Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three.
How are the three regressors being handled? I can think of several scenarios:
1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6).
2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2.
3) The Calhoun et al (2004) approach is being used to combine the three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2.
Thanks for any help you can give me!
Joe
--------------------------------------------------------------------------------
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
On 07/09/2013 04:11 PM, Joseph Dien wrote:
Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three.
How are the three regressors being handled? I can think of several scenarios:
- the contrast weights are not actually in terms of conditions (the
documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6).
- the latency and dispersion regressors are being ignored (a common
practice). The contrast weights should therefore be specified as -a 1 -c 2.
This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug
- The Calhoun et al (2004) approach is being used to combine the
three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2.
Thanks for any help you can give me!
Joe
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable
sum(X(1:207,4).*X(1:207,5))
but not hugely non-zero so maybe just rounding errors?
On Jul 9, 2013, at 4:16 PM, Douglas N Greve greve@NMR.MGH.HARVARD.EDU wrote:
On 07/09/2013 04:11 PM, Joseph Dien wrote:
Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three.
How are the three regressors being handled? I can think of several scenarios:
- the contrast weights are not actually in terms of conditions (the
documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6).
- the latency and dispersion regressors are being ignored (a common
practice). The contrast weights should therefore be specified as -a 1 -c 2.
This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug
- The Calhoun et al (2004) approach is being used to combine the
three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2.
Thanks for any help you can give me!
Joe
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
--------------------------------------------------------------------------------
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
I tried correlations and the 2nd derivative is definitely not orthogonal.
corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1.0000 -0.0000 -0.5427 -0.0000 1.0000 -0.0298 -0.5427 -0.0298 1.0000
I looked at the regressors that SPM generates for the same data:
ans =
1.0000 0.0436 0.1740 0.0436 1.0000 -0.0226 0.1740 -0.0226 1.0000
The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power?
Thanks for the help!
Joe
On Jul 9, 2013, at 4:34 PM, Joseph Dien jdien07@mac.com wrote:
Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable
sum(X(1:207,4).*X(1:207,5))
but not hugely non-zero so maybe just rounding errors?
On Jul 9, 2013, at 4:16 PM, Douglas N Greve greve@NMR.MGH.HARVARD.EDU wrote:
On 07/09/2013 04:11 PM, Joseph Dien wrote:
Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three.
How are the three regressors being handled? I can think of several scenarios:
- the contrast weights are not actually in terms of conditions (the
documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6).
- the latency and dispersion regressors are being ignored (a common
practice). The contrast weights should therefore be specified as -a 1 -c 2.
This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug
- The Calhoun et al (2004) approach is being used to combine the
three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2.
Thanks for any help you can give me!
Joe
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
--------------------------------------------------------------------------------
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights?
Joe
On Jul 9, 2013, at 5:08 PM, Joseph Dien jdien07@mac.com wrote:
I tried correlations and the 2nd derivative is definitely not orthogonal.
corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1.0000 -0.0000 -0.5427-0.0000 1.0000 -0.0298 -0.5427 -0.0298 1.0000
I looked at the regressors that SPM generates for the same data:
ans =
1.0000 0.0436 0.1740 0.0436 1.0000 -0.0226 0.1740 -0.0226 1.0000The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power?
Thanks for the help!
Joe
On Jul 9, 2013, at 4:34 PM, Joseph Dien jdien07@mac.com wrote:
Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable
sum(X(1:207,4).*X(1:207,5))
but not hugely non-zero so maybe just rounding errors?
On Jul 9, 2013, at 4:16 PM, Douglas N Greve greve@NMR.MGH.HARVARD.EDU wrote:
On 07/09/2013 04:11 PM, Joseph Dien wrote:
Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three.
How are the three regressors being handled? I can think of several scenarios:
- the contrast weights are not actually in terms of conditions (the
documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6).
- the latency and dispersion regressors are being ignored (a common
practice). The contrast weights should therefore be specified as -a 1 -c 2.
This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug
- The Calhoun et al (2004) approach is being used to combine the
three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2.
Thanks for any help you can give me!
Joe
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
--------------------------------------------------------------------------------
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea
doug
On 07/09/2013 10:26 PM, Joseph Dien wrote:
It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights?
Joe
On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com> wrote:
I tried correlations and the 2nd derivative is definitely not orthogonal.
corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1.0000 -0.0000 -0.5427-0.0000 1.0000 -0.0298 -0.5427 -0.0298 1.0000
I looked at the regressors that SPM generates for the same data:
ans =
1.0000 0.0436 0.1740 0.0436 1.0000 -0.0226 0.1740 -0.0226 1.0000The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power?
Thanks for the help!
Joe
On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com> wrote:
Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable
sum(X(1:207,4).*X(1:207,5))
but not hugely non-zero so maybe just rounding errors?
On Jul 9, 2013, at 4:16 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
On 07/09/2013 04:11 PM, Joseph Dien wrote:
Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three.
How are the three regressors being handled? I can think of several scenarios:
- the contrast weights are not actually in terms of conditions (the
documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6).
- the latency and dispersion regressors are being ignored (a common
practice). The contrast weights should therefore be specified as -a 1 -c 2.
This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug
- The Calhoun et al (2004) approach is being used to combine the
three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2.
Thanks for any help you can give me!
Joe
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks!
Joe
On Jul 10, 2013, at 12:39 PM, Douglas N Greve greve@NMR.MGH.HARVARD.EDU wrote:
I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea
doug
On 07/09/2013 10:26 PM, Joseph Dien wrote:
It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights?
Joe
On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com> wrote:
I tried correlations and the 2nd derivative is definitely not orthogonal.
corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1.0000 -0.0000 -0.5427 -0.0000 1.0000 -0.0298 -0.5427 -0.0298 1.0000
I looked at the regressors that SPM generates for the same data:
ans =
1.0000 0.0436 0.1740 0.0436 1.0000 -0.0226 0.1740 -0.0226 1.0000
The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power?
Thanks for the help!
Joe
On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com> wrote:
Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable
sum(X(1:207,4).*X(1:207,5))
but not hugely non-zero so maybe just rounding errors?
On Jul 9, 2013, at 4:16 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
On 07/09/2013 04:11 PM, Joseph Dien wrote:
Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three.
How are the three regressors being handled? I can think of several scenarios:
- the contrast weights are not actually in terms of conditions (the
documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6).
- the latency and dispersion regressors are being ignored (a common
practice). The contrast weights should therefore be specified as -a 1 -c 2.
This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug
- The Calhoun et al (2004) approach is being used to combine the
three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2.
Thanks for any help you can give me!
Joe
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless.
As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative?
doug
On 07/10/2013 12:47 PM, Joseph Dien wrote:
I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks!
Joe
On Jul 10, 2013, at 12:39 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea
doug
On 07/09/2013 10:26 PM, Joseph Dien wrote:
It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights?
Joe
On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com> wrote:
I tried correlations and the 2nd derivative is definitely not orthogonal.
corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1.0000 -0.0000 -0.5427 -0.0000 1.0000 -0.0298 -0.5427 -0.0298 1.0000
I looked at the regressors that SPM generates for the same data:
ans =
1.0000 0.0436 0.1740 0.0436 1.0000 -0.0226 0.1740 -0.0226 1.0000
The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power?
Thanks for the help!
Joe
On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com> wrote:
Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable
sum(X(1:207,4).*X(1:207,5))
but not hugely non-zero so maybe just rounding errors?
On Jul 9, 2013, at 4:16 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
On 07/09/2013 04:11 PM, Joseph Dien wrote: > Hi, > I have a question about how mkcontrast-sess works. I ran an > analysis using the mkanalysis-sess option spmhrf 2 so there are > three > regressors for each predictor, the primary, the latency, and the > dispersion. When specifying the contrast weights for > mkcontrast-sess, > the documentation indicates that they are specified in terms of the > conditions as numbered in the paradigm file, not the individual > regressors. Furthermore there only appears to be one contrast value > output for each contrast, not three. > > How are the three regressors being handled? I can think of several > scenarios: > > 1) the contrast weights are not actually in terms of conditions (the > documentation is incorrect), they are actually in terms of the > regressors (so contrasting conditions 1 and 2 could be specified > as -a > 1 -a 2 -a 3 -c 4 -c 5 -c 6). > > 2) the latency and dispersion regressors are being ignored (a common > practice). The contrast weights should therefore be specified as > -a 1 > -c 2. This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug > > 3) The Calhoun et al (2004) approach is being used to combine the > three regressors into a "derivative boost" amplitude > measure. The contrast weights should therefore be specified as -a > 1 -c 2. > > Thanks for any help you can give me! > > Joe > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07@mac.com mailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > Phone: 202-297-8117 > http://joedien.com// > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Sorry, not following what you are suggesting?
I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf.
However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step.
On Jul 10, 2013, at 1:21 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless.
As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative?
doug
On 07/10/2013 12:47 PM, Joseph Dien wrote:
I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks!
Joe
On Jul 10, 2013, at 12:39 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea
doug
On 07/09/2013 10:26 PM, Joseph Dien wrote:
It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights?
Joe
On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com> wrote:
I tried correlations and the 2nd derivative is definitely not orthogonal.
> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1.0000 -0.0000 -0.5427 -0.0000 1.0000 -0.0298 -0.5427 -0.0298 1.0000
I looked at the regressors that SPM generates for the same data:
ans =
1.0000 0.0436 0.1740 0.0436 1.0000 -0.0226 0.1740 -0.0226 1.0000
The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power?
Thanks for the help!
Joe
On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com> wrote:
Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable
sum(X(1:207,4).*X(1:207,5))
but not hugely non-zero so maybe just rounding errors?
On Jul 9, 2013, at 4:16 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
> > On 07/09/2013 04:11 PM, Joseph Dien wrote: >> Hi, >> I have a question about how mkcontrast-sess works. I ran an >> analysis using the mkanalysis-sess option spmhrf 2 so there are >> three >> regressors for each predictor, the primary, the latency, and the >> dispersion. When specifying the contrast weights for >> mkcontrast-sess, >> the documentation indicates that they are specified in terms of the >> conditions as numbered in the paradigm file, not the individual >> regressors. Furthermore there only appears to be one contrast value >> output for each contrast, not three. >> >> How are the three regressors being handled? I can think of several >> scenarios: >> >> 1) the contrast weights are not actually in terms of conditions (the >> documentation is incorrect), they are actually in terms of the >> regressors (so contrasting conditions 1 and 2 could be specified >> as -a >> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >> >> 2) the latency and dispersion regressors are being ignored (a common >> practice). The contrast weights should therefore be specified as >> -a 1 >> -c 2. > This is what happens. If you want to use the derivatives, then you > need > to spec -setwdelay. When you run the command, it will prompt you > for 3 > values to use. If you spec 1 0 0, then it will be the same as the > default. If you want to test only the first derivative, then you > would > spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt > time, > not the first derivative wrt the dispersion parameter. You cannot get > the Calhoun 2004 value using a contrast (it is non-linear). > doug >> >> 3) The Calhoun et al (2004) approach is being used to combine the >> three regressors into a "derivative boost" amplitude >> measure. The contrast weights should therefore be specified as -a >> 1 -c 2. >> >> Thanks for any help you can give me! >> >> Joe >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07@mac.com mailto:jdien07@mac.com >> mailto:jdien07@mac.com >> mailto:jdien07@mac.com >> Phone: 202-297-8117 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. >
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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E-mail: jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
On 07/10/2013 01:29 PM, Joseph Dien wrote:
Sorry, not following what you are suggesting?
I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf.
Sorry, it had been a while since I read that paper. I did not know that they had a formulation that included the 2nd derivative.
However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step.
I don't know how much it will hurt the power. You'd have to look at the efficiency. doug
On Jul 10, 2013, at 1:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless.
As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative?
doug
On 07/10/2013 12:47 PM, Joseph Dien wrote:
I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks!
Joe
On Jul 10, 2013, at 12:39 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea
doug
On 07/09/2013 10:26 PM, Joseph Dien wrote:
It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights?
Joe
On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com> wrote:
I tried correlations and the 2nd derivative is definitely not orthogonal.
>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1.0000 -0.0000 -0.5427 -0.0000 1.0000 -0.0298 -0.5427 -0.0298 1.0000
I looked at the regressors that SPM generates for the same data:
ans =
1.0000 0.0436 0.1740 0.0436 1.0000 -0.0226 0.1740 -0.0226 1.0000
The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power?
Thanks for the help!
Joe
On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com> wrote:
> Thanks for the quick response! So if I wanted to use the Calhoun > 2004 approach, I should be able to use the Steffener 2010 correction > to address the violation of the assumption that the regressors were > standardized and generate a new beta.nii.gz file where the primary > beta values have been replaced with the Calhoun 2004 measure. Can I > assume the three regressors are more or less orthogonal? I got > non-zero numbers when I tried to test the assumption in the Xtmp.X > variable > > sum(X(1:207,4).*X(1:207,5)) > > but not hugely non-zero so maybe just rounding errors? > > > On Jul 9, 2013, at 4:16 PM, Douglas N Greve > <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU > mailto:greve@NMR.MGH.HARVARD.EDU > mailto:greve@NMR.MGH.HARVARD.EDU> wrote: > >> >> On 07/09/2013 04:11 PM, Joseph Dien wrote: >>> Hi, >>> I have a question about how mkcontrast-sess works. I ran an >>> analysis using the mkanalysis-sess option spmhrf 2 so there are >>> three >>> regressors for each predictor, the primary, the latency, and the >>> dispersion. When specifying the contrast weights for >>> mkcontrast-sess, >>> the documentation indicates that they are specified in terms >>> of the >>> conditions as numbered in the paradigm file, not the individual >>> regressors. Furthermore there only appears to be one contrast >>> value >>> output for each contrast, not three. >>> >>> How are the three regressors being handled? I can think of >>> several >>> scenarios: >>> >>> 1) the contrast weights are not actually in terms of >>> conditions (the >>> documentation is incorrect), they are actually in terms of the >>> regressors (so contrasting conditions 1 and 2 could be specified >>> as -a >>> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >>> >>> 2) the latency and dispersion regressors are being ignored (a >>> common >>> practice). The contrast weights should therefore be specified as >>> -a 1 >>> -c 2. >> This is what happens. If you want to use the derivatives, then you >> need >> to spec -setwdelay. When you run the command, it will prompt you >> for 3 >> values to use. If you spec 1 0 0, then it will be the same as the >> default. If you want to test only the first derivative, then you >> would >> spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt >> time, >> not the first derivative wrt the dispersion parameter. You >> cannot get >> the Calhoun 2004 value using a contrast (it is non-linear). >> doug >>> >>> 3) The Calhoun et al (2004) approach is being used to combine the >>> three regressors into a "derivative boost" amplitude >>> measure. The contrast weights should therefore be specified as -a >>> 1 -c 2. >>> >>> Thanks for any help you can give me! >>> >>> Joe >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07@mac.com mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> Phone: 202-297-8117 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07@mac.com mailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > Phone: 202-297-8117 > http://joedien.com// > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 07/10/2013 01:29 PM, Joseph Dien wrote:
Sorry, not following what you are suggesting?
I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf.
Sorry, it had been a while since I read that paper. I did not know that they had a formulation that included the 2nd derivative.
However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step.
I don't know how much it will hurt the power. You'd have to look at the efficiency. doug
On Jul 10, 2013, at 1:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless.
As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative?
doug
On 07/10/2013 12:47 PM, Joseph Dien wrote:
I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks!
Joe
On Jul 10, 2013, at 12:39 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea
doug
On 07/09/2013 10:26 PM, Joseph Dien wrote:
It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights?
Joe
On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com> wrote:
> I tried correlations and the 2nd derivative is definitely not > orthogonal. > >>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) > > ans = > > 1.0000 -0.0000 -0.5427 > -0.0000 1.0000 -0.0298 > -0.5427 -0.0298 1.0000 > > I looked at the regressors that SPM generates for the same data: > > ans = > > 1.0000 0.0436 0.1740 > 0.0436 1.0000 -0.0226 > 0.1740 -0.0226 1.0000 > > The first derivative is not as orthogonal but the second derivative > was much more orthogonal. > Does this have to do with what you noted below about how the second > derivative is being calculated? > So does this mean I should avoid the spmhrf 2 option entirely to > avoid loss of statistical power? > > Thanks for the help! > > Joe > > > On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com> wrote: > >> Thanks for the quick response! So if I wanted to use the Calhoun >> 2004 approach, I should be able to use the Steffener 2010 correction >> to address the violation of the assumption that the regressors were >> standardized and generate a new beta.nii.gz file where the primary >> beta values have been replaced with the Calhoun 2004 measure. Can I >> assume the three regressors are more or less orthogonal? I got >> non-zero numbers when I tried to test the assumption in the Xtmp.X >> variable >> >> sum(X(1:207,4).*X(1:207,5)) >> >> but not hugely non-zero so maybe just rounding errors? >> >> >> On Jul 9, 2013, at 4:16 PM, Douglas N Greve >> <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU >> mailto:greve@NMR.MGH.HARVARD.EDU >> mailto:greve@NMR.MGH.HARVARD.EDU> wrote: >> >>> >>> On 07/09/2013 04:11 PM, Joseph Dien wrote: >>>> Hi, >>>> I have a question about how mkcontrast-sess works. I ran an >>>> analysis using the mkanalysis-sess option spmhrf 2 so there are >>>> three >>>> regressors for each predictor, the primary, the latency, and the >>>> dispersion. When specifying the contrast weights for >>>> mkcontrast-sess, >>>> the documentation indicates that they are specified in terms >>>> of the >>>> conditions as numbered in the paradigm file, not the individual >>>> regressors. Furthermore there only appears to be one contrast >>>> value >>>> output for each contrast, not three. >>>> >>>> How are the three regressors being handled? I can think of >>>> several >>>> scenarios: >>>> >>>> 1) the contrast weights are not actually in terms of >>>> conditions (the >>>> documentation is incorrect), they are actually in terms of the >>>> regressors (so contrasting conditions 1 and 2 could be specified >>>> as -a >>>> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >>>> >>>> 2) the latency and dispersion regressors are being ignored (a >>>> common >>>> practice). The contrast weights should therefore be specified as >>>> -a 1 >>>> -c 2. >>> This is what happens. If you want to use the derivatives, then you >>> need >>> to spec -setwdelay. When you run the command, it will prompt you >>> for 3 >>> values to use. If you spec 1 0 0, then it will be the same as the >>> default. If you want to test only the first derivative, then you >>> would >>> spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt >>> time, >>> not the first derivative wrt the dispersion parameter. You >>> cannot get >>> the Calhoun 2004 value using a contrast (it is non-linear). >>> doug >>>> >>>> 3) The Calhoun et al (2004) approach is being used to combine the >>>> three regressors into a "derivative boost" amplitude >>>> measure. The contrast weights should therefore be specified as -a >>>> 1 -c 2. >>>> >>>> Thanks for any help you can give me! >>>> >>>> Joe >>>> >>>> -------------------------------------------------------------------------------- >>>> >>>> Joseph Dien, >>>> Senior Research Scientist >>>> University of Maryland >>>> >>>> E-mail: jdien07@mac.com mailto:jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> Phone: 202-297-8117 >>>> http://joedien.com// >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom it is >>> addressed. If you believe this e-mail was sent to you in error and >>> the e-mail >>> contains patient information, please contact the Partners >>> Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> but does not contain patient information, please contact the sender >>> and properly >>> dispose of the e-mail. >>> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07@mac.com mailto:jdien07@mac.com >> mailto:jdien07@mac.com >> mailto:jdien07@mac.com >> Phone: 202-297-8117 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07@mac.com mailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > Phone: 202-297-8117 > http://joedien.com// > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail.
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume
On 07/10/2013 01:40 PM, Joseph Dien wrote:
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 07/10/2013 01:29 PM, Joseph Dien wrote:
Sorry, not following what you are suggesting?
I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf.
Sorry, it had been a while since I read that paper. I did not know that they had a formulation that included the 2nd derivative.
However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step.
I don't know how much it will hurt the power. You'd have to look at the efficiency. doug
On Jul 10, 2013, at 1:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless.
As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative?
doug
On 07/10/2013 12:47 PM, Joseph Dien wrote:
I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks!
Joe
On Jul 10, 2013, at 12:39 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea
doug
On 07/09/2013 10:26 PM, Joseph Dien wrote: > It looks as though selxavg3-sess generates the contrast analyses at > the same time as the beta weights. Would it be possible to > run selxavg3-sess once to obtain the beta weights, modify the > beta.nii.gz file, and then rerun selxavg3-sess to obtain the > contrast > statistics using the modified beta weights? > > Joe > > On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com> wrote: > >> I tried correlations and the 2nd derivative is definitely not >> orthogonal. >> >>>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) >> >> ans = >> >> 1.0000 -0.0000 -0.5427 >> -0.0000 1.0000 -0.0298 >> -0.5427 -0.0298 1.0000 >> >> I looked at the regressors that SPM generates for the same data: >> >> ans = >> >> 1.0000 0.0436 0.1740 >> 0.0436 1.0000 -0.0226 >> 0.1740 -0.0226 1.0000 >> >> The first derivative is not as orthogonal but the second derivative >> was much more orthogonal. >> Does this have to do with what you noted below about how the second >> derivative is being calculated? >> So does this mean I should avoid the spmhrf 2 option entirely to >> avoid loss of statistical power? >> >> Thanks for the help! >> >> Joe >> >> >> On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com >> mailto:jdien07@mac.com >> mailto:jdien07@mac.com >> mailto:jdien07@mac.com >> mailto:jdien07@mac.com> wrote: >> >>> Thanks for the quick response! So if I wanted to use the Calhoun >>> 2004 approach, I should be able to use the Steffener 2010 >>> correction >>> to address the violation of the assumption that the regressors >>> were >>> standardized and generate a new beta.nii.gz file where the primary >>> beta values have been replaced with the Calhoun 2004 measure. >>> Can I >>> assume the three regressors are more or less orthogonal? I got >>> non-zero numbers when I tried to test the assumption in the Xtmp.X >>> variable >>> >>> sum(X(1:207,4).*X(1:207,5)) >>> >>> but not hugely non-zero so maybe just rounding errors? >>> >>> >>> On Jul 9, 2013, at 4:16 PM, Douglas N Greve >>> <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU >>> mailto:greve@NMR.MGH.HARVARD.EDU >>> mailto:greve@NMR.MGH.HARVARD.EDU >>> mailto:greve@NMR.MGH.HARVARD.EDU> wrote: >>> >>>> >>>> On 07/09/2013 04:11 PM, Joseph Dien wrote: >>>>> Hi, >>>>> I have a question about how mkcontrast-sess works. I ran an >>>>> analysis using the mkanalysis-sess option spmhrf 2 so there are >>>>> three >>>>> regressors for each predictor, the primary, the latency, and the >>>>> dispersion. When specifying the contrast weights for >>>>> mkcontrast-sess, >>>>> the documentation indicates that they are specified in terms >>>>> of the >>>>> conditions as numbered in the paradigm file, not the individual >>>>> regressors. Furthermore there only appears to be one contrast >>>>> value >>>>> output for each contrast, not three. >>>>> >>>>> How are the three regressors being handled? I can think of >>>>> several >>>>> scenarios: >>>>> >>>>> 1) the contrast weights are not actually in terms of >>>>> conditions (the >>>>> documentation is incorrect), they are actually in terms of the >>>>> regressors (so contrasting conditions 1 and 2 could be specified >>>>> as -a >>>>> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >>>>> >>>>> 2) the latency and dispersion regressors are being ignored (a >>>>> common >>>>> practice). The contrast weights should therefore be >>>>> specified as >>>>> -a 1 >>>>> -c 2. >>>> This is what happens. If you want to use the derivatives, >>>> then you >>>> need >>>> to spec -setwdelay. When you run the command, it will prompt you >>>> for 3 >>>> values to use. If you spec 1 0 0, then it will be the same as the >>>> default. If you want to test only the first derivative, then you >>>> would >>>> spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt >>>> time, >>>> not the first derivative wrt the dispersion parameter. You >>>> cannot get >>>> the Calhoun 2004 value using a contrast (it is non-linear). >>>> doug >>>>> >>>>> 3) The Calhoun et al (2004) approach is being used to >>>>> combine the >>>>> three regressors into a "derivative boost" amplitude >>>>> measure. The contrast weights should therefore be specified >>>>> as -a >>>>> 1 -c 2. >>>>> >>>>> Thanks for any help you can give me! >>>>> >>>>> Joe >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> >>>>> Joseph Dien, >>>>> Senior Research Scientist >>>>> University of Maryland >>>>> >>>>> E-mail: jdien07@mac.com mailto:jdien07@mac.com >>>>> mailto:jdien07@mac.com >>>>> mailto:jdien07@mac.com >>>>> mailto:jdien07@mac.com >>>>> mailto:jdien07@mac.com >>>>> Phone: 202-297-8117 >>>>> http://joedien.com// >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it is >>>> addressed. If you believe this e-mail was sent to you in >>>> error and >>>> the e-mail >>>> contains patient information, please contact the Partners >>>> Compliance HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was >>>> sent to >>>> you in error >>>> but does not contain patient information, please contact the >>>> sender >>>> and properly >>>> dispose of the e-mail. >>>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07@mac.com mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> Phone: 202-297-8117 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom it is >>> addressed. If you believe this e-mail was sent to you in error and >>> the e-mail >>> contains patient information, please contact the Partners >>> Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> but does not contain patient information, please contact the >>> sender >>> and properly >>> dispose of the e-mail. >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07@mac.com mailto:jdien07@mac.com >> mailto:jdien07@mac.com >> mailto:jdien07@mac.com >> mailto:jdien07@mac.com >> Phone: 202-297-8117 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners >> Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdien07@mac.com mailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > Phone: 202-297-8117 > http://joedien.com// > > > > > > > > > > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
After a long break, back to this…
My goal is still to get the betas for the first and maybe second spm hrf so I can calculate a Calhoun derivative boost measure.
As a first step I ran:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
to use the SPM HRF with one derivative.
Then:
selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh
I got the following error:
ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch This condition has 2 regressors, but evrm has 1 Struct contents reference from a non-struct array object.
Error in flac_conmat (line 37) if(nthcon > length(flac.con))
Error in flac_customize (line 369) flacnew = flac_conmat(flacnew,nthcon);
Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0);
ERROR: fast_selxavg3() failed\n
This ran fine with spmhrf 0
based on your prior response below that:
"This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear).”
I tried:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay
but I just got the error:
ERROR: Flag -setwdelay unrecognized.
I also tried using the flag when setting up the contrasts but that didn’t work either.
so not quite sure what I’m doing wrong. I had understood from your response below that the contrast weights didn’t need to be changed from the spmhrf 0 case but perhaps I misunderstood?
any help would be welcome!
Joe
On Jul 10, 2013, at 13:58, Douglas N Greve greve@NMR.MGH.HARVARD.EDU wrote:
I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume
On 07/10/2013 01:40 PM, Joseph Dien wrote:
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
On 07/10/2013 01:29 PM, Joseph Dien wrote:
Sorry, not following what you are suggesting?
I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf.
Sorry, it had been a while since I read that paper. I did not know that they had a formulation that included the 2nd derivative.
However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step.
I don't know how much it will hurt the power. You'd have to look at the efficiency. doug
On Jul 10, 2013, at 1:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless.
As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative?
doug
On 07/10/2013 12:47 PM, Joseph Dien wrote:
I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks!
Joe
On Jul 10, 2013, at 12:39 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU>> wrote:
> > I think that would work. You would need to change the time stamps > on the > .mat file in the analysis folder. When you re-run selxavg3-sess, it > will > see that the .mat files are newer than the beta and regenerate the > contrasts. But what are you planning to do the the beta file? It > sounds > like a potentially bad idea > > doug > > > On 07/09/2013 10:26 PM, Joseph Dien wrote: >> It looks as though selxavg3-sess generates the contrast analyses at >> the same time as the beta weights. Would it be possible to >> run selxavg3-sess once to obtain the beta weights, modify the >> beta.nii.gz file, and then rerun selxavg3-sess to obtain the >> contrast >> statistics using the modified beta weights? >> >> Joe >> >> On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com >> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> <mailto:jdien07@mac.com mailto:jdien07@mac.com>> wrote: >> >>> I tried correlations and the 2nd derivative is definitely not >>> orthogonal. >>> >>>>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) >>> >>> ans = >>> >>> 1.0000 -0.0000 -0.5427 >>> -0.0000 1.0000 -0.0298 >>> -0.5427 -0.0298 1.0000 >>> >>> I looked at the regressors that SPM generates for the same data: >>> >>> ans = >>> >>> 1.0000 0.0436 0.1740 >>> 0.0436 1.0000 -0.0226 >>> 0.1740 -0.0226 1.0000 >>> >>> The first derivative is not as orthogonal but the second derivative >>> was much more orthogonal. >>> Does this have to do with what you noted below about how the second >>> derivative is being calculated? >>> So does this mean I should avoid the spmhrf 2 option entirely to >>> avoid loss of statistical power? >>> >>> Thanks for the help! >>> >>> Joe >>> >>> >>> On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com>> wrote: >>> >>>> Thanks for the quick response! So if I wanted to use the Calhoun >>>> 2004 approach, I should be able to use the Steffener 2010 >>>> correction >>>> to address the violation of the assumption that the regressors >>>> were >>>> standardized and generate a new beta.nii.gz file where the primary >>>> beta values have been replaced with the Calhoun 2004 measure. >>>> Can I >>>> assume the three regressors are more or less orthogonal? I got >>>> non-zero numbers when I tried to test the assumption in the Xtmp.X >>>> variable >>>> >>>> sum(X(1:207,4).*X(1:207,5)) >>>> >>>> but not hugely non-zero so maybe just rounding errors? >>>> >>>> >>>> On Jul 9, 2013, at 4:16 PM, Douglas N Greve >>>> <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU>> wrote: >>>> >>>>> >>>>> On 07/09/2013 04:11 PM, Joseph Dien wrote: >>>>>> Hi, >>>>>> I have a question about how mkcontrast-sess works. I ran an >>>>>> analysis using the mkanalysis-sess option spmhrf 2 so there are >>>>>> three >>>>>> regressors for each predictor, the primary, the latency, and the >>>>>> dispersion. When specifying the contrast weights for >>>>>> mkcontrast-sess, >>>>>> the documentation indicates that they are specified in terms >>>>>> of the >>>>>> conditions as numbered in the paradigm file, not the individual >>>>>> regressors. Furthermore there only appears to be one contrast >>>>>> value >>>>>> output for each contrast, not three. >>>>>> >>>>>> How are the three regressors being handled? I can think of >>>>>> several >>>>>> scenarios: >>>>>> >>>>>> 1) the contrast weights are not actually in terms of >>>>>> conditions (the >>>>>> documentation is incorrect), they are actually in terms of the >>>>>> regressors (so contrasting conditions 1 and 2 could be specified >>>>>> as -a >>>>>> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >>>>>> >>>>>> 2) the latency and dispersion regressors are being ignored (a >>>>>> common >>>>>> practice). The contrast weights should therefore be >>>>>> specified as >>>>>> -a 1 >>>>>> -c 2. >>>>> This is what happens. If you want to use the derivatives, >>>>> then you >>>>> need >>>>> to spec -setwdelay. When you run the command, it will prompt you >>>>> for 3 >>>>> values to use. If you spec 1 0 0, then it will be the same as the >>>>> default. If you want to test only the first derivative, then you >>>>> would >>>>> spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt >>>>> time, >>>>> not the first derivative wrt the dispersion parameter. You >>>>> cannot get >>>>> the Calhoun 2004 value using a contrast (it is non-linear). >>>>> doug >>>>>> >>>>>> 3) The Calhoun et al (2004) approach is being used to >>>>>> combine the >>>>>> three regressors into a "derivative boost" amplitude >>>>>> measure. The contrast weights should therefore be specified >>>>>> as -a >>>>>> 1 -c 2. >>>>>> >>>>>> Thanks for any help you can give me! >>>>>> >>>>>> Joe >>>>>> >>>>>> -------------------------------------------------------------------------------- >>>>>> >>>>>> Joseph Dien, >>>>>> Senior Research Scientist >>>>>> University of Maryland >>>>>> >>>>>> E-mail: jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> Phone: 202-297-8117 >>>>>> http://joedien.com// http://joedien.com// >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to >>>>> whom it is >>>>> addressed. If you believe this e-mail was sent to you in >>>>> error and >>>>> the e-mail >>>>> contains patient information, please contact the Partners >>>>> Compliance HelpLine at >>>>> http://www.partners.org/complianceline . 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If the e-mail was sent to >>>> you in error >>>> but does not contain patient information, please contact the >>>> sender >>>> and properly >>>> dispose of the e-mail. >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> Phone: 202-297-8117 >>> http://joedien.com// http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom it is >>> addressed. If you believe this e-mail was sent to you in error and >>> the e-mail >>> contains patient information, please contact the Partners >>> Compliance >>> HelpLine at >>> http://www.partners.org/complianceline http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> but does not contain patient information, please contact the sender >>> and properly >>> dispose of the e-mail. >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> Phone: 202-297-8117 >> http://joedien.com// http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com> <mailto:jdien07@mac.com mailto:jdien07@mac.com> <mailto:jdien07@mac.com mailto:jdien07@mac.com> Phone: 202-297-8117 http://joedien.com// http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com> <mailto:jdien07@mac.com mailto:jdien07@mac.com> Phone: 202-297-8117 http://joedien.com// http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail: jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com> Phone: 202-297-8117 http://joedien.com// http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
On 03/13/2016 10:29 PM, Joseph Dien wrote:
After a long break, back to this…
My goal is still to get the betas for the first and maybe second spm hrf so I can calculate a Calhoun derivative boost measure.
As a first step I ran:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
to use the SPM HRF with one derivative.
Then:
selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh
I got the following error:
ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch This condition has 2 regressors, but evrm has 1 Struct contents reference from a non-struct array object.
Error in flac_conmat (line 37) if(nthcon > length(flac.con))
Error in flac_customize (line 369) flacnew = flac_conmat(flacnew,nthcon);
Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0);
ERROR: fast_selxavg3() failed\n
This ran fine with spmhrf 0
based on your prior response below that:
"This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear).”
I tried:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay
but I just got the error:
ERROR: Flag -setwdelay unrecognized.
I also tried using the flag when setting up the contrasts but that didn’t work either.
so not quite sure what I’m doing wrong. I had understood from your response below that the contrast weights didn’t need to be changed from the spmhrf 0 case but perhaps I misunderstood?
any help would be welcome!
Joe
On Jul 10, 2013, at 13:58, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu> wrote:
I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume
On 07/10/2013 01:40 PM, Joseph Dien wrote:
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
On 07/10/2013 01:29 PM, Joseph Dien wrote:
Sorry, not following what you are suggesting?
I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf.
Sorry, it had been a while since I read that paper. I did not know that they had a formulation that included the 2nd derivative.
However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step.
I don't know how much it will hurt the power. You'd have to look at the efficiency. doug
On Jul 10, 2013, at 1:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless.
As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative?
doug
On 07/10/2013 12:47 PM, Joseph Dien wrote: > I'm thinking of generating a modified beta.nii.gz file where the > primary betas have been replaced with the Calhoun et al (2004) > derivative boost measure. What do you think? Also, please note my > question below about the second derivative as it is causing me > concern > about my analysis. Thanks! > > Joe > > > On Jul 10, 2013, at 12:39 PM, Douglas N Greve > <greve@NMR.MGH.HARVARD.EDU > mailto:greve@nmr.mgh.harvard.edumailto:greve@NMR.MGH.HARVARD.EDU > mailto:greve@NMR.MGH.HARVARD.EDU > mailto:greve@NMR.MGH.HARVARD.EDU> wrote: > >> >> I think that would work. You would need to change the time stamps >> on the >> .mat file in the analysis folder. When you re-run selxavg3-sess, it >> will >> see that the .mat files are newer than the beta and regenerate the >> contrasts. But what are you planning to do the the beta file? It >> sounds >> like a potentially bad idea >> >> doug >> >> >> On 07/09/2013 10:26 PM, Joseph Dien wrote: >>> It looks as though selxavg3-sess generates the contrast >>> analyses at >>> the same time as the beta weights. Would it be possible to >>> run selxavg3-sess once to obtain the beta weights, modify the >>> beta.nii.gz file, and then rerun selxavg3-sess to obtain the >>> contrast >>> statistics using the modified beta weights? >>> >>> Joe >>> >>> On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com> wrote: >>> >>>> I tried correlations and the 2nd derivative is definitely not >>>> orthogonal. >>>> >>>>>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) >>>> >>>> ans = >>>> >>>> 1.0000 -0.0000 -0.5427 >>>> -0.0000 1.0000 -0.0298 >>>> -0.5427 -0.0298 1.0000 >>>> >>>> I looked at the regressors that SPM generates for the same data: >>>> >>>> ans = >>>> >>>> 1.0000 0.0436 0.1740 >>>> 0.0436 1.0000 -0.0226 >>>> 0.1740 -0.0226 1.0000 >>>> >>>> The first derivative is not as orthogonal but the second >>>> derivative >>>> was much more orthogonal. >>>> Does this have to do with what you noted below about how the >>>> second >>>> derivative is being calculated? >>>> So does this mean I should avoid the spmhrf 2 option entirely to >>>> avoid loss of statistical power? >>>> >>>> Thanks for the help! >>>> >>>> Joe >>>> >>>> >>>> On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> mailto:jdien07@mac.com> wrote: >>>> >>>>> Thanks for the quick response! So if I wanted to use the >>>>> Calhoun >>>>> 2004 approach, I should be able to use the Steffener 2010 >>>>> correction >>>>> to address the violation of the assumption that the regressors >>>>> were >>>>> standardized and generate a new beta.nii.gz file where the >>>>> primary >>>>> beta values have been replaced with the Calhoun 2004 measure. >>>>> Can I >>>>> assume the three regressors are more or less orthogonal? I got >>>>> non-zero numbers when I tried to test the assumption in the >>>>> Xtmp.X >>>>> variable >>>>> >>>>> sum(X(1:207,4).*X(1:207,5)) >>>>> >>>>> but not hugely non-zero so maybe just rounding errors? >>>>> >>>>> >>>>> On Jul 9, 2013, at 4:16 PM, Douglas N Greve >>>>> <greve@NMR.MGH.HARVARD.EDU >>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@NMR.MGH.HARVARD.EDU >>>>> mailto:greve@NMR.MGH.HARVARD.EDU >>>>> mailto:greve@NMR.MGH.HARVARD.EDU >>>>> mailto:greve@NMR.MGH.HARVARD.EDU> wrote: >>>>> >>>>>> >>>>>> On 07/09/2013 04:11 PM, Joseph Dien wrote: >>>>>>> Hi, >>>>>>> I have a question about how mkcontrast-sess works. I ran an >>>>>>> analysis using the mkanalysis-sess option spmhrf 2 so >>>>>>> there are >>>>>>> three >>>>>>> regressors for each predictor, the primary, the latency, >>>>>>> and the >>>>>>> dispersion. When specifying the contrast weights for >>>>>>> mkcontrast-sess, >>>>>>> the documentation indicates that they are specified in terms >>>>>>> of the >>>>>>> conditions as numbered in the paradigm file, not the >>>>>>> individual >>>>>>> regressors. Furthermore there only appears to be one contrast >>>>>>> value >>>>>>> output for each contrast, not three. >>>>>>> >>>>>>> How are the three regressors being handled? I can think of >>>>>>> several >>>>>>> scenarios: >>>>>>> >>>>>>> 1) the contrast weights are not actually in terms of >>>>>>> conditions (the >>>>>>> documentation is incorrect), they are actually in terms of the >>>>>>> regressors (so contrasting conditions 1 and 2 could be >>>>>>> specified >>>>>>> as -a >>>>>>> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >>>>>>> >>>>>>> 2) the latency and dispersion regressors are being ignored (a >>>>>>> common >>>>>>> practice). The contrast weights should therefore be >>>>>>> specified as >>>>>>> -a 1 >>>>>>> -c 2. >>>>>> This is what happens. If you want to use the derivatives, >>>>>> then you >>>>>> need >>>>>> to spec -setwdelay. When you run the command, it will >>>>>> prompt you >>>>>> for 3 >>>>>> values to use. If you spec 1 0 0, then it will be the same >>>>>> as the >>>>>> default. If you want to test only the first derivative, >>>>>> then you >>>>>> would >>>>>> spec 0 1 0. Note that the 3rd regressor is the 2nd >>>>>> derivative wrt >>>>>> time, >>>>>> not the first derivative wrt the dispersion parameter. You >>>>>> cannot get >>>>>> the Calhoun 2004 value using a contrast (it is non-linear). >>>>>> doug >>>>>>> >>>>>>> 3) The Calhoun et al (2004) approach is being used to >>>>>>> combine the >>>>>>> three regressors into a "derivative boost" amplitude >>>>>>> measure. The contrast weights should therefore be specified >>>>>>> as -a >>>>>>> 1 -c 2. >>>>>>> >>>>>>> Thanks for any help you can give me! >>>>>>> >>>>>>> Joe >>>>>>> >>>>>>> -------------------------------------------------------------------------------- >>>>>>> >>>>>>> Joseph Dien, >>>>>>> Senior Research Scientist >>>>>>> University of Maryland >>>>>>> >>>>>>> E-mail:jdien07@mac.com >>>>>>> mailto:jdien07@mac.commailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> Phone: 202-297-8117 >>>>>>> http://joedien.com// >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: >>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the >>>>>> person to >>>>>> whom it is >>>>>> addressed. If you believe this e-mail was sent to you in >>>>>> error and >>>>>> the e-mail >>>>>> contains patient information, please contact the Partners >>>>>> Compliance HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>> sent to >>>>>> you in error >>>>>> but does not contain patient information, please contact the >>>>>> sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> >>>>> Joseph Dien, >>>>> Senior Research Scientist >>>>> University of Maryland >>>>> >>>>> E-mail:jdien07@mac.com >>>>> mailto:jdien07@mac.commailto:jdien07@mac.com >>>>> mailto:jdien07@mac.com >>>>> mailto:jdien07@mac.com >>>>> mailto:jdien07@mac.com >>>>> Phone: 202-297-8117 >>>>> http://joedien.com// >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> The information in this e-mail is intended only for the >>>>> person to >>>>> whom it is >>>>> addressed. If you believe this e-mail was sent to you in >>>>> error and >>>>> the e-mail >>>>> contains patient information, please contact the Partners >>>>> Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline. If the e-mail was >>>>> sent to >>>>> you in error >>>>> but does not contain patient information, please contact the >>>>> sender >>>>> and properly >>>>> dispose of the e-mail. >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> >>>> Joseph Dien, >>>> Senior Research Scientist >>>> University of Maryland >>>> >>>> E-mail:jdien07@mac.com >>>> mailto:jdien07@mac.commailto:jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> mailto:jdien07@mac.com >>>> Phone: 202-297-8117 >>>> http://joedien.com// >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it is >>>> addressed. If you believe this e-mail was sent to you in >>>> error and >>>> the e-mail >>>> contains patient information, please contact the Partners >>>> Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline. If the e-mail was sent to >>>> you in error >>>> but does not contain patient information, please contact the >>>> sender >>>> and properly >>>> dispose of the e-mail. >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail:jdien07@mac.com >>> mailto:jdien07@mac.commailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> Phone: 202-297-8117 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail:jdien07@mac.com > mailto:jdien07@mac.commailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > Phone: 202-297-8117 > http://joedien.com// > > > > > > > > > > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
oh duh! Sorry, wasn’t thinking clearly. Okay, I see how to generate the betas now. I don’t even need to mess with the mkcontrast-sess command. I just run selxavg3-sess with the -no-con-ok flag. With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex. With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex. With 12 conditions, 12 more betas is exactly right. So how do I know which of the betas is which? I looked through the files and couldn’t find any labels. I’m guessing the first twelve are the condition betas for "spmhrf 0". If so, for "spmhrf 1", is it arranged as:
1) c1 c2 c3…d1 d2 d3...
or
2) c1 d1 c2 d2...
(where d is the first derivative term)
also, when I asked you earlier about implementing this procedure, I had suggested reading the betas, computing the Calhoun, then generating new beta.nii.gz files with the new betas replacing the original spmhrf0 betas and then continuing with the regular analysis stream but you said it would result in invalid p-values. Instead, you suggested:
"I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume”
can you expand on how one might “compute the contrasts” and “write out the new volume”?
Thanks again for this help!
Joe
On Mar 15, 2016, at 12:43, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
On 03/13/2016 10:29 PM, Joseph Dien wrote:
After a long break, back to this…
My goal is still to get the betas for the first and maybe second spm hrf so I can calculate a Calhoun derivative boost measure.
As a first step I ran:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
to use the SPM HRF with one derivative.
Then:
selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh
I got the following error:
ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch This condition has 2 regressors, but evrm has 1 Struct contents reference from a non-struct array object.
Error in flac_conmat (line 37) if(nthcon > length(flac.con))
Error in flac_customize (line 369) flacnew = flac_conmat(flacnew,nthcon);
Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0);
ERROR: fast_selxavg3() failed\n
This ran fine with spmhrf 0
based on your prior response below that:
"This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear).”
I tried:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay
but I just got the error:
ERROR: Flag -setwdelay unrecognized.
I also tried using the flag when setting up the contrasts but that didn’t work either.
so not quite sure what I’m doing wrong. I had understood from your response below that the contrast weights didn’t need to be changed from the spmhrf 0 case but perhaps I misunderstood?
any help would be welcome!
Joe
On Jul 10, 2013, at 13:58, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume
On 07/10/2013 01:40 PM, Joseph Dien wrote:
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
On 07/10/2013 01:29 PM, Joseph Dien wrote:
Sorry, not following what you are suggesting?
I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf.
Sorry, it had been a while since I read that paper. I did not know that they had a formulation that included the 2nd derivative.
However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step.
I don't know how much it will hurt the power. You'd have to look at the efficiency. doug
On Jul 10, 2013, at 1:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
> > Why not just create a new volume and then compute contrasts from > the new > volume? What you are suggesting will work I think, but it leaves me a > little nervous. The p-values will be meaningless. > > > As for the 2nd derivative, I think it must be a numerical issue > (it is > not computed analytically). Why do you need the 2nd derivative? > > doug > > > > On 07/10/2013 12:47 PM, Joseph Dien wrote: >> I'm thinking of generating a modified beta.nii.gz file where the >> primary betas have been replaced with the Calhoun et al (2004) >> derivative boost measure. What do you think? Also, please note my >> question below about the second derivative as it is causing me >> concern >> about my analysis. Thanks! >> >> Joe >> >> >> On Jul 10, 2013, at 12:39 PM, Douglas N Greve >> <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU>> wrote: >> >>> >>> I think that would work. You would need to change the time stamps >>> on the >>> .mat file in the analysis folder. When you re-run selxavg3-sess, it >>> will >>> see that the .mat files are newer than the beta and regenerate the >>> contrasts. But what are you planning to do the the beta file? It >>> sounds >>> like a potentially bad idea >>> >>> doug >>> >>> >>> On 07/09/2013 10:26 PM, Joseph Dien wrote: >>>> It looks as though selxavg3-sess generates the contrast >>>> analyses at >>>> the same time as the beta weights. Would it be possible to >>>> run selxavg3-sess once to obtain the beta weights, modify the >>>> beta.nii.gz file, and then rerun selxavg3-sess to obtain the >>>> contrast >>>> statistics using the modified beta weights? >>>> >>>> Joe >>>> >>>> On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com>> wrote: >>>> >>>>> I tried correlations and the 2nd derivative is definitely not >>>>> orthogonal. >>>>> >>>>>>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) >>>>> >>>>> ans = >>>>> >>>>> 1.0000 -0.0000 -0.5427 >>>>> -0.0000 1.0000 -0.0298 >>>>> -0.5427 -0.0298 1.0000 >>>>> >>>>> I looked at the regressors that SPM generates for the same data: >>>>> >>>>> ans = >>>>> >>>>> 1.0000 0.0436 0.1740 >>>>> 0.0436 1.0000 -0.0226 >>>>> 0.1740 -0.0226 1.0000 >>>>> >>>>> The first derivative is not as orthogonal but the second >>>>> derivative >>>>> was much more orthogonal. >>>>> Does this have to do with what you noted below about how the >>>>> second >>>>> derivative is being calculated? >>>>> So does this mean I should avoid the spmhrf 2 option entirely to >>>>> avoid loss of statistical power? >>>>> >>>>> Thanks for the help! >>>>> >>>>> Joe >>>>> >>>>> >>>>> On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com>> wrote: >>>>> >>>>>> Thanks for the quick response! So if I wanted to use the >>>>>> Calhoun >>>>>> 2004 approach, I should be able to use the Steffener 2010 >>>>>> correction >>>>>> to address the violation of the assumption that the regressors >>>>>> were >>>>>> standardized and generate a new beta.nii.gz file where the >>>>>> primary >>>>>> beta values have been replaced with the Calhoun 2004 measure. >>>>>> Can I >>>>>> assume the three regressors are more or less orthogonal? I got >>>>>> non-zero numbers when I tried to test the assumption in the >>>>>> Xtmp.X >>>>>> variable >>>>>> >>>>>> sum(X(1:207,4).*X(1:207,5)) >>>>>> >>>>>> but not hugely non-zero so maybe just rounding errors? >>>>>> >>>>>> >>>>>> On Jul 9, 2013, at 4:16 PM, Douglas N Greve >>>>>> <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu >>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU>> wrote: >>>>>> >>>>>>> >>>>>>> On 07/09/2013 04:11 PM, Joseph Dien wrote: >>>>>>>> Hi, >>>>>>>> I have a question about how mkcontrast-sess works. I ran an >>>>>>>> analysis using the mkanalysis-sess option spmhrf 2 so >>>>>>>> there are >>>>>>>> three >>>>>>>> regressors for each predictor, the primary, the latency, >>>>>>>> and the >>>>>>>> dispersion. When specifying the contrast weights for >>>>>>>> mkcontrast-sess, >>>>>>>> the documentation indicates that they are specified in terms >>>>>>>> of the >>>>>>>> conditions as numbered in the paradigm file, not the >>>>>>>> individual >>>>>>>> regressors. Furthermore there only appears to be one contrast >>>>>>>> value >>>>>>>> output for each contrast, not three. >>>>>>>> >>>>>>>> How are the three regressors being handled? I can think of >>>>>>>> several >>>>>>>> scenarios: >>>>>>>> >>>>>>>> 1) the contrast weights are not actually in terms of >>>>>>>> conditions (the >>>>>>>> documentation is incorrect), they are actually in terms of the >>>>>>>> regressors (so contrasting conditions 1 and 2 could be >>>>>>>> specified >>>>>>>> as -a >>>>>>>> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >>>>>>>> >>>>>>>> 2) the latency and dispersion regressors are being ignored (a >>>>>>>> common >>>>>>>> practice). The contrast weights should therefore be >>>>>>>> specified as >>>>>>>> -a 1 >>>>>>>> -c 2. >>>>>>> This is what happens. If you want to use the derivatives, >>>>>>> then you >>>>>>> need >>>>>>> to spec -setwdelay. When you run the command, it will >>>>>>> prompt you >>>>>>> for 3 >>>>>>> values to use. If you spec 1 0 0, then it will be the same >>>>>>> as the >>>>>>> default. If you want to test only the first derivative, >>>>>>> then you >>>>>>> would >>>>>>> spec 0 1 0. Note that the 3rd regressor is the 2nd >>>>>>> derivative wrt >>>>>>> time, >>>>>>> not the first derivative wrt the dispersion parameter. You >>>>>>> cannot get >>>>>>> the Calhoun 2004 value using a contrast (it is non-linear). >>>>>>> doug >>>>>>>> >>>>>>>> 3) The Calhoun et al (2004) approach is being used to >>>>>>>> combine the >>>>>>>> three regressors into a "derivative boost" amplitude >>>>>>>> measure. The contrast weights should therefore be specified >>>>>>>> as -a >>>>>>>> 1 -c 2. >>>>>>>> >>>>>>>> Thanks for any help you can give me! >>>>>>>> >>>>>>>> Joe >>>>>>>> >>>>>>>> -------------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Joseph Dien, >>>>>>>> Senior Research Scientist >>>>>>>> University of Maryland >>>>>>>> >>>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>> Phone: 202-297-8117 >>>>>>>> http://joedien.com// http://joedien.com// >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> >>>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>> Outgoing: >>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the >>>>>>> person to >>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>> error and >>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners >>>>>>> Compliance HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>>> sent to >>>>>>> you in error >>>>>>> but does not contain patient information, please contact the >>>>>>> sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>>> >>>>>> >>>>>> >>>>>> -------------------------------------------------------------------------------- >>>>>> >>>>>> Joseph Dien, >>>>>> Senior Research Scientist >>>>>> University of Maryland >>>>>> >>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> Phone: 202-297-8117 >>>>>> http://joedien.com// http://joedien.com// >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the >>>>>> person to >>>>>> whom it is >>>>>> addressed. If you believe this e-mail was sent to you in >>>>>> error and >>>>>> the e-mail >>>>>> contains patient information, please contact the Partners >>>>>> Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline http://www.partners.org/complianceline. If the e-mail was >>>>>> sent to >>>>>> you in error >>>>>> but does not contain patient information, please contact the >>>>>> sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> >>>>> Joseph Dien, >>>>> Senior Research Scientist >>>>> University of Maryland >>>>> >>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> Phone: 202-297-8117 >>>>> http://joedien.com// http://joedien.com// >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to >>>>> whom it is >>>>> addressed. If you believe this e-mail was sent to you in >>>>> error and >>>>> the e-mail >>>>> contains patient information, please contact the Partners >>>>> Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline http://www.partners.org/complianceline. If the e-mail was sent to >>>>> you in error >>>>> but does not contain patient information, please contact the >>>>> sender >>>>> and properly >>>>> dispose of the e-mail. >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> >>>> Joseph Dien, >>>> Senior Research Scientist >>>> University of Maryland >>>> >>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> Phone: 202-297-8117 >>>> http://joedien.com// http://joedien.com// >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail:jdien07@mac.com mailto:jdien07@mac.com >> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> Phone: 202-297-8117 >> http://joedien.com// http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Joseph Dien, Senior Research Scientist University of Maryland
E-mail:jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> <mailto:jdien07@mac.com mailto:jdien07@mac.com> Phone: 202-297-8117 http://joedien.com// http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail:jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> Phone: 202-297-8117 http://joedien.com// http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com> Cell Phone: 202-297-8117 http://joedien.com http://joedien.com/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
I did more digging around and came up with a procedure. Please let me know if it would cause any problems. Looking at the contents of the X.mat files (which contain the predictors), it appears that the betas are indeed arranged as c1 d1 c2 d2… I also found that isxconcat-sess requires the contrast output of mkcontrast-sess so I can’t just bypass it.
So my thought is:
1) run mkanalysis-sess with -spmhrf 1 2) run selxavg3-sess with the -no-con-ok flag to get the spmhrf1 betas without bothering with the contrasts 3) run mkanalysis-sess with -spmhrf 0 4) run selxavg3-sess again but with the contrasts to get everything set up 5) read in the spmhrf1 betas with MRIread and compute the Calhoun derivative boost with the beta values in mri.vol 6) use these values to compute the desired contrasts. From my examination of a sample ces.nii.gz file, a simple linear combination based on the contrast weights is all that is needed. 7) replace the contents of the corresponding spmhrf0 ces.nii.gz files’ mri.vol with these new values 8) write out the new ces.nii.gz files. 9) proceed with the analysis stream, using isxconcat-sess to set up the second level analysis
So the question is, would this work? Am I neglecting files other than ces.nii.gz that would need to be modified? or other fields in the mri data structure? When you referred to writing “out a new volume” is this what you meant?
Thanks again for this help!
Joe
On Mar 15, 2016, at 17:32, Joseph Dien jdien07@mac.com wrote:
oh duh! Sorry, wasn’t thinking clearly. Okay, I see how to generate the betas now. I don’t even need to mess with the mkcontrast-sess command. I just run selxavg3-sess with the -no-con-ok flag. With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex. With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex. With 12 conditions, 12 more betas is exactly right. So how do I know which of the betas is which? I looked through the files and couldn’t find any labels. I’m guessing the first twelve are the condition betas for "spmhrf 0". If so, for "spmhrf 1", is it arranged as:
- c1 c2 c3…d1 d2 d3...
or
- c1 d1 c2 d2...
(where d is the first derivative term)
also, when I asked you earlier about implementing this procedure, I had suggested reading the betas, computing the Calhoun, then generating new beta.nii.gz files with the new betas replacing the original spmhrf0 betas and then continuing with the regular analysis stream but you said it would result in invalid p-values. Instead, you suggested:
"I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume”
can you expand on how one might “compute the contrasts” and “write out the new volume”?
Thanks again for this help!
Joe
On Mar 15, 2016, at 12:43, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
On 03/13/2016 10:29 PM, Joseph Dien wrote:
After a long break, back to this…
My goal is still to get the betas for the first and maybe second spm hrf so I can calculate a Calhoun derivative boost measure.
As a first step I ran:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
to use the SPM HRF with one derivative.
Then:
selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh
I got the following error:
ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch This condition has 2 regressors, but evrm has 1 Struct contents reference from a non-struct array object.
Error in flac_conmat (line 37) if(nthcon > length(flac.con))
Error in flac_customize (line 369) flacnew = flac_conmat(flacnew,nthcon);
Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0);
ERROR: fast_selxavg3() failed\n
This ran fine with spmhrf 0
based on your prior response below that:
"This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear).”
I tried:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay
but I just got the error:
ERROR: Flag -setwdelay unrecognized.
I also tried using the flag when setting up the contrasts but that didn’t work either.
so not quite sure what I’m doing wrong. I had understood from your response below that the contrast weights didn’t need to be changed from the spmhrf 0 case but perhaps I misunderstood?
any help would be welcome!
Joe
On Jul 10, 2013, at 13:58, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume
On 07/10/2013 01:40 PM, Joseph Dien wrote:
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
On 07/10/2013 01:29 PM, Joseph Dien wrote: > Sorry, not following what you are suggesting? > > I want the second derivative for calculating the Calhoun et al 2004 > derivative boost measure. > My understanding is that to the extent that the BOLD signal deviates > from the canonical hrf, the amplitude of the primary regressor will be > attenuated and the variance will instead end up in the first and > second derivatives (to the extent that they are able to accommodate > the divergence). By using a Calhoun measure that incorporates both > the first and second derivatives, in principle I'll have a BOLD > measure that is more robust to deviations from the canonical hrf. Sorry, it had been a while since I read that paper. I did not know that they had a formulation that included the 2nd derivative. > > However, if the way FSFAST is calculating the second derivative > regressor is resulting in loss of statistical power due to shared > variance with the primary regressor, then it would be best to just not > include it at all in the estimation step. I don't know how much it will hurt the power. You'd have to look at the efficiency. doug
> > > On Jul 10, 2013, at 1:21 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote: > >> >> Why not just create a new volume and then compute contrasts from >> the new >> volume? What you are suggesting will work I think, but it leaves me a >> little nervous. The p-values will be meaningless. >> >> >> As for the 2nd derivative, I think it must be a numerical issue >> (it is >> not computed analytically). Why do you need the 2nd derivative? >> >> doug >> >> >> >> On 07/10/2013 12:47 PM, Joseph Dien wrote: >>> I'm thinking of generating a modified beta.nii.gz file where the >>> primary betas have been replaced with the Calhoun et al (2004) >>> derivative boost measure. What do you think? Also, please note my >>> question below about the second derivative as it is causing me >>> concern >>> about my analysis. Thanks! >>> >>> Joe >>> >>> >>> On Jul 10, 2013, at 12:39 PM, Douglas N Greve >>> <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU>> wrote: >>> >>>> >>>> I think that would work. You would need to change the time stamps >>>> on the >>>> .mat file in the analysis folder. When you re-run selxavg3-sess, it >>>> will >>>> see that the .mat files are newer than the beta and regenerate the >>>> contrasts. But what are you planning to do the the beta file? It >>>> sounds >>>> like a potentially bad idea >>>> >>>> doug >>>> >>>> >>>> On 07/09/2013 10:26 PM, Joseph Dien wrote: >>>>> It looks as though selxavg3-sess generates the contrast >>>>> analyses at >>>>> the same time as the beta weights. Would it be possible to >>>>> run selxavg3-sess once to obtain the beta weights, modify the >>>>> beta.nii.gz file, and then rerun selxavg3-sess to obtain the >>>>> contrast >>>>> statistics using the modified beta weights? >>>>> >>>>> Joe >>>>> >>>>> On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com>> wrote: >>>>> >>>>>> I tried correlations and the 2nd derivative is definitely not >>>>>> orthogonal. >>>>>> >>>>>>>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) >>>>>> >>>>>> ans = >>>>>> >>>>>> 1.0000 -0.0000 -0.5427 >>>>>> -0.0000 1.0000 -0.0298 >>>>>> -0.5427 -0.0298 1.0000 >>>>>> >>>>>> I looked at the regressors that SPM generates for the same data: >>>>>> >>>>>> ans = >>>>>> >>>>>> 1.0000 0.0436 0.1740 >>>>>> 0.0436 1.0000 -0.0226 >>>>>> 0.1740 -0.0226 1.0000 >>>>>> >>>>>> The first derivative is not as orthogonal but the second >>>>>> derivative >>>>>> was much more orthogonal. >>>>>> Does this have to do with what you noted below about how the >>>>>> second >>>>>> derivative is being calculated? >>>>>> So does this mean I should avoid the spmhrf 2 option entirely to >>>>>> avoid loss of statistical power? >>>>>> >>>>>> Thanks for the help! >>>>>> >>>>>> Joe >>>>>> >>>>>> >>>>>> On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com>> wrote: >>>>>> >>>>>>> Thanks for the quick response! So if I wanted to use the >>>>>>> Calhoun >>>>>>> 2004 approach, I should be able to use the Steffener 2010 >>>>>>> correction >>>>>>> to address the violation of the assumption that the regressors >>>>>>> were >>>>>>> standardized and generate a new beta.nii.gz file where the >>>>>>> primary >>>>>>> beta values have been replaced with the Calhoun 2004 measure. >>>>>>> Can I >>>>>>> assume the three regressors are more or less orthogonal? I got >>>>>>> non-zero numbers when I tried to test the assumption in the >>>>>>> Xtmp.X >>>>>>> variable >>>>>>> >>>>>>> sum(X(1:207,4).*X(1:207,5)) >>>>>>> >>>>>>> but not hugely non-zero so maybe just rounding errors? >>>>>>> >>>>>>> >>>>>>> On Jul 9, 2013, at 4:16 PM, Douglas N Greve >>>>>>> <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu >>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>>>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>>>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>>>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU>> wrote: >>>>>>> >>>>>>>> >>>>>>>> On 07/09/2013 04:11 PM, Joseph Dien wrote: >>>>>>>>> Hi, >>>>>>>>> I have a question about how mkcontrast-sess works. I ran an >>>>>>>>> analysis using the mkanalysis-sess option spmhrf 2 so >>>>>>>>> there are >>>>>>>>> three >>>>>>>>> regressors for each predictor, the primary, the latency, >>>>>>>>> and the >>>>>>>>> dispersion. When specifying the contrast weights for >>>>>>>>> mkcontrast-sess, >>>>>>>>> the documentation indicates that they are specified in terms >>>>>>>>> of the >>>>>>>>> conditions as numbered in the paradigm file, not the >>>>>>>>> individual >>>>>>>>> regressors. Furthermore there only appears to be one contrast >>>>>>>>> value >>>>>>>>> output for each contrast, not three. >>>>>>>>> >>>>>>>>> How are the three regressors being handled? I can think of >>>>>>>>> several >>>>>>>>> scenarios: >>>>>>>>> >>>>>>>>> 1) the contrast weights are not actually in terms of >>>>>>>>> conditions (the >>>>>>>>> documentation is incorrect), they are actually in terms of the >>>>>>>>> regressors (so contrasting conditions 1 and 2 could be >>>>>>>>> specified >>>>>>>>> as -a >>>>>>>>> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >>>>>>>>> >>>>>>>>> 2) the latency and dispersion regressors are being ignored (a >>>>>>>>> common >>>>>>>>> practice). The contrast weights should therefore be >>>>>>>>> specified as >>>>>>>>> -a 1 >>>>>>>>> -c 2. >>>>>>>> This is what happens. If you want to use the derivatives, >>>>>>>> then you >>>>>>>> need >>>>>>>> to spec -setwdelay. When you run the command, it will >>>>>>>> prompt you >>>>>>>> for 3 >>>>>>>> values to use. If you spec 1 0 0, then it will be the same >>>>>>>> as the >>>>>>>> default. If you want to test only the first derivative, >>>>>>>> then you >>>>>>>> would >>>>>>>> spec 0 1 0. Note that the 3rd regressor is the 2nd >>>>>>>> derivative wrt >>>>>>>> time, >>>>>>>> not the first derivative wrt the dispersion parameter. You >>>>>>>> cannot get >>>>>>>> the Calhoun 2004 value using a contrast (it is non-linear). >>>>>>>> doug >>>>>>>>> >>>>>>>>> 3) The Calhoun et al (2004) approach is being used to >>>>>>>>> combine the >>>>>>>>> three regressors into a "derivative boost" amplitude >>>>>>>>> measure. The contrast weights should therefore be specified >>>>>>>>> as -a >>>>>>>>> 1 -c 2. >>>>>>>>> >>>>>>>>> Thanks for any help you can give me! >>>>>>>>> >>>>>>>>> Joe >>>>>>>>> >>>>>>>>> -------------------------------------------------------------------------------- >>>>>>>>> >>>>>>>>> Joseph Dien, >>>>>>>>> Senior Research Scientist >>>>>>>>> University of Maryland >>>>>>>>> >>>>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>> Phone: 202-297-8117 >>>>>>>>> http://joedien.com// http://joedien.com// >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>> Outgoing: >>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> The information in this e-mail is intended only for the >>>>>>>> person to >>>>>>>> whom it is >>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>> error and >>>>>>>> the e-mail >>>>>>>> contains patient information, please contact the Partners >>>>>>>> Compliance HelpLine at >>>>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>>>> sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the >>>>>>>> sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------------- >>>>>>> >>>>>>> Joseph Dien, >>>>>>> Senior Research Scientist >>>>>>> University of Maryland >>>>>>> >>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> Phone: 202-297-8117 >>>>>>> http://joedien.com// http://joedien.com// >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the >>>>>>> person to >>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>> error and >>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners >>>>>>> Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline http://www.partners.org/complianceline. If the e-mail was >>>>>>> sent to >>>>>>> you in error >>>>>>> but does not contain patient information, please contact the >>>>>>> sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> -------------------------------------------------------------------------------- >>>>>> >>>>>> Joseph Dien, >>>>>> Senior Research Scientist >>>>>> University of Maryland >>>>>> >>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> Phone: 202-297-8117 >>>>>> http://joedien.com// http://joedien.com// >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom it is >>>>>> addressed. If you believe this e-mail was sent to you in >>>>>> error and >>>>>> the e-mail >>>>>> contains patient information, please contact the Partners >>>>>> Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline http://www.partners.org/complianceline. If the e-mail was sent to >>>>>> you in error >>>>>> but does not contain patient information, please contact the >>>>>> sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> >>>>> Joseph Dien, >>>>> Senior Research Scientist >>>>> University of Maryland >>>>> >>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>> Phone: 202-297-8117 >>>>> http://joedien.com// http://joedien.com// >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>> Phone: 202-297-8117 >>> http://joedien.com// http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail:jdien07@mac.com mailto:jdien07@mac.com > <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> > <mailto:jdien07@mac.com mailto:jdien07@mac.com> > Phone: 202-297-8117 > http://joedien.com// http://joedien.com// > > > > > > > > > > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, Senior Research Scientist University of Maryland
E-mail:jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> Phone: 202-297-8117 http://joedien.com// http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
Doug, I see now what your concern was with just adjusting the beta weights. Since FSFAST is using a pseudo-mixed effects model, there is also a need to pass the cesvar statistics up to the second level. How that might accommodate the derivative boost computation is not straightforward to me. I need to understand better what fsfast is doing. I was wondering if you could answer a couple questions about how cesvar is computed;
1) The cesvar computations in the fast_fratio.m function provided a good guide. According to it: cescvm = inv(C*inv(X'*X)*X'*Sn*X*inv(X'*X)*C’); where Sn is the covariance matrix of the noise after the whitening (which is on by default). cesvar=rvar./cescvm.
How is Sn computed?
2) I need to understand what fsfast is doing conceptually but I couldn’t reconcile the Thirion et al (2007) Equation #5 and the equations above, specifically the inclusion of the rvar term. Can you throw some light on this?
I greatly appreciate your helpful tips and this amazing software that you have written.
Respectfully,
Joe
On Mar 17, 2016, at 15:48, Joseph Dien jdien07@mac.com wrote:
I did more digging around and came up with a procedure. Please let me know if it would cause any problems. Looking at the contents of the X.mat files (which contain the predictors), it appears that the betas are indeed arranged as c1 d1 c2 d2… I also found that isxconcat-sess requires the contrast output of mkcontrast-sess so I can’t just bypass it.
So my thought is:
- run mkanalysis-sess with -spmhrf 1
- run selxavg3-sess with the -no-con-ok flag to get the spmhrf1 betas without bothering with the contrasts
- run mkanalysis-sess with -spmhrf 0
- run selxavg3-sess again but with the contrasts to get everything set up
- read in the spmhrf1 betas with MRIread and compute the Calhoun derivative boost with the beta values in mri.vol
- use these values to compute the desired contrasts. From my examination of a sample ces.nii.gz file, a simple linear combination based on the contrast weights is all that is needed.
- replace the contents of the corresponding spmhrf0 ces.nii.gz files’ mri.vol with these new values
- write out the new ces.nii.gz files.
- proceed with the analysis stream, using isxconcat-sess to set up the second level analysis
So the question is, would this work? Am I neglecting files other than ces.nii.gz that would need to be modified? or other fields in the mri data structure? When you referred to writing “out a new volume” is this what you meant?
Thanks again for this help!
Joe
On Mar 15, 2016, at 17:32, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com> wrote:
oh duh! Sorry, wasn’t thinking clearly. Okay, I see how to generate the betas now. I don’t even need to mess with the mkcontrast-sess command. I just run selxavg3-sess with the -no-con-ok flag. With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex. With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex. With 12 conditions, 12 more betas is exactly right. So how do I know which of the betas is which? I looked through the files and couldn’t find any labels. I’m guessing the first twelve are the condition betas for "spmhrf 0". If so, for "spmhrf 1", is it arranged as:
- c1 c2 c3…d1 d2 d3...
or
- c1 d1 c2 d2...
(where d is the first derivative term)
also, when I asked you earlier about implementing this procedure, I had suggested reading the betas, computing the Calhoun, then generating new beta.nii.gz files with the new betas replacing the original spmhrf0 betas and then continuing with the regular analysis stream but you said it would result in invalid p-values. Instead, you suggested:
"I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume”
can you expand on how one might “compute the contrasts” and “write out the new volume”?
Thanks again for this help!
Joe
On Mar 15, 2016, at 12:43, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
On 03/13/2016 10:29 PM, Joseph Dien wrote:
After a long break, back to this…
My goal is still to get the betas for the first and maybe second spm hrf so I can calculate a Calhoun derivative boost measure.
As a first step I ran:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
to use the SPM HRF with one derivative.
Then:
selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh
I got the following error:
ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch This condition has 2 regressors, but evrm has 1 Struct contents reference from a non-struct array object.
Error in flac_conmat (line 37) if(nthcon > length(flac.con))
Error in flac_customize (line 369) flacnew = flac_conmat(flacnew,nthcon);
Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0);
ERROR: fast_selxavg3() failed\n
This ran fine with spmhrf 0
based on your prior response below that:
"This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear).”
I tried:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay
but I just got the error:
ERROR: Flag -setwdelay unrecognized.
I also tried using the flag when setting up the contrasts but that didn’t work either.
so not quite sure what I’m doing wrong. I had understood from your response below that the contrast weights didn’t need to be changed from the spmhrf 0 case but perhaps I misunderstood?
any help would be welcome!
Joe
On Jul 10, 2013, at 13:58, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume
On 07/10/2013 01:40 PM, Joseph Dien wrote:
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
> > On 07/10/2013 01:29 PM, Joseph Dien wrote: >> Sorry, not following what you are suggesting? >> >> I want the second derivative for calculating the Calhoun et al 2004 >> derivative boost measure. >> My understanding is that to the extent that the BOLD signal deviates >> from the canonical hrf, the amplitude of the primary regressor will be >> attenuated and the variance will instead end up in the first and >> second derivatives (to the extent that they are able to accommodate >> the divergence). By using a Calhoun measure that incorporates both >> the first and second derivatives, in principle I'll have a BOLD >> measure that is more robust to deviations from the canonical hrf. > Sorry, it had been a while since I read that paper. I did not know that > they had a formulation that included the 2nd derivative. >> >> However, if the way FSFAST is calculating the second derivative >> regressor is resulting in loss of statistical power due to shared >> variance with the primary regressor, then it would be best to just not >> include it at all in the estimation step. > I don't know how much it will hurt the power. You'd have to look at the > efficiency. > doug > >> >> >> On Jul 10, 2013, at 1:21 PM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >>> >>> Why not just create a new volume and then compute contrasts from >>> the new >>> volume? What you are suggesting will work I think, but it leaves me a >>> little nervous. The p-values will be meaningless. >>> >>> >>> As for the 2nd derivative, I think it must be a numerical issue >>> (it is >>> not computed analytically). Why do you need the 2nd derivative? >>> >>> doug >>> >>> >>> >>> On 07/10/2013 12:47 PM, Joseph Dien wrote: >>>> I'm thinking of generating a modified beta.nii.gz file where the >>>> primary betas have been replaced with the Calhoun et al (2004) >>>> derivative boost measure. What do you think? Also, please note my >>>> question below about the second derivative as it is causing me >>>> concern >>>> about my analysis. Thanks! >>>> >>>> Joe >>>> >>>> >>>> On Jul 10, 2013, at 12:39 PM, Douglas N Greve >>>> <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU>> wrote: >>>> >>>>> >>>>> I think that would work. You would need to change the time stamps >>>>> on the >>>>> .mat file in the analysis folder. When you re-run selxavg3-sess, it >>>>> will >>>>> see that the .mat files are newer than the beta and regenerate the >>>>> contrasts. But what are you planning to do the the beta file? It >>>>> sounds >>>>> like a potentially bad idea >>>>> >>>>> doug >>>>> >>>>> >>>>> On 07/09/2013 10:26 PM, Joseph Dien wrote: >>>>>> It looks as though selxavg3-sess generates the contrast >>>>>> analyses at >>>>>> the same time as the beta weights. Would it be possible to >>>>>> run selxavg3-sess once to obtain the beta weights, modify the >>>>>> beta.nii.gz file, and then rerun selxavg3-sess to obtain the >>>>>> contrast >>>>>> statistics using the modified beta weights? >>>>>> >>>>>> Joe >>>>>> >>>>>> On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com>> wrote: >>>>>> >>>>>>> I tried correlations and the 2nd derivative is definitely not >>>>>>> orthogonal. >>>>>>> >>>>>>>>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) >>>>>>> >>>>>>> ans = >>>>>>> >>>>>>> 1.0000 -0.0000 -0.5427 >>>>>>> -0.0000 1.0000 -0.0298 >>>>>>> -0.5427 -0.0298 1.0000 >>>>>>> >>>>>>> I looked at the regressors that SPM generates for the same data: >>>>>>> >>>>>>> ans = >>>>>>> >>>>>>> 1.0000 0.0436 0.1740 >>>>>>> 0.0436 1.0000 -0.0226 >>>>>>> 0.1740 -0.0226 1.0000 >>>>>>> >>>>>>> The first derivative is not as orthogonal but the second >>>>>>> derivative >>>>>>> was much more orthogonal. >>>>>>> Does this have to do with what you noted below about how the >>>>>>> second >>>>>>> derivative is being calculated? >>>>>>> So does this mean I should avoid the spmhrf 2 option entirely to >>>>>>> avoid loss of statistical power? >>>>>>> >>>>>>> Thanks for the help! >>>>>>> >>>>>>> Joe >>>>>>> >>>>>>> >>>>>>> On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com>> wrote: >>>>>>> >>>>>>>> Thanks for the quick response! So if I wanted to use the >>>>>>>> Calhoun >>>>>>>> 2004 approach, I should be able to use the Steffener 2010 >>>>>>>> correction >>>>>>>> to address the violation of the assumption that the regressors >>>>>>>> were >>>>>>>> standardized and generate a new beta.nii.gz file where the >>>>>>>> primary >>>>>>>> beta values have been replaced with the Calhoun 2004 measure. >>>>>>>> Can I >>>>>>>> assume the three regressors are more or less orthogonal? I got >>>>>>>> non-zero numbers when I tried to test the assumption in the >>>>>>>> Xtmp.X >>>>>>>> variable >>>>>>>> >>>>>>>> sum(X(1:207,4).*X(1:207,5)) >>>>>>>> >>>>>>>> but not hugely non-zero so maybe just rounding errors? >>>>>>>> >>>>>>>> >>>>>>>> On Jul 9, 2013, at 4:16 PM, Douglas N Greve >>>>>>>> <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>>>>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>>>>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> >>>>>>>> <mailto:greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU>> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> On 07/09/2013 04:11 PM, Joseph Dien wrote: >>>>>>>>>> Hi, >>>>>>>>>> I have a question about how mkcontrast-sess works. I ran an >>>>>>>>>> analysis using the mkanalysis-sess option spmhrf 2 so >>>>>>>>>> there are >>>>>>>>>> three >>>>>>>>>> regressors for each predictor, the primary, the latency, >>>>>>>>>> and the >>>>>>>>>> dispersion. When specifying the contrast weights for >>>>>>>>>> mkcontrast-sess, >>>>>>>>>> the documentation indicates that they are specified in terms >>>>>>>>>> of the >>>>>>>>>> conditions as numbered in the paradigm file, not the >>>>>>>>>> individual >>>>>>>>>> regressors. Furthermore there only appears to be one contrast >>>>>>>>>> value >>>>>>>>>> output for each contrast, not three. >>>>>>>>>> >>>>>>>>>> How are the three regressors being handled? I can think of >>>>>>>>>> several >>>>>>>>>> scenarios: >>>>>>>>>> >>>>>>>>>> 1) the contrast weights are not actually in terms of >>>>>>>>>> conditions (the >>>>>>>>>> documentation is incorrect), they are actually in terms of the >>>>>>>>>> regressors (so contrasting conditions 1 and 2 could be >>>>>>>>>> specified >>>>>>>>>> as -a >>>>>>>>>> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >>>>>>>>>> >>>>>>>>>> 2) the latency and dispersion regressors are being ignored (a >>>>>>>>>> common >>>>>>>>>> practice). The contrast weights should therefore be >>>>>>>>>> specified as >>>>>>>>>> -a 1 >>>>>>>>>> -c 2. >>>>>>>>> This is what happens. If you want to use the derivatives, >>>>>>>>> then you >>>>>>>>> need >>>>>>>>> to spec -setwdelay. When you run the command, it will >>>>>>>>> prompt you >>>>>>>>> for 3 >>>>>>>>> values to use. If you spec 1 0 0, then it will be the same >>>>>>>>> as the >>>>>>>>> default. If you want to test only the first derivative, >>>>>>>>> then you >>>>>>>>> would >>>>>>>>> spec 0 1 0. Note that the 3rd regressor is the 2nd >>>>>>>>> derivative wrt >>>>>>>>> time, >>>>>>>>> not the first derivative wrt the dispersion parameter. You >>>>>>>>> cannot get >>>>>>>>> the Calhoun 2004 value using a contrast (it is non-linear). >>>>>>>>> doug >>>>>>>>>> >>>>>>>>>> 3) The Calhoun et al (2004) approach is being used to >>>>>>>>>> combine the >>>>>>>>>> three regressors into a "derivative boost" amplitude >>>>>>>>>> measure. The contrast weights should therefore be specified >>>>>>>>>> as -a >>>>>>>>>> 1 -c 2. >>>>>>>>>> >>>>>>>>>> Thanks for any help you can give me! >>>>>>>>>> >>>>>>>>>> Joe >>>>>>>>>> >>>>>>>>>> -------------------------------------------------------------------------------- >>>>>>>>>> >>>>>>>>>> Joseph Dien, >>>>>>>>>> Senior Research Scientist >>>>>>>>>> University of Maryland >>>>>>>>>> >>>>>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>>>> Phone: 202-297-8117 >>>>>>>>>> http://joedien.com// http://joedien.com// >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>> MGH-NMR Center >>>>>>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>> Fax: 617-726-7422 >>>>>>>>> >>>>>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>>>> Outgoing: >>>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>>> The information in this e-mail is intended only for the >>>>>>>>> person to >>>>>>>>> whom it is >>>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>>> error and >>>>>>>>> the e-mail >>>>>>>>> contains patient information, please contact the Partners >>>>>>>>> Compliance HelpLine at >>>>>>>>> http://www.partners.org/complianceline http://www.partners.org/complianceline . If the e-mail was >>>>>>>>> sent to >>>>>>>>> you in error >>>>>>>>> but does not contain patient information, please contact the >>>>>>>>> sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Joseph Dien, >>>>>>>> Senior Research Scientist >>>>>>>> University of Maryland >>>>>>>> >>>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>>> Phone: 202-297-8117 >>>>>>>> http://joedien.com// http://joedien.com// >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> The information in this e-mail is intended only for the >>>>>>>> person to >>>>>>>> whom it is >>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>> error and >>>>>>>> the e-mail >>>>>>>> contains patient information, please contact the Partners >>>>>>>> Compliance >>>>>>>> HelpLine at >>>>>>>> http://www.partners.org/complianceline http://www.partners.org/complianceline. If the e-mail was >>>>>>>> sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the >>>>>>>> sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------------- >>>>>>> >>>>>>> Joseph Dien, >>>>>>> Senior Research Scientist >>>>>>> University of Maryland >>>>>>> >>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>>> Phone: 202-297-8117 >>>>>>> http://joedien.com// http://joedien.com// >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the person to >>>>>>> whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>> error and >>>>>>> the e-mail >>>>>>> contains patient information, please contact the Partners >>>>>>> Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline http://www.partners.org/complianceline. If the e-mail was sent to >>>>>>> you in error >>>>>>> but does not contain patient information, please contact the >>>>>>> sender >>>>>>> and properly >>>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> -------------------------------------------------------------------------------- >>>>>> >>>>>> Joseph Dien, >>>>>> Senior Research Scientist >>>>>> University of Maryland >>>>>> >>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>>>> Phone: 202-297-8117 >>>>>> http://joedien.com// http://joedien.com// >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> >>>> Joseph Dien, >>>> Senior Research Scientist >>>> University of Maryland >>>> >>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >>>> Phone: 202-297-8117 >>>> http://joedien.com// http://joedien.com// >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail:jdien07@mac.com mailto:jdien07@mac.com >> <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> >> <mailto:jdien07@mac.com mailto:jdien07@mac.com> >> Phone: 202-297-8117 >> http://joedien.com// http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Joseph Dien, Senior Research Scientist University of Maryland
E-mail:jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com><mailto:jdien07@mac.com mailto:jdien07@mac.com> Phone: 202-297-8117 http://joedien.com// http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com mailto:jdien07@mac.com <mailto:jdien07@mac.com mailto:jdien07@mac.com> Cell Phone: 202-297-8117 http://joedien.com http://joedien.com/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com http://joedien.com/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com http://joedien.com/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
On 03/24/2016 07:37 PM, Joseph Dien wrote:
Doug, I see now what your concern was with just adjusting the beta weights. Since FSFAST is using a pseudo-mixed effects model, there is also a need to pass the cesvar statistics up to the second level. How that might accommodate the derivative boost computation is not straightforward to me. I need to understand better what fsfast is doing. I was wondering if you could answer a couple questions about how cesvar is computed;
- The cesvar computations in the fast_fratio.m function provided a
good guide. According to it: cescvm = inv(C*inv(X'*X)*X'*Sn*X*inv(X'*X)*C’); where Sn is the covariance matrix of the noise after the whitening (which is on by default). cesvar=rvar./cescvm.
How is Sn computed?
The autocorrelation function is computed at each voxel from the residual, these are fit to an AR1 model and adjusted for residual bias. They are spatially clustered based on AR1 value. The Sn is computed as a toeplitz matrix of the autocorrelation function derived from the best-fit AR1 model (that matrix is multipled by the residual variance to get the final Sn).
- I need to understand what fsfast is doing conceptually but I
couldn’t reconcile the Thirion et al (2007) Equation #5 and the equations above, specifically the inclusion of the rvar term. Can you throw some light on this?
It is really nothing fancy, just down-weighting each subject by the residual standard deviation.
I greatly appreciate your helpful tips and this amazing software that you have written.
Respectfully,
Joe
On Mar 17, 2016, at 15:48, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com> wrote:
I did more digging around and came up with a procedure. Please let me know if it would cause any problems. Looking at the contents of the X.mat files (which contain the predictors), it appears that the betas are indeed arranged as c1 d1 c2 d2… I also found that isxconcat-sess requires the contrast output of mkcontrast-sess so I can’t just bypass it.
So my thought is:
- run mkanalysis-sess with -spmhrf 1
- run selxavg3-sess with the -no-con-ok flag to get the spmhrf1
betas without bothering with the contrasts 3) run mkanalysis-sess with -spmhrf 0 4) run selxavg3-sess again but with the contrasts to get everything set up 5) read in the spmhrf1 betas with MRIread and compute the Calhoun derivative boost with the beta values in mri.vol 6) use these values to compute the desired contrasts. From my examination of a sample ces.nii.gz file, a simple linear combination based on the contrast weights is all that is needed. 7) replace the contents of the corresponding spmhrf0 ces.nii.gz files’ mri.vol with these new values 8) write out the new ces.nii.gz files. 9) proceed with the analysis stream, using isxconcat-sess to set up the second level analysis
So the question is, would this work? Am I neglecting files other than ces.nii.gz that would need to be modified? or other fields in the mri data structure? When you referred to writing “out a new volume” is this what you meant?
Thanks again for this help!
Joe
On Mar 15, 2016, at 17:32, Joseph Dien <jdien07@mac.com mailto:jdien07@mac.com> wrote:
oh duh! Sorry, wasn’t thinking clearly. Okay, I see how to generate the betas now. I don’t even need to mess with the mkcontrast-sess command. I just run selxavg3-sess with the -no-con-ok flag. With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex. With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex. With 12 conditions, 12 more betas is exactly right. So how do I know which of the betas is which? I looked through the files and couldn’t find any labels. I’m guessing the first twelve are the condition betas for "spmhrf 0". If so, for "spmhrf 1", is it arranged as:
- c1 c2 c3…d1 d2 d3...
or
- c1 d1 c2 d2...
(where d is the first derivative term)
also, when I asked you earlier about implementing this procedure, I had suggested reading the betas, computing the Calhoun, then generating new beta.nii.gz files with the new betas replacing the original spmhrf0 betas and then continuing with the regular analysis stream but you said it would result in invalid p-values. Instead, you suggested:
"I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume”
can you expand on how one might “compute the contrasts” and “write out the new volume”?
Thanks again for this help!
Joe
On Mar 15, 2016, at 12:43, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
On 03/13/2016 10:29 PM, Joseph Dien wrote:
After a long break, back to this…
My goal is still to get the betas for the first and maybe second spm hrf so I can calculate a Calhoun derivative boost measure.
As a first step I ran:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
to use the SPM HRF with one derivative.
Then:
selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh
I got the following error:
ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch This condition has 2 regressors, but evrm has 1 Struct contents reference from a non-struct array object.
Error in flac_conmat (line 37) if(nthcon > length(flac.con))
Error in flac_customize (line 369) flacnew = flac_conmat(flacnew,nthcon);
Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0);
> ------------------------------------------
ERROR: fast_selxavg3() failed\n
This ran fine with spmhrf 0
based on your prior response below that:
"This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear).”
I tried:
mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay
but I just got the error:
ERROR: Flag -setwdelay unrecognized.
I also tried using the flag when setting up the contrasts but that didn’t work either.
so not quite sure what I’m doing wrong. I had understood from your response below that the contrast weights didn’t need to be changed from the spmhrf 0 case but perhaps I misunderstood?
any help would be welcome!
Joe
On Jul 10, 2013, at 13:58, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume
On 07/10/2013 01:40 PM, Joseph Dien wrote: > Sounds good! > > Regarding creating a new volume and computing contrasts from it, > what > do you mean? I didn't follow that. > > Thanks! > > Joe > > > On Jul 10, 2013, at 1:33 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> > wrote: > >> >> On 07/10/2013 01:29 PM, Joseph Dien wrote: >>> Sorry, not following what you are suggesting? >>> >>> I want the second derivative for calculating the Calhoun et al >>> 2004 >>> derivative boost measure. >>> My understanding is that to the extent that the BOLD signal >>> deviates >>> from the canonical hrf, the amplitude of the primary regressor >>> will be >>> attenuated and the variance will instead end up in the first and >>> second derivatives (to the extent that they are able to >>> accommodate >>> the divergence). By using a Calhoun measure that incorporates >>> both >>> the first and second derivatives, in principle I'll have a BOLD >>> measure that is more robust to deviations from the canonical hrf. >> Sorry, it had been a while since I read that paper. I did not >> know that >> they had a formulation that included the 2nd derivative. >>> >>> However, if the way FSFAST is calculating the second derivative >>> regressor is resulting in loss of statistical power due to shared >>> variance with the primary regressor, then it would be best to >>> just not >>> include it at all in the estimation step. >> I don't know how much it will hurt the power. You'd have to >> look at the >> efficiency. >> doug >> >>> >>> >>> On Jul 10, 2013, at 1:21 PM, Douglas N Greve >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu> wrote: >>> >>>> >>>> Why not just create a new volume and then compute contrasts from >>>> the new >>>> volume? What you are suggesting will work I think, but it >>>> leaves me a >>>> little nervous. The p-values will be meaningless. >>>> >>>> >>>> As for the 2nd derivative, I think it must be a numerical issue >>>> (it is >>>> not computed analytically). Why do you need the 2nd derivative? >>>> >>>> doug >>>> >>>> >>>> >>>> On 07/10/2013 12:47 PM, Joseph Dien wrote: >>>>> I'm thinking of generating a modified beta.nii.gz file where the >>>>> primary betas have been replaced with the Calhoun et al (2004) >>>>> derivative boost measure. What do you think? Also, please >>>>> note my >>>>> question below about the second derivative as it is causing me >>>>> concern >>>>> about my analysis. Thanks! >>>>> >>>>> Joe >>>>> >>>>> >>>>> On Jul 10, 2013, at 12:39 PM, Douglas N Greve >>>>> <greve@NMR.MGH.HARVARD.EDU mailto:greve@nmr.mgh.harvard.edu >>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@NMR.MGH.HARVARD.EDU >>>>> mailto:greve@NMR.MGH.HARVARD.EDU >>>>> mailto:greve@NMR.MGH.HARVARD.EDU> wrote: >>>>> >>>>>> >>>>>> I think that would work. You would need to change the time >>>>>> stamps >>>>>> on the >>>>>> .mat file in the analysis folder. When you re-run >>>>>> selxavg3-sess, it >>>>>> will >>>>>> see that the .mat files are newer than the beta and >>>>>> regenerate the >>>>>> contrasts. But what are you planning to do the the beta >>>>>> file? It >>>>>> sounds >>>>>> like a potentially bad idea >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> On 07/09/2013 10:26 PM, Joseph Dien wrote: >>>>>>> It looks as though selxavg3-sess generates the contrast >>>>>>> analyses at >>>>>>> the same time as the beta weights. Would it be possible to >>>>>>> run selxavg3-sess once to obtain the beta weights, modify the >>>>>>> beta.nii.gz file, and then rerun selxavg3-sess to obtain the >>>>>>> contrast >>>>>>> statistics using the modified beta weights? >>>>>>> >>>>>>> Joe >>>>>>> >>>>>>> On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com> wrote: >>>>>>> >>>>>>>> I tried correlations and the 2nd derivative is definitely not >>>>>>>> orthogonal. >>>>>>>> >>>>>>>>>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) >>>>>>>> >>>>>>>> ans = >>>>>>>> >>>>>>>> 1.0000 -0.0000 -0.5427 >>>>>>>> -0.0000 1.0000 -0.0298 >>>>>>>> -0.5427 -0.0298 1.0000 >>>>>>>> >>>>>>>> I looked at the regressors that SPM generates for the >>>>>>>> same data: >>>>>>>> >>>>>>>> ans = >>>>>>>> >>>>>>>> 1.0000 0.0436 0.1740 >>>>>>>> 0.0436 1.0000 -0.0226 >>>>>>>> 0.1740 -0.0226 1.0000 >>>>>>>> >>>>>>>> The first derivative is not as orthogonal but the second >>>>>>>> derivative >>>>>>>> was much more orthogonal. >>>>>>>> Does this have to do with what you noted below about how the >>>>>>>> second >>>>>>>> derivative is being calculated? >>>>>>>> So does this mean I should avoid the spmhrf 2 option >>>>>>>> entirely to >>>>>>>> avoid loss of statistical power? >>>>>>>> >>>>>>>> Thanks for the help! >>>>>>>> >>>>>>>> Joe >>>>>>>> >>>>>>>> >>>>>>>> On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdien07@mac.com >>>>>>>> mailto:jdien07@mac.com >>>>>>>> mailto:jdien07@mac.com >>>>>>>> mailto:jdien07@mac.com >>>>>>>> mailto:jdien07@mac.com >>>>>>>> mailto:jdien07@mac.com >>>>>>>> mailto:jdien07@mac.com> wrote: >>>>>>>> >>>>>>>>> Thanks for the quick response! So if I wanted to use the >>>>>>>>> Calhoun >>>>>>>>> 2004 approach, I should be able to use the Steffener 2010 >>>>>>>>> correction >>>>>>>>> to address the violation of the assumption that the >>>>>>>>> regressors >>>>>>>>> were >>>>>>>>> standardized and generate a new beta.nii.gz file where the >>>>>>>>> primary >>>>>>>>> beta values have been replaced with the Calhoun 2004 >>>>>>>>> measure. >>>>>>>>> Can I >>>>>>>>> assume the three regressors are more or less orthogonal? >>>>>>>>> I got >>>>>>>>> non-zero numbers when I tried to test the assumption in the >>>>>>>>> Xtmp.X >>>>>>>>> variable >>>>>>>>> >>>>>>>>> sum(X(1:207,4).*X(1:207,5)) >>>>>>>>> >>>>>>>>> but not hugely non-zero so maybe just rounding errors? >>>>>>>>> >>>>>>>>> >>>>>>>>> On Jul 9, 2013, at 4:16 PM, Douglas N Greve >>>>>>>>> <greve@NMR.MGH.HARVARD.EDU >>>>>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@NMR.MGH.HARVARD.EDU >>>>>>>>> mailto:greve@NMR.MGH.HARVARD.EDU >>>>>>>>> mailto:greve@NMR.MGH.HARVARD.EDU >>>>>>>>> mailto:greve@NMR.MGH.HARVARD.EDU> wrote: >>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 07/09/2013 04:11 PM, Joseph Dien wrote: >>>>>>>>>>> Hi, >>>>>>>>>>> I have a question about how mkcontrast-sess works. I >>>>>>>>>>> ran an >>>>>>>>>>> analysis using the mkanalysis-sess option spmhrf 2 so >>>>>>>>>>> there are >>>>>>>>>>> three >>>>>>>>>>> regressors for each predictor, the primary, the latency, >>>>>>>>>>> and the >>>>>>>>>>> dispersion. When specifying the contrast weights for >>>>>>>>>>> mkcontrast-sess, >>>>>>>>>>> the documentation indicates that they are specified in >>>>>>>>>>> terms >>>>>>>>>>> of the >>>>>>>>>>> conditions as numbered in the paradigm file, not the >>>>>>>>>>> individual >>>>>>>>>>> regressors. Furthermore there only appears to be one >>>>>>>>>>> contrast >>>>>>>>>>> value >>>>>>>>>>> output for each contrast, not three. >>>>>>>>>>> >>>>>>>>>>> How are the three regressors being handled? I can >>>>>>>>>>> think of >>>>>>>>>>> several >>>>>>>>>>> scenarios: >>>>>>>>>>> >>>>>>>>>>> 1) the contrast weights are not actually in terms of >>>>>>>>>>> conditions (the >>>>>>>>>>> documentation is incorrect), they are actually in >>>>>>>>>>> terms of the >>>>>>>>>>> regressors (so contrasting conditions 1 and 2 could be >>>>>>>>>>> specified >>>>>>>>>>> as -a >>>>>>>>>>> 1 -a 2 -a 3 -c 4 -c 5 -c 6). >>>>>>>>>>> >>>>>>>>>>> 2) the latency and dispersion regressors are being >>>>>>>>>>> ignored (a >>>>>>>>>>> common >>>>>>>>>>> practice). The contrast weights should therefore be >>>>>>>>>>> specified as >>>>>>>>>>> -a 1 >>>>>>>>>>> -c 2. >>>>>>>>>> This is what happens. If you want to use the derivatives, >>>>>>>>>> then you >>>>>>>>>> need >>>>>>>>>> to spec -setwdelay. When you run the command, it will >>>>>>>>>> prompt you >>>>>>>>>> for 3 >>>>>>>>>> values to use. If you spec 1 0 0, then it will be the same >>>>>>>>>> as the >>>>>>>>>> default. If you want to test only the first derivative, >>>>>>>>>> then you >>>>>>>>>> would >>>>>>>>>> spec 0 1 0. Note that the 3rd regressor is the 2nd >>>>>>>>>> derivative wrt >>>>>>>>>> time, >>>>>>>>>> not the first derivative wrt the dispersion parameter. You >>>>>>>>>> cannot get >>>>>>>>>> the Calhoun 2004 value using a contrast (it is non-linear). >>>>>>>>>> doug >>>>>>>>>>> >>>>>>>>>>> 3) The Calhoun et al (2004) approach is being used to >>>>>>>>>>> combine the >>>>>>>>>>> three regressors into a "derivative boost" amplitude >>>>>>>>>>> measure. The contrast weights should therefore be >>>>>>>>>>> specified >>>>>>>>>>> as -a >>>>>>>>>>> 1 -c 2. >>>>>>>>>>> >>>>>>>>>>> Thanks for any help you can give me! >>>>>>>>>>> >>>>>>>>>>> Joe >>>>>>>>>>> >>>>>>>>>>> -------------------------------------------------------------------------------- >>>>>>>>>>> >>>>>>>>>>> Joseph Dien, >>>>>>>>>>> Senior Research Scientist >>>>>>>>>>> University of Maryland >>>>>>>>>>> >>>>>>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>>>>>> mailto:jdien07@mac.commailto:jdien07@mac.com >>>>>>>>>>> mailto:jdien07@mac.com >>>>>>>>>>> mailto:jdien07@mac.com >>>>>>>>>>> mailto:jdien07@mac.com >>>>>>>>>>> mailto:jdien07@mac.com >>>>>>>>>>> Phone: 202-297-8117 >>>>>>>>>>> http://joedien.com// >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>> MGH-NMR Center >>>>>>>>>> greve@nmr.mgh.harvard.edu >>>>>>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>> >>>>>>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>>> http://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> Outgoing: >>>>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the >>>>>>>>>> person to >>>>>>>>>> whom it is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>>>> error and >>>>>>>>>> the e-mail >>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>> Compliance HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>>>>>> sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please >>>>>>>>>> contact the >>>>>>>>>> sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -------------------------------------------------------------------------------- >>>>>>>>> >>>>>>>>> Joseph Dien, >>>>>>>>> Senior Research Scientist >>>>>>>>> University of Maryland >>>>>>>>> >>>>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>>>> mailto:jdien07@mac.commailto:jdien07@mac.com >>>>>>>>> mailto:jdien07@mac.com >>>>>>>>> mailto:jdien07@mac.com >>>>>>>>> mailto:jdien07@mac.com >>>>>>>>> Phone: 202-297-8117 >>>>>>>>> http://joedien.com// >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>>> The information in this e-mail is intended only for the >>>>>>>>> person to >>>>>>>>> whom it is >>>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>>> error and >>>>>>>>> the e-mail >>>>>>>>> contains patient information, please contact the Partners >>>>>>>>> Compliance >>>>>>>>> HelpLine at >>>>>>>>> http://www.partners.org/complianceline. If the e-mail was >>>>>>>>> sent to >>>>>>>>> you in error >>>>>>>>> but does not contain patient information, please contact the >>>>>>>>> sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Joseph Dien, >>>>>>>> Senior Research Scientist >>>>>>>> University of Maryland >>>>>>>> >>>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>>> mailto:jdien07@mac.commailto:jdien07@mac.com >>>>>>>> mailto:jdien07@mac.com >>>>>>>> mailto:jdien07@mac.com >>>>>>>> mailto:jdien07@mac.com >>>>>>>> Phone: 202-297-8117 >>>>>>>> http://joedien.com// >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> The information in this e-mail is intended only for the >>>>>>>> person to >>>>>>>> whom it is >>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>> error and >>>>>>>> the e-mail >>>>>>>> contains patient information, please contact the Partners >>>>>>>> Compliance >>>>>>>> HelpLine at >>>>>>>> http://www.partners.org/complianceline. If the e-mail was >>>>>>>> sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the >>>>>>>> sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------------- >>>>>>> >>>>>>> Joseph Dien, >>>>>>> Senior Research Scientist >>>>>>> University of Maryland >>>>>>> >>>>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.commailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> mailto:jdien07@mac.com >>>>>>> Phone: 202-297-8117 >>>>>>> http://joedien.com// >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> http://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: >>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> >>>>> Joseph Dien, >>>>> Senior Research Scientist >>>>> University of Maryland >>>>> >>>>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>>>> mailto:jdien07@mac.commailto:jdien07@mac.com >>>>> mailto:jdien07@mac.com >>>>> mailto:jdien07@mac.com >>>>> Phone: 202-297-8117 >>>>> http://joedien.com// >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> http://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail:jdien07@mac.com mailto:jdien07@mac.com >>> mailto:jdien07@mac.commailto:jdien07@mac.com >>> mailto:jdien07@mac.com >>> Phone: 202-297-8117 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >> http://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail:jdien07@mac.com > mailto:jdien07@mac.commailto:jdien07@mac.commailto:jdien07@mac.com > Phone: 202-297-8117 > http://joedien.com// > > > > > > > > > > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07@mac.com mailto:jdien07@mac.com Cell Phone: 202-297-8117 http://joedien.com
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Joseph Dien