Courtney,
if i understand your question, i think one way to do that is to use qdec to draw a label on the blob of interest, and the run 'map label to subjects', which creates a label file in each subjects label dir, then you can run stats on that with mris_anatomical_stats.
(btw, i'm putting this answer on the list, as others may have better ideas.)
n.
On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi Nick
Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer.
A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance?
Thanks in advance! Courtney
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, December 30, 2010 2:44 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Interpreting results from Qdec
ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a plot of the data at that surface vertex will appear. the group will be apparent from that (say, demented group is thinner than non-demented group). this data is significance data (log p, so '2' is 0.01), so mean and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data of all subjects in the analysis, so you could extract mean and stdev from that.
ans. 2. - slide the 'annotation' opacity slider to show the annotation data (cortical parcellation). the ctrl left click will also put the region info for that vertex on the lower left of the display.
see also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
n.
On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi,
I’m currently running analyses in Qdec and have identified areas that show significant effects in my contrasts. I have two questions related to interpreting these results.
How can you interpret the effect in each “blob?” (i.e., whichgroup has a greater cortical surface area, etc.). Right now, all I know is that there is an effect in certain areas. Can you export this data to get means and standard errors?
Is there a way to localize where these effects are? E.g., atool that tells you this effect is located in __ area of the brain?
Thanks in advance
Courtney
Courtney Gallen
Post-baccalaureate IRTA
Neuroimaging Research Branch
National Institute on Drug Abuse (IRP)
251 Bayview Blvd
Suite 200
Baltimore, MD 21224
Tel: (443) 740-2631
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.
Hi Nick
I'm revisiting this issue and have a few more questions. First, I have a significant interaction between two variables on cortical volume. I drew a label on this ROI and ran mris_anatomical_stats on the label (thank you for that suggestion).
For stats in the output table file, is the column 'GrayVol' the same thing as the cortical volume I looked at in Qdec? I'm asking because when I export GrayVol values into SPSS, there is no longer a significant interaction between my variables (and if this ROI is significant after multiple comparisons across the brain, I'd expect the mean volume from the ROI to be very significant in SPSS).
Please let me know if my questions aren't clear. Thanks in advance Courtney
Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, January 13, 2011 3:08 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Interpreting results from Qdec
Courtney,
if i understand your question, i think one way to do that is to use qdec to draw a label on the blob of interest, and the run 'map label to subjects', which creates a label file in each subjects label dir, then you can run stats on that with mris_anatomical_stats.
(btw, i'm putting this answer on the list, as others may have better ideas.)
n.
On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi Nick
Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer.
A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance?
Thanks in advance! Courtney
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, December 30, 2010 2:44 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Interpreting results from Qdec
ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a plot of the data at that surface vertex will appear. the group will be apparent from that (say, demented group is thinner than non-demented group). this data is significance data (log p, so '2' is 0.01), so mean and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data of all subjects in the analysis, so you could extract mean and stdev from that.
ans. 2. - slide the 'annotation' opacity slider to show the annotation data (cortical parcellation). the ctrl left click will also put the region info for that vertex on the lower left of the display.
see also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
n.
On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi,
I’m currently running analyses in Qdec and have identified areas that show significant effects in my contrasts. I have two questions related to interpreting these results.
How can you interpret the effect in each “blob?” (i.e., whichgroup has a greater cortical surface area, etc.). Right now, all I know is that there is an effect in certain areas. Can you export this data to get means and standard errors?
Is there a way to localize where these effects are? E.g., atool that tells you this effect is located in __ area of the brain?
Thanks in advance
Courtney
Courtney Gallen
Post-baccalaureate IRTA
Neuroimaging Research Branch
National Institute on Drug Abuse (IRP)
251 Bayview Blvd
Suite 200
Baltimore, MD 21224
Tel: (443) 740-2631
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Courtney, did you transfer the label to each individual subject using mri_label2label? A better way to replicate your qdec results is to run mri_segstats on the input data to qdec (y.mgh usually). Specify the label with "--slabel subject hemi yourlabel". Also specify "--avgwf subjectdata.txt". This will create this text file with a list of the input data for each subject averaged over your label.
doug
Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi Nick
I'm revisiting this issue and have a few more questions. First, I have a significant interaction between two variables on cortical volume. I drew a label on this ROI and ran mris_anatomical_stats on the label (thank you for that suggestion).
For stats in the output table file, is the column 'GrayVol' the same thing as the cortical volume I looked at in Qdec? I'm asking because when I export GrayVol values into SPSS, there is no longer a significant interaction between my variables (and if this ROI is significant after multiple comparisons across the brain, I'd expect the mean volume from the ROI to be very significant in SPSS).
Please let me know if my questions aren't clear. Thanks in advance Courtney
Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, January 13, 2011 3:08 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Interpreting results from Qdec
Courtney,
if i understand your question, i think one way to do that is to use qdec to draw a label on the blob of interest, and the run 'map label to subjects', which creates a label file in each subjects label dir, then you can run stats on that with mris_anatomical_stats.
(btw, i'm putting this answer on the list, as others may have better ideas.)
n.
On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi Nick
Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer.
A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance?
Thanks in advance! Courtney
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, December 30, 2010 2:44 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Interpreting results from Qdec
ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a plot of the data at that surface vertex will appear. the group will be apparent from that (say, demented group is thinner than non-demented group). this data is significance data (log p, so '2' is 0.01), so mean and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data of all subjects in the analysis, so you could extract mean and stdev from that.
ans. 2. - slide the 'annotation' opacity slider to show the annotation data (cortical parcellation). the ctrl left click will also put the region info for that vertex on the lower left of the display.
see also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
n.
On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi,
I’m currently running analyses in Qdec and have identified areas that show significant effects in my contrasts. I have two questions related to interpreting these results.
How can you interpret the effect in each “blob?” (i.e., whichgroup has a greater cortical surface area, etc.). Right now, all I know is that there is an effect in certain areas. Can you export this data to get means and standard errors?
Is there a way to localize where these effects are? E.g., atool that tells you this effect is located in __ area of the brain?
Thanks in advance
Courtney
Courtney Gallen
Post-baccalaureate IRTA
Neuroimaging Research Branch
National Institute on Drug Abuse (IRP)
251 Bayview Blvd
Suite 200
Baltimore, MD 21224
Tel: (443) 740-2631
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.
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 for helping me with this!
First time around I did everything as is outlined in 'Define a Region of Interest' here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis.
I'll try your suggestion now. The input data would be something like ?h.volume.fwhm10.fsaverage.mgh, correct?
Thanks again Courtney
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, March 31, 2011 5:44 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: Nick Schmansky; Freesurfer Mailing List Subject: Re: [Freesurfer] Interpreting results from Qdec
Hi Courtney, did you transfer the label to each individual subject using mri_label2label? A better way to replicate your qdec results is to run mri_segstats on the input data to qdec (y.mgh usually). Specify the label with "--slabel subject hemi yourlabel". Also specify "--avgwf subjectdata.txt". This will create this text file with a list of the input data for each subject averaged over your label.
doug
Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi Nick
I'm revisiting this issue and have a few more questions. First, I have a significant interaction between two variables on cortical volume. I drew a label on this ROI and ran mris_anatomical_stats on the label (thank you for that suggestion).
For stats in the output table file, is the column 'GrayVol' the same thing as the cortical volume I looked at in Qdec? I'm asking because when I export GrayVol values into SPSS, there is no longer a significant interaction between my variables (and if this ROI is significant after multiple comparisons across the brain, I'd expect the mean volume from the ROI to be very significant in SPSS).
Please let me know if my questions aren't clear. Thanks in advance Courtney
Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, January 13, 2011 3:08 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Interpreting results from Qdec
Courtney,
if i understand your question, i think one way to do that is to use qdec to draw a label on the blob of interest, and the run 'map label to subjects', which creates a label file in each subjects label dir, then you can run stats on that with mris_anatomical_stats.
(btw, i'm putting this answer on the list, as others may have better ideas.)
n.
On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi Nick
Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer.
A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance?
Thanks in advance! Courtney
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, December 30, 2010 2:44 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Interpreting results from Qdec
ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a plot of the data at that surface vertex will appear. the group will be apparent from that (say, demented group is thinner than non-demented group). this data is significance data (log p, so '2' is 0.01), so mean and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data of all subjects in the analysis, so you could extract mean and stdev from that.
ans. 2. - slide the 'annotation' opacity slider to show the annotation data (cortical parcellation). the ctrl left click will also put the region info for that vertex on the lower left of the display.
see also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
n.
On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi,
I’m currently running analyses in Qdec and have identified areas that show significant effects in my contrasts. I have two questions related to interpreting these results.
How can you interpret the effect in each “blob?” (i.e., whichgroup has a greater cortical surface area, etc.). Right now, all I know is that there is an effect in certain areas. Can you export this data to get means and standard errors?
Is there a way to localize where these effects are? E.g., atool that tells you this effect is located in __ area of the brain?
Thanks in advance
Courtney
Courtney Gallen
Post-baccalaureate IRTA
Neuroimaging Research Branch
National Institute on Drug Abuse (IRP)
251 Bayview Blvd
Suite 200
Baltimore, MD 21224
Tel: (443) 740-2631
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.
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
yes, something like ?h.volume.fwhm10.fsaverage.mgh doug
Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi Doug
Thanks for helping me with this!
First time around I did everything as is outlined in 'Define a Region of Interest' here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis.
I'll try your suggestion now. The input data would be something like ?h.volume.fwhm10.fsaverage.mgh, correct?
Thanks again Courtney
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, March 31, 2011 5:44 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: Nick Schmansky; Freesurfer Mailing List Subject: Re: [Freesurfer] Interpreting results from Qdec
Hi Courtney, did you transfer the label to each individual subject using mri_label2label? A better way to replicate your qdec results is to run mri_segstats on the input data to qdec (y.mgh usually). Specify the label with "--slabel subject hemi yourlabel". Also specify "--avgwf subjectdata.txt". This will create this text file with a list of the input data for each subject averaged over your label.
doug
Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi Nick
I'm revisiting this issue and have a few more questions. First, I have a significant interaction between two variables on cortical volume. I drew a label on this ROI and ran mris_anatomical_stats on the label (thank you for that suggestion).
For stats in the output table file, is the column 'GrayVol' the same thing as the cortical volume I looked at in Qdec? I'm asking because when I export GrayVol values into SPSS, there is no longer a significant interaction between my variables (and if this ROI is significant after multiple comparisons across the brain, I'd expect the mean volume from the ROI to be very significant in SPSS).
Please let me know if my questions aren't clear. Thanks in advance Courtney
Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, January 13, 2011 3:08 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Interpreting results from Qdec
Courtney,
if i understand your question, i think one way to do that is to use qdec to draw a label on the blob of interest, and the run 'map label to subjects', which creates a label file in each subjects label dir, then you can run stats on that with mris_anatomical_stats.
(btw, i'm putting this answer on the list, as others may have better ideas.)
n.
On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi Nick
Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer.
A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance?
Thanks in advance! Courtney
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, December 30, 2010 2:44 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Interpreting results from Qdec
ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a plot of the data at that surface vertex will appear. the group will be apparent from that (say, demented group is thinner than non-demented group). this data is significance data (log p, so '2' is 0.01), so mean and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data of all subjects in the analysis, so you could extract mean and stdev from that.
ans. 2. - slide the 'annotation' opacity slider to show the annotation data (cortical parcellation). the ctrl left click will also put the region info for that vertex on the lower left of the display.
see also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
n.
On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote:
Hi,
I’m currently running analyses in Qdec and have identified areas that show significant effects in my contrasts. I have two questions related to interpreting these results.
How can you interpret the effect in each “blob?” (i.e., whichgroup has a greater cortical surface area, etc.). Right now, all I know is that there is an effect in certain areas. Can you export this data to get means and standard errors?
Is there a way to localize where these effects are? E.g., atool that tells you this effect is located in __ area of the brain?
Thanks in advance
Courtney
Courtney Gallen
Post-baccalaureate IRTA
Neuroimaging Research Branch
National Institute on Drug Abuse (IRP)
251 Bayview Blvd
Suite 200
Baltimore, MD 21224
Tel: (443) 740-2631
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.
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@nmr.mgh.harvard.edu
-
Douglas N Greve -
Gallen, Courtney (NIH/NIDA) [F] -
Nick Schmansky