Re: [HCP-Users] thresholding the data to p-value
Hi Tim,
After you turn the threshold on and set values for a high and a low threshold
for a map, selecting the "Show Data Inside Thresholds" button will display data
from the map that falls between those values and selecting "Show Data Outside
Thresholds" will display data from the map that have values lower than the low
threshold value and higher than the high threshold value. The purple shaded
region of histogram on the right should indicate the parts of the data that are
not being shown when the threshold is on.
Hope that's clear.
Best,
Jenn
Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>
From: hcp-users-boun...@humanconnectome.org
on behalf of Timothy Hendrickson
Sent: Wednesday, December 7, 2016 10:08:49 AM
To: Dierker, Donna
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] thresholding the data to p-value
Can you please clarify what the fields "Show Data Inside Thresholds" and "Show
Data Outside Thresholds" represent?
I'm confused by the wording...
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
On Tue, Dec 6, 2016 at 8:21 AM, Timothy Hendrickson
mailto:hendr...@umn.edu>> wrote:
Yes thank you!
On Dec 6, 2016 8:13 AM, "Dierker, Donna"
mailto:do...@wustl.edu>> wrote:
TimH - you mean this one?
On Jul 7, 2016, at 10:26 AM, Dierker, Donna
mailto:do...@wustl.edu>> wrote:
You need to adjust your overlay settings; see attached capture. Make sure
Threshold Type is set to On.
[cid:B7646768-2537-4828-8045-A6B646996AD8@wustl.edu]
On Dec 5, 2016, at 11:16 AM, Timothy Hendrickson
mailto:hendr...@umn.edu>> wrote:
Hi Donna,
Could you please re-attach the screen capture that you took for Vasudev? I
cannot find it...
I also am looking into how to observe significance levels with a threshold of
p<0.05.
Respectfully,
-Tim
You need to adjust your overlay settings; see attached capture. Make sure
Threshold Type is set to On.
From:
hcp-users-boun...@humanconnectome.org<http://humanconnectome.org>
<
hcp-users-boun...@humanconnectome.org<http://humanconnectome.org>
> on behalf of Dev vasu
<
vasudevamurthy.devulapa...@gmail.com<http://gmail.com>
>
Sent: Thursday, July 7, 2016 10:03:28 AM
To: Dierker, Donna
Cc: <
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
>
Subject: Re: [HCP-Users] thresholding the data to p-value
Dear madam,
I don't want to write to an ROI volume, i just want to observe activation
levels with a threshold of p<0.05.
Thanks
Vasudev
On 7 July 2016 at 16:31, Dierker, Donna
<
do...@wustl.edu<mailto:do...@wustl.edu><mailto:do...@wustl.edu<mailto:do...@wustl.edu>
>> wrote:
Hi Vasudev,
I'm pretty sure wb_view can display voxels within a range of values (inside
upper and lower limit), but I think you mean threshold and write a ROI volume.
For that, try:
wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile}
Donna
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org><mailto:hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
>
<
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org><mailto:hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
>>
on behalf of Dev vasu
<
vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurthy.devulapa...@gmail.com><mailto:vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurthy.devulapa...@gmail.com>
>>
Sent: Wednesday, July 6, 2016 12:04:50 PM
To: Harms, Michael;
<
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org><mailto:hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
>>
Subject: [HCP-Users] thresholding the data to p-value
Dear sir,
I would like to threshold my results to a p-value of p<0.05 and i couldn't do
it from workbench GUI, I can only threshold the data to percentage changes.
Please kindly let me know how i can possibly threshold the results to real
p-stats.
Thanks
Vasudev
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
___
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HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailm
Re: [HCP-Users] thresholding the data to p-value
Can you please clarify what the fields "Show Data Inside Thresholds" and
"Show Data Outside Thresholds" represent?
I'm confused by the wording...
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
On Tue, Dec 6, 2016 at 8:21 AM, Timothy Hendrickson
wrote:
> Yes thank you!
>
> On Dec 6, 2016 8:13 AM, "Dierker, Donna" wrote:
>
>> TimH - you mean this one?
>>
>> On Jul 7, 2016, at 10:26 AM, Dierker, Donna wrote:
>>
>> You need to adjust your overlay settings; see attached capture. Make
>> sure Threshold Type is set to On.
>>
>>
>>
>>
>> On Dec 5, 2016, at 11:16 AM, Timothy Hendrickson
>> wrote:
>>
>> Hi Donna,
>>
>> Could you please re-attach the screen capture that you took for Vasudev?
>> I cannot find it...
>> I also am looking into how to observe significance levels with a
>> threshold of p<0.05.
>>
>> Respectfully,
>>
>> -Tim
>>
>> You need to adjust your overlay settings; see attached capture. Make
>> sure
>> Threshold Type is set to On.
>>
>>
>> From:
>> hcp-users-boun...@humanconnectome.org
>>
>> <
>> hcp-users-boun...@humanconnectome.org
>> > on behalf of Dev vasu
>> <
>> vasudevamurthy.devulapa...@gmail.com
>> >
>> Sent: Thursday, July 7, 2016 10:03:28 AM
>> To: Dierker, Donna
>> Cc: <
>> hcp-users@humanconnectome.org
>> >
>> Subject: Re: [HCP-Users] thresholding the data to p-value
>>
>> Dear madam,
>>
>> I don't want to write to an ROI volume, i just want to observe activation
>> levels with a threshold of p<0.05.
>>
>>
>> Thanks
>> Vasudev
>>
>> On 7 July 2016 at 16:31, Dierker, Donna
>> <
>> do...@wustl.edu<mailto:do...@wustl.edu
>> >> wrote:
>>
>> Hi Vasudev,
>>
>>
>> I'm pretty sure wb_view can display voxels within a range of values
>> (inside
>> upper and lower limit), but I think you mean threshold and write a ROI
>> volume.
>> For that, try:
>>
>>
>> wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x
>> ${PstatFile}
>>
>>
>> Donna
>>
>> ________
>> From:
>>
>> hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun.
>> ..@humanconnectome.org
>> >
>>
>> <
>> hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun.
>> ..@humanconnectome.org
>> >>
>> on behalf of Dev vasu
>> <
>> vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurthy.
>> devulapa...@gmail.com
>> >>
>> Sent: Wednesday, July 6, 2016 12:04:50 PM
>> To: Harms, Michael;
>> <
>> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org
>> >>
>> Subject: [HCP-Users] thresholding the data to p-value
>>
>>
>>
>> Dear sir,
>>
>> I would like to threshold my results to a p-value of p<0.05 and i
>> couldn't do
>> it from workbench GUI, I can only threshold the data to percentage
>> changes.
>>
>> Please kindly let me know how i can possibly threshold the results to
>> real
>> p-stats.
>>
>>
>>
>> Thanks
>> Vasudev
>>
>>
>>
>>
>> Timothy Hendrickson
>> Department of Psychiatry
>> University of Minnesota
>> Office: 612-624-6441
>> Mobile: 507-259-3434 (texts okay)
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
>>
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] thresholding the data to p-value
Yes thank you!
On Dec 6, 2016 8:13 AM, "Dierker, Donna" wrote:
> TimH - you mean this one?
>
> On Jul 7, 2016, at 10:26 AM, Dierker, Donna wrote:
>
> You need to adjust your overlay settings; see attached capture. Make sure
> Threshold Type is set to On.
>
>
>
>
> On Dec 5, 2016, at 11:16 AM, Timothy Hendrickson wrote:
>
> Hi Donna,
>
> Could you please re-attach the screen capture that you took for Vasudev? I
> cannot find it...
> I also am looking into how to observe significance levels with a threshold
> of p<0.05.
>
> Respectfully,
>
> -Tim
>
> You need to adjust your overlay settings; see attached capture. Make sure
> Threshold Type is set to On.
>
>
> From:
> hcp-users-boun...@humanconnectome.org
>
> <
> hcp-users-boun...@humanconnectome.org
> > on behalf of Dev vasu
> <
> vasudevamurthy.devulapa...@gmail.com
> >
> Sent: Thursday, July 7, 2016 10:03:28 AM
> To: Dierker, Donna
> Cc: <
> hcp-users@humanconnectome.org
> >
> Subject: Re: [HCP-Users] thresholding the data to p-value
>
> Dear madam,
>
> I don't want to write to an ROI volume, i just want to observe activation
> levels with a threshold of p<0.05.
>
>
> Thanks
> Vasudev
>
> On 7 July 2016 at 16:31, Dierker, Donna
> <
> do...@wustl.edu<mailto:do...@wustl.edu
> >> wrote:
>
> Hi Vasudev,
>
>
> I'm pretty sure wb_view can display voxels within a range of values
> (inside
> upper and lower limit), but I think you mean threshold and write a ROI
> volume.
> For that, try:
>
>
> wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x
> ${PstatFile}
>
>
> Donna
>
>
> From:
>
> hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@
> humanconnectome.org
> >
>
> <
> hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@
> humanconnectome.org
> >>
> on behalf of Dev vasu
> <
> vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurth
> y.devulapa...@gmail.com
> >>
> Sent: Wednesday, July 6, 2016 12:04:50 PM
> To: Harms, Michael;
> <
> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org
> >>
> Subject: [HCP-Users] thresholding the data to p-value
>
>
>
> Dear sir,
>
> I would like to threshold my results to a p-value of p<0.05 and i couldn't
> do
> it from workbench GUI, I can only threshold the data to percentage changes.
>
> Please kindly let me know how i can possibly threshold the results to real
> p-stats.
>
>
>
> Thanks
> Vasudev
>
>
>
>
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Office: 612-624-6441
> Mobile: 507-259-3434 (texts okay)
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] thresholding the data to p-value
TimH - you mean this one?
On Jul 7, 2016, at 10:26 AM, Dierker, Donna
mailto:do...@wustl.edu>> wrote:
You need to adjust your overlay settings; see attached capture. Make sure
Threshold Type is set to On.
[cid:B7646768-2537-4828-8045-A6B646996AD8@wustl.edu]
On Dec 5, 2016, at 11:16 AM, Timothy Hendrickson
mailto:hendr...@umn.edu>> wrote:
Hi Donna,
Could you please re-attach the screen capture that you took for Vasudev? I
cannot find it...
I also am looking into how to observe significance levels with a threshold of
p<0.05.
Respectfully,
-Tim
You need to adjust your overlay settings; see attached capture. Make sure
Threshold Type is set to On.
From:
hcp-users-boun...@humanconnectome.org<http://humanconnectome.org>
<
hcp-users-boun...@humanconnectome.org<http://humanconnectome.org>
> on behalf of Dev vasu
<
vasudevamurthy.devulapa...@gmail.com<http://gmail.com>
>
Sent: Thursday, July 7, 2016 10:03:28 AM
To: Dierker, Donna
Cc: <
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
>
Subject: Re: [HCP-Users] thresholding the data to p-value
Dear madam,
I don't want to write to an ROI volume, i just want to observe activation
levels with a threshold of p<0.05.
Thanks
Vasudev
On 7 July 2016 at 16:31, Dierker, Donna
<
do...@wustl.edu<mailto:do...@wustl.edu
>> wrote:
Hi Vasudev,
I'm pretty sure wb_view can display voxels within a range of values (inside
upper and lower limit), but I think you mean threshold and write a ROI volume.
For that, try:
wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile}
Donna
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org
>
<
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org
>>
on behalf of Dev vasu
<
vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurthy.devulapa...@gmail.com
>>
Sent: Wednesday, July 6, 2016 12:04:50 PM
To: Harms, Michael;
<
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org
>>
Subject: [HCP-Users] thresholding the data to p-value
Dear sir,
I would like to threshold my results to a p-value of p<0.05 and i couldn't do
it from workbench GUI, I can only threshold the data to percentage changes.
Please kindly let me know how i can possibly threshold the results to real
p-stats.
Thanks
Vasudev
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] thresholding the data to p-value
Hi Donna,
Could you please re-attach the screen capture that you took for
Vasudev? I cannot find it...
I also am looking into how to observe significance levels with a
threshold of p<0.05.
Respectfully,
-Tim
You need to adjust your overlay settings; see attached capture. Make sure
Threshold Type is set to On.
From: hcp-users-boun...@humanconnectome.org
on behalf of Dev vasu
Sent: Thursday, July 7, 2016 10:03:28 AM
To: Dierker, Donna
Cc:
Subject: Re: [HCP-Users] thresholding the data to p-value
Dear madam,
I don't want to write to an ROI volume, i just want to observe activation
levels with a threshold of p<0.05.
Thanks
Vasudev
On 7 July 2016 at 16:31, Dierker, Donna
mailto:do...@wustl.edu >> wrote:
Hi Vasudev,
I'm pretty sure wb_view can display voxels within a range of values (inside
upper and lower limit), but I think you mean threshold and write a ROI volume.
For that, try:
wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile}
Donna
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org
>
mailto:hcp-users-boun...@humanconnectome.org
>>
on behalf of Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com
>>
Sent: Wednesday, July 6, 2016 12:04:50 PM
To: Harms, Michael;
mailto:hcp-users@humanconnectome.org
>>
Subject: [HCP-Users] thresholding the data to p-value
Dear sir,
I would like to threshold my results to a p-value of p<0.05 and i couldn't do
it from workbench GUI, I can only threshold the data to percentage changes.
Please kindly let me know how i can possibly threshold the results to real
p-stats.
Thanks
Vasudev
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] thresholding the data to p-value
You need to adjust your overlay settings; see attached capture. Make sure
Threshold Type is set to On.
From: hcp-users-boun...@humanconnectome.org
on behalf of Dev vasu
Sent: Thursday, July 7, 2016 10:03:28 AM
To: Dierker, Donna
Cc:
Subject: Re: [HCP-Users] thresholding the data to p-value
Dear madam,
I don't want to write to an ROI volume, i just want to observe activation
levels with a threshold of p<0.05.
Thanks
Vasudev
On 7 July 2016 at 16:31, Dierker, Donna
mailto:do...@wustl.edu>> wrote:
Hi Vasudev,
I'm pretty sure wb_view can display voxels within a range of values (inside
upper and lower limit), but I think you mean threshold and write a ROI volume.
For that, try:
wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile}
Donna
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Sent: Wednesday, July 6, 2016 12:04:50 PM
To: Harms, Michael;
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] thresholding the data to p-value
Dear sir,
I would like to threshold my results to a p-value of p<0.05 and i couldn't do
it from workbench GUI, I can only threshold the data to percentage changes.
Please kindly let me know how i can possibly threshold the results to real
p-stats.
Thanks
Vasudev
___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] thresholding the data to p-value
Dear madam,
I don't want to write to an ROI volume, i just want to observe activation
levels with a threshold of p<0.05.
Thanks
Vasudev
On 7 July 2016 at 16:31, Dierker, Donna wrote:
> Hi Vasudev,
>
>
> I'm pretty sure wb_view can display voxels within a range of values
> (inside upper and lower limit), but I think you mean threshold and write a
> ROI volume. For that, try:
>
>
> wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x
> ${PstatFile}
>
>
> Donna
> --
> *From:* hcp-users-boun...@humanconnectome.org <
> hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu <
> vasudevamurthy.devulapa...@gmail.com>
> *Sent:* Wednesday, July 6, 2016 12:04:50 PM
> *To:* Harms, Michael;
> *Subject:* [HCP-Users] thresholding the data to p-value
>
>
>
> Dear sir,
>
> I would like to threshold my results to a p-value of p<0.05 and i couldn't
> do it from workbench GUI, I can only threshold the data to percentage
> changes.
>
> Please kindly let me know how i can possibly threshold the results to real
> p-stats.
>
>
>
> Thanks
> Vasudev
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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Re: [HCP-Users] thresholding the data to p-value
Hi Vasudev,
I'm pretty sure wb_view can display voxels within a range of values (inside
upper and lower limit), but I think you mean threshold and write a ROI volume.
For that, try:
wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile}
Donna
From: hcp-users-boun...@humanconnectome.org
on behalf of Dev vasu
Sent: Wednesday, July 6, 2016 12:04:50 PM
To: Harms, Michael;
Subject: [HCP-Users] thresholding the data to p-value
Dear sir,
I would like to threshold my results to a p-value of p<0.05 and i couldn't do
it from workbench GUI, I can only threshold the data to percentage changes.
Please kindly let me know how i can possibly threshold the results to real
p-stats.
Thanks
Vasudev
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] thresholding the data to p-value
Dear sir, I would like to threshold my results to a p-value of p<0.05 and i couldn't do it from workbench GUI, I can only threshold the data to percentage changes. Please kindly let me know how i can possibly threshold the results to real p-stats. Thanks Vasudev ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
