hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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.
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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 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
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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 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
mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces
________________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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 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
-- 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/
not sure what is happening. Can you tar up the glmfit folder and send it to me at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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 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
-- 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/
this is the contrast file with the corrected and uncorrected map right? miracle
________________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is happening. Can you tar up the glmfit folder and send it to me at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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 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
-- 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/
-- 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/
also, i do require a username and password in order to send you the folder.
________________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is happening. Can you tar up the glmfit folder and send it to me at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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 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
-- 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/
-- 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/
Hello Douglas, I have sent the files to you. Thank you. Best, Miracle
________________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is happening. Can you tar up the glmfit folder and send it to me at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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 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
-- 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/
-- 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/
I meant the glmfit folder, which is
lh.firstsessionscore1.glmdir
On 03/25/2016 02:29 PM, Miracle Ozzoude wrote:
Hello Douglas, I have sent the files to you. Thank you. Best, Miracle
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is happening. Can you tar up the glmfit folder and send it to me at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ 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
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 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
-- 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/
-- 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/
Hello Douglas, I just sent you the current file. Thank you. Best, Miracle
________________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 9:35 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
I meant the glmfit folder, which is
lh.firstsessionscore1.glmdir
On 03/25/2016 02:29 PM, Miracle Ozzoude wrote:
Hello Douglas, I have sent the files to you. Thank you. Best, Miracle
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is happening. Can you tar up the glmfit folder and send it to me at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center 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 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/
-- 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/
-- 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/
What command did you use to visualize? There are no significant clusters so the brain should have been totally blank
On 03/25/2016 05:42 PM, Miracle Ozzoude wrote:
Hello Douglas, I just sent you the current file. Thank you. Best, Miracle
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 9:35 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
I meant the glmfit folder, which is
lh.firstsessionscore1.glmdir
On 03/25/2016 02:29 PM, Miracle Ozzoude wrote:
Hello Douglas, I have sent the files to you. Thank you. Best, Miracle
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is happening. Can you tar up the glmfit folder and send it to me at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces
From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Bruce and Douglas, This is what my design looks like. GroupDescriptorFile 1 Class Group1 Class Group2 Variables Age Firstsessionscore Input subj1 Group1 72 0.76 Input subj2 Group1 67 0.43 Input subj3 Group2 80 1.23 The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate if thickness correlates with the score removing the effects of group and age. The uncorrected map had blue and red colors in some areas of the brain. The blue color (thickness decreases withe score) seems unlike because i was expecting all red color(thickness increases with score). After I correcting for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the corrected map however, my entire left hemisphere was yellow with no clusters. how do i fix this?Thanks Miracle ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 24, 2016 6:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow
Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like?
On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? Also, when I tried to view the cluster summary for the entire hemisphere results, I did not see a single cluster unlike, the cluster summary for the precuneus results
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 9:48 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] whole hemisphere is yellow
Hi Miracle
have you tried changing the thresholds? What kinds of values are you seeing?
Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
> hello doug, > i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? > Best, > Miracle > _______________________________________________ > 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
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 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
-- 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/
-- 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/
-- 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@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Miracle Ozzoude