Dear Mailing List,
I have just completed a QDEC (v5.1.0) analysis of the following design: Measure: thickness Smoothing (FWHM): 10 Hemisphere: lh 2 Discrete (Fixed Factors): group (2 levels, AtRisk & Control) and gene (2 levels, CC & TTorTC) 1 Nuisance Factos: age
On completion of the analysis, I have selected the following results in the display tab: "Does the average thickness, acounting for group, differ between CC and TTorTC?". I have then completed an FDR correction by clicking the "Set Using FDR" (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit "Find Clusters and Goto Max" and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2.
I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained?
Create a label of the cluster, then run
mri_segstats --slabel fsaverage lh /path/to/your.label --i y.mgh --id 1 --avgwf cluster.dat
where y.mgh is the file created by qdec in the qdec output folder and make sure to use the full path to the label. The output will be cluster.dat and it will have have a value for each subject. Does this work for you?
doug
On 08/20/2014 07:36 PM, Bronwyn Overs wrote:
Dear Mailing List,
I have just completed a QDEC (v5.1.0) analysis of the following design: Measure: thickness Smoothing (FWHM): 10 Hemisphere: lh 2 Discrete (Fixed Factors): group (2 levels, AtRisk & Control) and gene (2 levels, CC & TTorTC) 1 Nuisance Factos: age
On completion of the analysis, I have selected the following results in the display tab: "Does the average thickness, acounting for group, differ between CC and TTorTC?". I have then completed an FDR correction by clicking the "Set Using FDR" (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit "Find Clusters and Goto Max" and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2.
I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained?
--
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for your response. I was able to follow the steps you detailed and have ended up with a .dat file containing a list of values for each subject. Just a couple of follow up questions:
1. In my analysis I was using rh thickness as a dependent measure. So, do the individual values I have generated (using the below command) represent average thickness of the labelled area for each subject? 2. If I where using area or volume as the dependant measure, how would i generate label specific stats for those measures? 2. Are the generated stats measured in mm2? 3. What is the function of the flag "--id 1"?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 22/08/2014 3:27 am, Douglas N Greve wrote:
Create a label of the cluster, then run
mri_segstats --slabel fsaverage lh /path/to/your.label --i y.mgh --id 1 --avgwf cluster.dat
where y.mgh is the file created by qdec in the qdec output folder and make sure to use the full path to the label. The output will be cluster.dat and it will have have a value for each subject. Does this work for you?
doug
On 08/20/2014 07:36 PM, Bronwyn Overs wrote:
Dear Mailing List,
I have just completed a QDEC (v5.1.0) analysis of the following design: Measure: thickness Smoothing (FWHM): 10 Hemisphere: lh 2 Discrete (Fixed Factors): group (2 levels, AtRisk & Control) and gene (2 levels, CC & TTorTC) 1 Nuisance Factos: age
On completion of the analysis, I have selected the following results in the display tab: "Does the average thickness, acounting for group, differ between CC and TTorTC?". I have then completed an FDR correction by clicking the "Set Using FDR" (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit "Find Clusters and Goto Max" and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2.
I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained?
--
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 8/24/14 8:54 PM, Bronwyn Overs wrote:
Hi Doug,
Thanks for your response. I was able to follow the steps you detailed and have ended up with a .dat file containing a list of values for each subject. Just a couple of follow up questions:
- In my analysis I was using rh thickness as a dependent measure. So,
do the individual values I have generated (using the below command) represent average thickness of the labelled area for each subject?
Yes
- If I where using area or volume as the dependant measure, how would
i generate label specific stats for those measures?
Do you mean you want to run qdec using area or volume to generate a new label or that you want to get area and volume measures for the thickness-based label? If the latter, then run qdec with area/volume as the dependent measure making sure to spec a different output folder. This will create a new y.mgh file. Then run the mri_segstats command on it.
- Are the generated stats measured in mm2?
For thickness, they will be mm, area mm2, volume mm3.
- What is the function of the flag "--id 1"?
It just says to generate stats for the label. If you don't include that flag, then it will generate 2 numbers, one for all the vertices in the label, and one for all vertices not in the label doug
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 22/08/2014 3:27 am, Douglas N Greve wrote:
Create a label of the cluster, then run
mri_segstats --slabel fsaverage lh /path/to/your.label --i y.mgh --id 1 --avgwf cluster.dat
where y.mgh is the file created by qdec in the qdec output folder and make sure to use the full path to the label. The output will be cluster.dat and it will have have a value for each subject. Does this work for you?
doug
On 08/20/2014 07:36 PM, Bronwyn Overs wrote:
Dear Mailing List,
I have just completed a QDEC (v5.1.0) analysis of the following design: Measure: thickness Smoothing (FWHM): 10 Hemisphere: lh 2 Discrete (Fixed Factors): group (2 levels, AtRisk & Control) and gene (2 levels, CC & TTorTC) 1 Nuisance Factos: age
On completion of the analysis, I have selected the following results in the display tab: "Does the average thickness, acounting for group, differ between CC and TTorTC?". I have then completed an FDR correction by clicking the "Set Using FDR" (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit "Find Clusters and Goto Max" and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2.
I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained?
--
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks again for your prompt response. That is all very clear!
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 25/08/2014 12:21 pm, Douglas Greve wrote:
On 8/24/14 8:54 PM, Bronwyn Overs wrote:
Hi Doug,
Thanks for your response. I was able to follow the steps you detailed and have ended up with a .dat file containing a list of values for each subject. Just a couple of follow up questions:
- In my analysis I was using rh thickness as a dependent measure.
So, do the individual values I have generated (using the below command) represent average thickness of the labelled area for each subject?
Yes
- If I where using area or volume as the dependant measure, how
would i generate label specific stats for those measures?
Do you mean you want to run qdec using area or volume to generate a new label or that you want to get area and volume measures for the thickness-based label? If the latter, then run qdec with area/volume as the dependent measure making sure to spec a different output folder. This will create a new y.mgh file. Then run the mri_segstats command on it.
- Are the generated stats measured in mm2?
For thickness, they will be mm, area mm2, volume mm3.
- What is the function of the flag "--id 1"?
It just says to generate stats for the label. If you don't include that flag, then it will generate 2 numbers, one for all the vertices in the label, and one for all vertices not in the label doug
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 22/08/2014 3:27 am, Douglas N Greve wrote:
Create a label of the cluster, then run
mri_segstats --slabel fsaverage lh /path/to/your.label --i y.mgh --id 1 --avgwf cluster.dat
where y.mgh is the file created by qdec in the qdec output folder and make sure to use the full path to the label. The output will be cluster.dat and it will have have a value for each subject. Does this work for you?
doug
On 08/20/2014 07:36 PM, Bronwyn Overs wrote:
Dear Mailing List,
I have just completed a QDEC (v5.1.0) analysis of the following design: Measure: thickness Smoothing (FWHM): 10 Hemisphere: lh 2 Discrete (Fixed Factors): group (2 levels, AtRisk & Control) and gene (2 levels, CC & TTorTC) 1 Nuisance Factos: age
On completion of the analysis, I have selected the following results in the display tab: "Does the average thickness, acounting for group, differ between CC and TTorTC?". I have then completed an FDR correction by clicking the "Set Using FDR" (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit "Find Clusters and Goto Max" and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2.
I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained?
--
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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