Re: [Freesurfer] Volume comparison between groups and QDEC
On 5/11/17 3:25 PM, John Anderson wrote:
Hi Doug,
Why Qdec offer "volume, area, thickness ,...etc " in the drop down
menu "measures"?
In this menu there are many measures and I understand that I can run
surface based analysis depending on the choice of this drop down menu.
Is this Correct? Please see attached. Thank you for any clarification
volume in this context is "surface volume". The volume at a vertex is
the volume of the triangles (truncated pyramids) adjacent to the vertex.
So you are still doing map-based analysis
I'm not sure I follow. If I understand, you are finding sig diff in
PCG volume when you extract it the volume value for each subject
(scaled by
etiv) and process in SPSS. The part I don't understand is what you are
doing with QDEC. I don't think QDEC can be used to test ROI volume.
On 05/09/2017 05:58 PM, John Anderson wrote:
> Dear Dr Doug,
> I have two groups of subjects (80 patients and 40 controls). I
> analyzed the data using Freesurfer v6.0.
> I want to study the difference between the groups in "precentral gyrus
> volume". After "recon-all" I built Qdec table and I used Qdec to
> compute the comparison by including eTIV a covariate. After correcting
> the results using Monte Carlo simulation or adjusting for FDR I found
> no difference between the groups in volume neither in surface area.
>
> I adjusted the precentral gyrus volume values for eTIV using the
commands:
>
> mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm
> 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2017 mri_label_volume -eTIV
> $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm
> 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2024
>
> I extracted the adjusted volume values to SPSS then I ran box plots
> comparison between the groups and I found difference at (P<0.0001) Why
> Qdec doesn't show the difference between the groups although the p
> value is very small. What I am doing wrong in Qdec? Is it wrong to
> include eTIV a covariate?
>
> Thank you for any advice
> John
>
>
> ___
> 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
gr...@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
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Re: [Freesurfer] Volume comparison between groups and QDEC
Hi Doug,
Why Qdec offer "volume, area, thickness ,...etc " in the drop down menu
"measures"?
In this menu there are many measures and I understand that I can run surface
based analysis depending on the choice of this drop down menu. Is this Correct?
Please see attached. Thank you for any clarification
I'm not sure I follow. If I understand, you are finding sig diff in PCG volume
when you extract it the volume value for each subject (scaled by
etiv) and process in SPSS. The part I don't understand is what you are doing
with QDEC. I don't think QDEC can be used to test ROI volume.
On 05/09/2017 05:58 PM, John Anderson wrote:
> Dear Dr Doug,
> I have two groups of subjects (80 patients and 40 controls). I
> analyzed the data using Freesurfer v6.0.
> I want to study the difference between the groups in "precentral gyrus
> volume". After "recon-all" I built Qdec table and I used Qdec to
> compute the comparison by including eTIV a covariate. After correcting
> the results using Monte Carlo simulation or adjusting for FDR I found
> no difference between the groups in volume neither in surface area.
>
> I adjusted the precentral gyrus volume values for eTIV using the commands:
>
> mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm
> 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2017 mri_label_volume -eTIV
> $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm
> 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2024
>
> I extracted the adjusted volume values to SPSS then I ran box plots
> comparison between the groups and I found difference at (P<0.0001) Why
> Qdec doesn't show the difference between the groups although the p
> value is very small. What I am doing wrong in Qdec? Is it wrong to
> include eTIV a covariate?
>
> Thank you for any advice
> John
>
>
> ___
> 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
gr...@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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
���1�E�___
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Volume comparison between groups and QDEC
I'm not sure I follow. If I understand, you are finding sig diff in PCG
volume when you extract it the volume value for each subject (scaled by
etiv) and process in SPSS. The part I don't understand is what you are
doing with QDEC. I don't think QDEC can be used to test ROI volume.
On 05/09/2017 05:58 PM, John Anderson wrote:
> Dear Dr Doug,
> I have two groups of subjects (80 patients and 40 controls). I
> analyzed the data using Freesurfer v6.0.
> I want to study the difference between the groups in "precentral gyrus
> volume". After "recon-all" I built Qdec table and I used Qdec to
> compute the comparison by including eTIV a covariate. After correcting
> the results using Monte Carlo simulation or adjusting for FDR I found
> no difference between the groups in volume neither in surface area.
>
> I adjusted the precentral gyrus volume values for eTIV using the commands:
>
> mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm
> 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2017
> mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm
> 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2024
>
> I extracted the adjusted volume values to SPSS then I ran box plots
> comparison between the groups and I found difference at (P<0.0001)
> Why Qdec doesn't show the difference between the groups although the p
> value is very small. What I am doing wrong in Qdec? Is it wrong to
> include eTIV a covariate?
>
> Thank you for any advice
> John
>
>
> ___
> 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
gr...@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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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.
[Freesurfer] Volume comparison between groups and QDEC
Dear Dr Doug,
I have two groups of subjects (80 patients and 40 controls). I analyzed the
data using Freesurfer v6.0.
I want to study the difference between the groups in "precentral gyrus volume".
After "recon-all" I built Qdec table and I used Qdec to compute the comparison
by including eTIV a covariate. After correcting the results using Monte Carlo
simulation or adjusting for FDR I found no difference between the groups in
volume neither in surface area.
I adjusted the precentral gyrus volume values for eTIV using the commands:
mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm 1948
$SUBJECTS_DIR/${i}/mri/wmparc.mgz 2017
mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm 1948
$SUBJECTS_DIR/${i}/mri/wmparc.mgz 2024
I extracted the adjusted volume values to SPSS then I ran box plots comparison
between the groups and I found difference at (P<0.0001)
Why Qdec doesn't show the difference between the groups although the p value is
very small. What I am doing wrong in Qdec? Is it wrong to include eTIV a
covariate?
Thank you for any advice
John___
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.
