Hi Dough,
I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii)
Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast.
Thanks, Maryam
Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug
On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote:
Hi Dough,
I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to
- compare the values in each voxel with 0.5 instead of 0
- how to make it ignore the fact that I dont have variance for each
subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii)
Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast.
Thanks, Maryam
Hi Doug,
The output of the analysis is a volume with performance values in each voxel. the performance ranges between 0 to 1 and I want to see if across subjects there is any region with above chance performance (Chance is 0.5).
Maryam
On Mon, Oct 1, 2012 at 6:10 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug
On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote:
Hi Dough,
I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to
- compare the values in each voxel with 0.5 instead of 0
- how to make it ignore the fact that I dont have variance for each
subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii)
Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast.
Thanks, Maryam
-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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/**compliancelinehttp://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.
So it is only one volume? This won't work with mri_glmfit. glmfit needs to have a value for each subject so that it can compute the variance across subjects (needed to infer whether a difference from 0 is significant). I don't know of any software that will do it.
doug
On 10/1/12 6:59 PM, Maryam Vaziri Pashkam wrote:
Hi Doug,
The output of the analysis is a volume with performance values in each voxel. the performance ranges between 0 to 1 and I want to see if across subjects there is any region with above chance performance (Chance is 0.5).
Maryam
On Mon, Oct 1, 2012 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote: Hi Dough, I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii) Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast. Thanks, Maryam -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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.
Its one value per voxel per subject. So there is variane across subjects. and I want to see weather that value is different from 0.5 instead of 0.
Maryam
On Mon, Oct 1, 2012 at 8:54 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
So it is only one volume? This won't work with mri_glmfit. glmfit needs to have a value for each subject so that it can compute the variance across subjects (needed to infer whether a difference from 0 is significant). I don't know of any software that will do it.
doug
On 10/1/12 6:59 PM, Maryam Vaziri Pashkam wrote:
Hi Doug,
The output of the analysis is a volume with performance values in each voxel. the performance ranges between 0 to 1 and I want to see if across subjects there is any region with above chance performance (Chance is 0.5).
Maryam
On Mon, Oct 1, 2012 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug
On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote:
Hi Dough,
I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to
- compare the values in each voxel with 0.5 instead of 0
- how to make it ignore the fact that I dont have variance for each
subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii)
Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast.
Thanks, Maryam
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
You can subtract .5 from the volume (fscalc vol.mgh sub .5 -o vol-minus.5.mgh), then do a one-sample group mean (--osgm). You should do a permutation test to correct for multiple comparisons because the residuals definitely won't be Gaussian. doug
On 10/1/12 9:11 PM, Maryam Vaziri Pashkam wrote:
Its one value per voxel per subject. So there is variane across subjects. and I want to see weather that value is different from 0.5 instead of 0.
Maryam
On Mon, Oct 1, 2012 at 8:54 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
So it is only one volume? This won't work with mri_glmfit. glmfit needs to have a value for each subject so that it can compute the variance across subjects (needed to infer whether a difference from 0 is significant). I don't know of any software that will do it. doug On 10/1/12 6:59 PM, Maryam Vaziri Pashkam wrote:Hi Doug, The output of the analysis is a volume with performance values in each voxel. the performance ranges between 0 to 1 and I want to see if across subjects there is any region with above chance performance (Chance is 0.5). Maryam On Mon, Oct 1, 2012 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote: Hi Dough, I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii) Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast. Thanks, Maryam -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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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Douglas N Greve
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Maryam Vaziri Pashkam