .nii file with as values the accuracies (range between 0 and 1). So, this is a brain map just like you usually feed to the second level.
What I want to test in the second level analysis is which brain areas have accuracies significantly higher than 0.5. So I want to test against the null-hypothesis that accuracies are 0.5 or lower. Now the problem is that the 1 sample t-test in spm on default tests against the null-hypothesis that the values are zero or higher.... So my first question is whether it is possible to set a custum value for the t-test to test against a manually set value?
I already tried a different approach, namely subtracting 0.5 from the values in my input images (to put them in the default spm t-test). However, when I trie to do this with the image calculator of spm (with as expression i1 - 0.5) I do not get correct results: I do not get a map with exactly 0.5 subtracted from each value but a range between 0.4-0.6. It seems that spm-image-calc is also doing something else with the image... So my second question is: how can I make image-calc subtract exactly 0.5 from all values in the image?
Thanks in advance!
Best regards,
Nynke van der Laan
--20cf3054a2f72ca08e049d4f4d70--
========================================================================Date: Mon, 28 Feb 2011 09:55:35 +0100
Reply-To: Marko Wilke <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Marko Wilke <[log in to unmask]>
Subject: Re: SPM8 error
Comments: To: Glen Lee <[log in to unmask]>
In-Reply-To: <[log in to unmask]>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: quoted-printable
Message-ID: <[log in to unmask]>
Hi Glen,
this could be an installation problem, perhaps try using a
newly-downloaded SPM, install the latest updates on top of it and
install it into a directory without spaces (say, 'C:\Test\SPM8'), and
then only add this directory to the Matlab path.
Cheers,
Marko
Glen Lee wrote:
> Hello SPMers,
> Does anybody help me figuring out what this error message (Error using
> ==> < a href="matlab: opentonline ('cfg_util.m',808,0)"> cfg_util at 808
> ) mean and how i can resolve this issue?
> I get this same error no matter what I try (e.g., realign, normalize,
> etc) in SPM8 (also see attached)
> Let me know. Thanks in advance.
>
> Glen
>
>
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn
____________________________________________________
========================================================================Date: Mon, 28 Feb 2011 09:06:14 +0000
Reply-To: John Ashburner <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: John Ashburner <[log in to unmask]>
Subject: Re: normalization failure (anterior posterior mismatch)
Comments: To: Yune Lee <[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]>
Before running the spatial normalisation, you'll need to ensure that
the image is in approximate alignment with the templates (Check Reg
button). For these images, it appears that they are either rotated by
180 degrees (about the z axis) or flipped in the anterior posterior
direction.
Best regards,
-John
On 28 February 2011 00:55, Yune Lee <[log in to unmask]> wrote:
>
> Dear SPM experts,
> I've encountered a normalization failure, such that there is a mismatch of
> anterior-posterior between a template (EPI.nii) and a source image
> (meanbold.nii)
> This is clearly shown in the attached PDF file.
> Any help wold be greatly appreciated.
>
> Thanks in advance,
> YSL
>
>
>
>
========================================================================Date: Mon, 28 Feb 2011 14:41:37 +0530
Reply-To: sarika cherodath <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: sarika cherodath <[log in to unmask]>
Subject: question on VOI analysis
MIME-Version: 1.0
Content-Type: multipart/alternative; boundaryMessage-ID: <[log in to unmask]>
--00248c05002ff8481b049d5412cf
Content-Type: text/plain; charset=ISO-8859-1
Hi SPMers,
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??
Thanks in advance,
--
Sarika Cherodath
Graduate Student
National Brain Research Centre
Manesar, Gurgaon -122050
India
--00248c05002ff8481b049d5412cf
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Hi SPMers,
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??
Thanks in advance,
--
Sarika Cherodath
Graduate Student
National Brain Research Centre
Manesar, Gurgaon -122050
India
Applications are invited for an 18
month postdoctoral
fellowship in
the human multimodal neuroimaging project “Linking the major system
markers for typical and atypical brain development: a multimodal imaging and
spectroscopy study” (http://www.zihp.uzh.ch/1610.php#45)
funded by the Zürich Institute of Human Physiology.
This study will investigate the
major physiological markers of brain development, using a combination of multimodal
brain imaging (e.g., simultaneous EEG-fMRI, see Lüchinger et al., 2011, NeuroImage,
in press)
and MR-spectroscopy methods (i.e., GABA, see O’Gorman et al., 2011, J. of
Mag. Reson. Img., in press). The initial phase of the study will establish
baseline neurotransmitter levels, cerebral blood flow (e.g., perfusion MRI) and
EEG frequency and power at rest in children, adolescents, and adults. Examining
the interactions between these markers and the changes they demonstrate with
age and hormone levels will allow to better understanding the global and
regional processes underlying brain maturation. In addition, we will
investigate changes in these physiological markers with (a) memory tasks (see
Michels et al., 2010, PLoS ONE) and (b) attention deficit hyperactivity disorder
(ADHD, see Doehnert et al., Biol Psychiatry, 2010). The starting
date of the position is May 2011.
Our department is equipped with 64-channel fMRI-compatible EEG equipment and a
3 Tesla GE scanner, which is mainly dedicated for research questions.
The successful applicant will have a
PhD research background in Cognitive Neuroscience, Neurophysiology, Psychology,
Neuropsychology, or related fields. Fluency in English and the ability to work within a
multidisciplinary team are essential. Applicants must be experienced at
conducting fMRI and/or EEG studies –demonstrated by at least 2 first
author publications in international peer-reviewed journals– and be
familiar with analysis software such as SPM/Matlab, BrainVoyager and/or
FSL. Experience with stimulus presentation software (such as Presentation),
UNIX, and programming languages a plus.
Salaries are in accordance with the
Swiss National Research Foundation.
APPLICATION INSTRUCTIONS: To apply, please send a
curriculum vitae, a personal statement describing research interests, 3 letters
of recommendations, and up to 3 article reprints/preprints (max. 2 MB!!!) to:
Dr Lars Michels
[log in to unmask]
MR-Zentrum
University Children’s Hospital
Steinwiesstrasse 75
Zürich 8032
Switzerland
Reviews of applications will begin
on the 1st of March and
will continue until the position is filled.
------_=_NextPart_001_01CBD727.BC9EDDD6--
========================================================================Date: Mon, 28 Feb 2011 09:48:36 +0000
Reply-To: Vincent Koppelmans <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Vincent Koppelmans <[log in to unmask]>
Subject: Adjusting Dartel for ICV: RC volumes or C volumes
Mime-Version: 1.0
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset="UTF-8"
Message-ID: <[log in to unmask]>
Dear SPM experts,
If you adjust for intra cranial volume in a dartel analyses on gray matter, would it be best to have your ICV calculated from the RC files or the C files. I have read that C files are a little bit more accurate than the RC files. Then again, the dartel analysis uses RC files, therefore volumes calculated from RC files would match the data best, right? Kind regards,
Vincent
========================================================================Date: Mon, 28 Feb 2011 11:43:44 +0100
Reply-To: =?ISO-8859-1?Q?Gemma_Monté?= <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: =?ISO-8859-1?Q?Gemma_Monté?= <[log in to unmask]>
Subject: Re: Adjusting Dartel for ICV: RC volumes or C volumes
Comments: To: Vincent Koppelmans <[log in to unmask]>
In-Reply-To: <[log in to unmask]>
MIME-Version: 1.0
Content-Type: multipart/alternative; boundaryMessage-ID: <[log in to unmask]>
--0015175cb1445b46e5049d555ca2
Content-Type: text/plain; charset=ISO-8859-1
Hi Vincent,
I suggest you use the c*.nii files. They are the tissue classes in native
space.
You are right, DARTEL takes information encoded in the rc*.nii files.
However, the flow fields u_rc1*.nii files are applied to the c1*.nii to
create the warped files. So finally, you obtain files in the form
swmc1*.nii, either in the DARTEL space or in the MNI space. You can check
that the volumes of the GM Jacobian scaled images (without smoothing) by
DARTEL are the same than the volume of the GM segments in native space
(c1*.nii files).
Hope this helps,
Gemma
On 28 February 2011 10:48, Vincent Koppelmans <[log in to unmask]>wrote:
> Dear SPM experts,
>
> If you adjust for intra cranial volume in a dartel analyses on gray matter,
> would it be best to have your ICV calculated from the RC files or the C
> files. I have read that C files are a little bit more accurate than the RC
> files. Then again, the dartel analysis uses RC files, therefore volumes
> calculated from RC files would match the data best, right? Kind regards,
>
> Vincent
>
<[log in to unmask]>
--0015175cb1445b46e5049d555ca2
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Hi Vincent,
I suggest you use the c*.nii files. They are the tissue classes in native space.
You are right, DARTEL takes information encoded in the rc*.nii files. However, the flow fields u_rc1*.nii files are applied to the c1*.nii to create the warped files. So finally, you obtain files in the form swmc1*.nii, either in the DARTEL space or in the MNI space. You can check that the volumes of the GM Jacobian scaled images (without smoothing) by DARTEL are the same than the volume of the GM segments in native space (c1*.nii files).
Hope this helps,
Gemma
On 28 February 2011 10:48, Vincent Koppelmans
<[log in to unmask]> wrote:
Dear SPM experts,
If you adjust for intra cranial volume in a dartel analyses on gray matter, would it be best to have your ICV calculated from the RC files or the C files. I have read that C files are a little bit more accurate than the RC files. Then again, the dartel analysis uses RC files, therefore volumes calculated from RC files would match the data best, right? Kind regards,
Vincent
--0015175cb1445b46e5049d555ca2--
========================================================================Date: Mon, 28 Feb 2011 11:50:23 +0100
Reply-To: michel grothe <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: michel grothe <[log in to unmask]>
Subject: Re: Adjusting Dartel for ICV: RC volumes or C volumes
Comments: To: [log in to unmask]
In-Reply-To: <[log in to unmask]>
Content-Type: multipart/alternative;
boundary="_90f969e0-6ae7-4793-8d3b-790a0b77c215_"
MIME-Version: 1.0
Message-ID: <[log in to unmask]>
--_90f969e0-6ae7-4793-8d3b-790a0b77c215_
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Content-Transfer-Encoding: quoted-printable
Dear Vincent,
the rc*-files are rigid-body (6-P) transformed versions of the c*-files and total tissue calculations should therefore be exactly the same between the two files. Given that modulation aims to preserve the native amount of tissue, totals calculated from mwrc*-files should also be equal to the ones calculated from c*- or rc*-files, although they might differ slightly because of interpolation issues. Do totals calculated from the different image-types differ in your case?
Best regards,
Michel
> Date: Mon, 28 Feb 2011 09:48:36 +0000
> From: [log in to unmask]
> Subject: [SPM] Adjusting Dartel for ICV: RC volumes or C volumes
> To: [log in to unmask]
>
> Dear SPM experts,
>
> If you adjust for intra cranial volume in a dartel analyses on gray matter, would it be best to have your ICV calculated from the RC files or the C files. I have read that C files are a little bit more accurate than the RC files. Then again, the dartel analysis uses RC files, therefore volumes calculated from RC files would match the data best, right? Kind regards,
>
> Vincent
--_90f969e0-6ae7-4793-8d3b-790a0b77c215_
Content-Type: text/html; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Dear Vincent,
the rc*-files are rigid-body (6-P) transformed versions of the c*-files and total tissue calculations should therefore be exactly the same between the two files. Given that modulation aims to preserve the native amount of tissue, totals calculated from mwrc*-files should also be equal to the ones calculated from c*- or rc*-files, although they might differ slightly because of interpolation issues. Do totals calculated from the different image-types differ in your case?
Best regards,
Michel
> Date: Mon, 28 Feb 2011 09:48:36 +0000
> From: [log in to unmask]
> Subject: [SPM] Adjusting Dartel for ICV: RC volumes or C volumes
> To: [log in to unmask]
>
> Dear SPM experts,
>
> If you adjust for intra cranial volume in a dartel analyses on gray matter, would it be best to have your ICV calculated from the RC files or the C files. I have read that C files are a little bit more accurate than the RC files. Then again, the dartel analysis uses RC files, therefore volumes calculated from RC files would match the data best, right? Kind regards,
>
> Vincent
--_90f969e0-6ae7-4793-8d3b-790a0b77c215_--
========================================================================Date: Mon, 28 Feb 2011 10:59:22 +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 DCM] how to specify the modulation?
Comments: To: =?UTF-8?B?6aOe6bif?= <[log in to unmask]>
In-Reply-To: <[log in to unmask]>
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable
Message-ID: <[log in to unmask]>
Dear Haoran,
2011/2/27 飞鸟 <[log in to unmask]>:
> Hello all,
> 　　When you analysis your data with the method of DCM, have you ever met the
> problem about how to specify the modulation? Now I choose 7 basic models,
> and then assume all the connections in each basic model are modulated by the
> experimental manipulation. What I want to know is that whether or not this
> is reasonable
Usually one would have a hypothesis about which specific connections
are affected by the experimental condition.
>In addition, is it possible that the connections
> between two sources could include forward connectivity, backward
> connectivity and lateral connectivity at the same time?
No. Every connection can only have one type.
Vladimir
> 　　Any help will be grateful!
>
> --
> Haoran LI (MS)
> Brain Imaging Lab,
> Research Center for Learning Science,
> Southeast University
> 2 Si Pai Lou , Nanjing, 210096, P.R.China
>
>
========================================================================Date: Mon, 28 Feb 2011 12:02:19 +0100
Reply-To: Marko Wilke <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Marko Wilke <[log in to unmask]>
Subject: F-values
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: quoted-printable
Message-ID: <[log in to unmask]>
Dear All,
at the risk of (once again) exhibiting my statistical ignorance, I
wanted to ask for feedback re: an effect I see when doing F-tests. I am
comparing sessions with different numbers of covariates and compute an
omnibus F-test in SPM (for the covariates only) and sum the resulting
F-values. As expected, I see that there seems to be an optimum number of
covariates as the sum of F-values first increases, then decreases when
adding more covariates. I expected this to be a function of the degrees
of freedom but I cannot seem to find the piece of code where these are
taken into account. Any input is appreciated.
Cheers,
Marko
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn
____________________________________________________
========================================================================Date: Mon, 28 Feb 2011 14:12:21 +0000
Reply-To: SUBSCRIBE FSL Patricia Pires <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: SUBSCRIBE FSL Patricia Pires <[log in to unmask]>
Subject: DTI with SPM
Mime-Version: 1.0
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset="UTF-8"
Message-ID: <[log in to unmask]>
Hello,
i am new in the SPM forum and i will be glad if somebody could help me. My question is concerning to preocess DTI images with SPM. I have processed DTI images (FA; MD, RD...) with FSL. Could anyone tell me some lecture to find how process (e.g. FA images) with SPM or where to find information concernig SPM and FSL procedures softwares differences?
Thank you very much,
Patricia.
========================================================================Date: Mon, 28 Feb 2011 15:25:26 +0100
Reply-To: Janani Dhinakaran <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Janani Dhinakaran <[log in to unmask]>
Subject: Unsubscribe me please
MIME-Version: 1.0
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Thank you.
--20cf3079b77ea0b2a8049d5874c7
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Thank you.
--20cf3079b77ea0b2a8049d5874c7--
========================================================================Date: Mon, 28 Feb 2011 15:29:46 +0100
Reply-To: Wolfgang Weber-Fahr <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Wolfgang Weber-Fahr <[log in to unmask]>
Subject: Job Anouncement ZI-Mannheim, Germany
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8; format=flowed
Content-Transfer-Encoding: quoted-printable
Message-ID: <[log in to unmask]>
The Central Institute of Mental Health (State Foundation) is an
internationally
renowned research institute in the field of psychiatry and neuroscience,
home
of the Department of Psychiatry of the Medical Faculty Mannheim of the
University of Heidelberg as well as psychiatric hospital with 255 inpatient
and 52 day-hospital beds.
Within several new projects funded by the European Union and the Federal
Ministry
of Education and Research we offer
2 Positions for PostDocs and PhD-Students
in the area of rodent magnetic resonance functional-, perfusion- and
diffusion tensor (DTI)
imaging at 9.4 Tesla.
The Central Institute of Mental Health is equipped with a latest
generation 210 mm
horizontalbore Bruker BioSpec animal system and additional cryogenic MR
coils for
1H and 13C detection in the mouse brain as well as two 3 Tesla human
whole body MR-scanners.
The positions are for two years initially and located in the research
group Translational Imaging.
Potential applicants should have a diploma or master in physics,
physical chemistry or neuroscience,
or an equivalent field. The ideal candidate from the quantitative
sciences has a solid background
in NMR physics, signal detection and processing theory, and is familiar
with the
Bruker Paravision environment. Experience in other computer languages,
Matlab or IDL,
is desirable.
We have openings in these primary fields of research:
• Establishment of manganese enhanced magnetic resonance imaging (MEMRI)
for a the longitudinal assessment of connectivity and neuronal activity
in experimental animals.
• Development of methods for the acquisition and post processing of
functional
BOLD imaging data with optogenetics for the identification and
investigation of brain networks.
• Diffusion Tensor Imaging for the investigation of structural integrity
in different
psychiatric mouse-models.
The candidate would also collaborate on several ongoing animal studies
of schizophrenia, depression,
substance abuse and other psychiatric disorders in mouse and rat models.
The assistance in the general supervision of the animal scanner would
also be part of the position.
More information can be found at
http://www.zi-mannheim.de/transl_imaging.html.
We offer an interesting job in a leading research hospital with a strong
emphasis on MR-Imaging,
salary is according to the German TV-L pay scale, including the social
benefits of the public service sector.
For further information please contact Dr. Wolfgang Weber-Fahr, Tel. +49
621 1703-2961,
E-Mail: [log in to unmask]
Homepage: www.zi-mannheim.de/start_en.html
----------------------------------------------------------
Wolfgang Weber-Fahr, Dr.rer.nat.
Head RG Translational Imaging
Neuroimaging Department
Central Institute of Mental Health
J5
68072 Mannheim
Germany
email:[log in to unmask]
phone: ++49 621 1703 2961
========================================================================Date: Mon, 28 Feb 2011 10:36:54 -0500
Reply-To: zao liu <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: zao liu <[log in to unmask]>
Subject: regions of brain corresponding to VBM coordinates
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*Dear All,*
**
*I did VBM analysis on our T1-w images and would like to know if there is a
way to get the names of regions of activation in the brain from the
coordinates (which comes as a report at the end of VBM, i.e voxelwise,
cluster wise and set level reports). One more clarification the coordinates
reported are in MNI right and are mm not voxel coordinates right.*
--0015174bf21c068a29049d5973e3
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Dear All,
I did VBM analysis on our T1-w images and would like to know if there is a way to get the names of regions of activation in the brain from the coordinates (which comes as a report at the end of VBM, i.e voxelwise, cluster wise and set level reports). One more clarification the coordinates reported are in MNI right and are mm not voxel coordinates right.
--0015174bf21c068a29049d5973e3--
========================================================================Date: Mon, 28 Feb 2011 16:35:44 +0000
Reply-To: Richard Binney <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: Richard Binney <[log in to unmask]>
Subject: PPI: adjust for effects of interest
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Hi Darren G/ Karl F/other PPI-ers,
I can't find any posts on this and wondered if you can clear it up for me.
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?
My impression was that the raw timecourse would be extracted always. The
option to adjust suggests this is not always true. Do you use this option
(only?) when you have time or dispersion derivatives and/or motion
regressors?
I have a parametric design with two conditions (tasks) and two parametric
modulations per condition. The design matrix therefore has 6 regressors of
interest. Motion regressors are also included. 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
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Hi Darren G/ Karl F/other PPI-ers,
I can't find any posts on this and wondered if you can clear it up for me.
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?
My impression was that the raw timecourse would be extracted always. The option to adjust suggests this is not always true. Do you use this option (only?) when you have time or dispersion derivatives and/or motion regressors?
I have a parametric design with two conditions (tasks) and two parametric modulations per condition. The design matrix therefore has 6 regressors of interest. Motion regressors are also included. 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
--90e6ba1efe9a7601f6049d5a45df--
========================================================================Date: Mon, 28 Feb 2011 11:42:00 -0500
Reply-To: "MCLAREN, Donald" <[log in to unmask]>
Sender: "SPM (Statistical Parametric Mapping)" <[log in to unmask]>
From: "MCLAREN, Donald" <[log in to unmask]>
Subject: Re: PPI: adjust for effects of interest
Comments: To: Richard Binney <[log in to unmask]>
In-Reply-To: <[log in to unmask]>
MIME-Version: 1.0
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Richard,
I'd use an F-contrast that is one row per condition/modulator. In your case:
1 0 0 0 0 0 ...
0 1 0 0 0 0 ...
0 0 1 0 0 0 ...
0 0 0 1 0 0 ...
0 0 0 0 1 0 ...
0 0 0 0 0 1 ...
The goal of the adjustment is to extract only the BOLD signal related to
neural activity and eliminate the activity due to motion.
Best Regards, Donald McLaren
================D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
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 Mon, Feb 28, 2011 at 11:35 AM, Richard Binney <
[log in to unmask]> wrote:
> Hi Darren G/ Karl F/other PPI-ers,
>
> I can't find any posts on this and wondered if you can clear it up for me.
>
> 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?
>
> My impression was that the raw timecourse would be extracted always. The
> option to adjust suggests this is not always true. Do you use this option
> (only?) when you have time or dispersion derivatives and/or motion
> regressors?
>
> I have a parametric design with two conditions (tasks) and two parametric
> modulations per condition. The design matrix therefore has 6 regressors of
> interest. Motion regressors are also included. 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
>
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Richard,
I'd use an F-contrast that is one row per condition/modulator. In your case:1 0 0 0 0 0 ...
0 1 0 0 0 0 ...
0 0 1 0 0 0 ...
0 0 0 1 0 0 ...
0 0 0 0 1 0 ...
0 0 0 0 0 1 ...
The goal of the adjustment is to extract only the BOLD signal related to neural activity and eliminate the activity due to motion.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School
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 Mon, Feb 28, 2011 at 11:35 AM, Richard Binney
<[log in to unmask]> wrote:
Hi Darren G/ Karl F/other PPI-ers,
I can't find any posts on this and wondered if you can clear it up for me.
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?
My impression was that the raw timecourse would be extracted always. The option to adjust suggests this is not always true. Do you use this option (only?) when you have time or dispersion derivatives and/or motion regressors?
I have a parametric design with two conditions (tasks) and two parametric modulations per condition. The design matrix therefore has 6 regressors of interest. Motion regressors are also included. 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
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.Â
--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; boundaryMessage-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.
>>
>
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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 =/
/
/
/ Â Â 4.9700 Â Â 0.9960 Â Â /*/ Â 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--
========================================================================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)
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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
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Chair in Functional Neuroimaging
Neurodis Foundation
http://www.fondation-neurodis.org/
Postal Address:
CERMEP – Imagerie du Vivant
Hôpital 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:
>
> Hi SPMers,
>
> 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??
>
> Thanks in advance,
> --
> Sarika Cherodath
> Graduate Student
> National Brain Research Centre
> Manesar, Gurgaon -122050
> India
>
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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.
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]
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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]ryland.edu
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========================================================================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
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Ehsan
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========================================================================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
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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 (à
> 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
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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 (à
>>> 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
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--bcaec51a894a8f7f93049d601f97
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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]
>
>
>
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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
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
What is the best strategy for processing this data?
Regards
John Ochoa
Universidad de Antioquia
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