Re: [HCP-Users] two maximum points using -metric-extrema

[Glasser, Matthew]

You can use wb_command -metric-merge to extract single maps from the file for 
use in the FSL command.

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Wednesday, August 29, 2018 at 2:10 AM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Hi, Tim.

Thank you very much for your detailed and helpful explanation. I finally 
understand how the two maps are stored in the .func.gii file.

The problem I met is that the FSL surf2surf command can only convert the format 
of one ROI map even though there are two. I haven't got their reply yet. Maybe 
I should ask again.

Best regards,
Xinyang


At 2018-08-29 12:36:17, "Timothy Coalson" 
mailto:tsc...@mst.edu>> wrote:
.func.gii files are simply arrays of values, where one dimension is the number 
of vertices in the surface, and the other is the number of maps in the file.  
Every vertex of the relevant surface gets a value.  The special case of "ROIs" 
is just that the values are all either 0 or 1.  So, while in the second ROI 
map, different vertices have values of 1 than the first ROI map, both maps span 
all vertices.

Surface coordinates are stored in .surf.gii files - neither .func.gii nor cifti 
files contain vertex coordinates.  Cifti does not support using a different set 
of brainordinates in different maps of the file - every map in a single cifti 
file uses the same set of brainordinates.  Internally cifti files are just 
another rectangular matrix, but used in a different way (and with different, 
more elaborate metadata).

Tim


On Tue, Aug 28, 2018 at 10:55 PM, Xinyang Liu 
mailto:xinyang_ie...@163.com>> wrote:
Dear experts,

Could I ask an additional question following my previous emails about the CIFTI 
data display?

If two surface ROIs of one .func.gii  file are displayed in separate maps of 
Connectome Workbench instead of simultaneously shown on one brain surface, does 
it mean the two ROIs are saved separately with two sets of global grayordinate 
coordinates? Thanks.

Best regards,
Xinyang


At 2018-08-27 11:16:42, "Glasser, Matthew" 
mailto:glass...@wustl.edu>> wrote:
Would have to ask that on the FSL list.

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Sunday, August 26, 2018 at 10:14 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>, HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Hi, Matt.
I saw the second ROI on WB as you said then. Thank you so much！

Then another left question is, when I use $FSL/surf2surf to change the 
.func.gii file (with two ROIs included) to .asc format, I only saw the  
coordinates information of one ROI (vertices with 1 values). The .func.gii 
showed vertex number of two ROIs, i.e. 127, 48. But when checking the 
transformed .asc file, I only found the ROI coordinates of the first ROI (127 
vertices), not the second.

Does it mean the two produced ROIs are saved separately in .func.gii, but the 
"surf2surf "command can only transform one of them to .asc?

Best regards,
Xinyang


At 2018-08-27 01:12:54, "Glasser, Matthew" 
mailto:glass...@wustl.edu>> wrote:
The other should be in the next map of the ROI file.

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Sunday, August 26, 2018 at 2:41 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>, HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Hi, Matt.
Sure. I attached two pictures and two produced GIFTI files here.

In data processing, I first used -metric-extrema to find the maximum point 
within a certain fMRI region. The "maximum_IPS.JPG" attached was among the 
condition that two maximum points were found (please see the two yellow points 
in the first attached picture). The corresponding GIFTI file is 
"L.maxima.func.gii".

Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to 
draw ROIs, the result only showed one created ROI based on one maximum point, 
as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" 
file is also attached.

I also used the -metric-stats to calculate the vertex number of the created 
ROI, but the result provided two values: 127, 48.

So I am quite confusing about what happened here.

Best regards,
Xinyang



At 2018-08-26 13:03:42, "Glasser, Matthew" 
mailto:glass...@wustl.edu>> wrote:
How about posting some screen captures so we know what is happening?

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson mail

Re: [HCP-Users] two maximum points using -metric-extrema

[Xinyang Liu]

Hi, Tim.


Thank you very much for your detailed and helpful explanation. I finally 
understand how the two maps are stored in the .func.gii file. 


The problem I met is that the FSL surf2surf command can only convert the format 
of one ROI map even though there are two. I haven't got their reply yet. Maybe 
I should ask again.


Best regards,
Xinyang



At 2018-08-29 12:36:17, "Timothy Coalson"  wrote:

.func.gii files are simply arrays of values, where one dimension is the number 
of vertices in the surface, and the other is the number of maps in the file.  
Every vertex of the relevant surface gets a value.  The special case of "ROIs" 
is just that the values are all either 0 or 1.  So, while in the second ROI 
map, different vertices have values of 1 than the first ROI map, both maps span 
all vertices.


Surface coordinates are stored in .surf.gii files - neither .func.gii nor cifti 
files contain vertex coordinates.  Cifti does not support using a different set 
of brainordinates in different maps of the file - every map in a single cifti 
file uses the same set of brainordinates.  Internally cifti files are just 
another rectangular matrix, but used in a different way (and with different, 
more elaborate metadata).


Tim




On Tue, Aug 28, 2018 at 10:55 PM, Xinyang Liu  wrote:

Dear experts,


Could I ask an additional question following my previous emails about the CIFTI 
data display? 


If two surface ROIs of one .func.gii  file are displayed in separate maps of 
Connectome Workbench instead of simultaneously shown on one brain surface, does 
it mean the two ROIs are saved separately with two sets of global grayordinate 
coordinates? Thanks.


Best regards,
Xinyang



At 2018-08-27 11:16:42, "Glasser, Matthew"  wrote:

Would have to ask that on the FSL list.


Matt.


From: Xinyang Liu 
Date: Sunday, August 26, 2018 at 10:14 PM
To: Matt Glasser 
Cc: Timothy Coalson , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Hi, Matt.
I saw the second ROI on WB as you said then. Thank you so much！


Then another left question is, when I use $FSL/surf2surf to change the 
.func.gii file (with two ROIs included) to .asc format, I only saw the  
coordinates information of one ROI (vertices with 1 values). The .func.gii 
showed vertex number of two ROIs, i.e. 127, 48. But when checking the 
transformed .asc file, I only found the ROI coordinates of the first ROI (127 
vertices), not the second. 


Does it mean the two produced ROIs are saved separately in .func.gii, but the 
"surf2surf "command can only transform one of them to .asc?



Best regards,
Xinyang



At 2018-08-27 01:12:54, "Glasser, Matthew"  wrote:

The other should be in the next map of the ROI file.


Matt.


From: Xinyang Liu 
Date: Sunday, August 26, 2018 at 2:41 AM
To: Matt Glasser 
Cc: Timothy Coalson , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Hi, Matt.
Sure. I attached two pictures and two produced GIFTI files here. 


In data processing, I first used -metric-extrema to find the maximum point 
within a certain fMRI region. The "maximum_IPS.JPG" attached was among the 
condition that two maximum points were found (please see the two yellow points 
in the first attached picture). The corresponding GIFTI file is 
"L.maxima.func.gii".


Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to 
draw ROIs, the result only showed one created ROI based on one maximum point, 
as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" 
file is also attached.


I also used the -metric-stats to calculate the vertex number of the created 
ROI, but the result provided two values: 127, 48.


So I am quite confusing about what happened here.


Best regards,
Xinyang





At 2018-08-26 13:03:42, "Glasser, Matthew"  wrote:

How about posting some screen captures so we know what is happening?


Matt.


From: Xinyang Liu 
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson 
Cc: Matt Glasser , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Dear Tim, dear Matt,


Thank you very much for your helpful answers.


Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file). 


Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connecto

Re: [HCP-Users] two maximum points using -metric-extrema

[Timothy Coalson]

.func.gii files are simply arrays of values, where one dimension is the
number of vertices in the surface, and the other is the number of maps in
the file.  Every vertex of the relevant surface gets a value.  The special
case of "ROIs" is just that the values are all either 0 or 1.  So, while in
the second ROI map, different vertices have values of 1 than the first ROI
map, both maps span all vertices.

Surface coordinates are stored in .surf.gii files - neither .func.gii nor
cifti files contain vertex coordinates.  Cifti does not support using a
different set of brainordinates in different maps of the file - every map
in a single cifti file uses the same set of brainordinates.  Internally
cifti files are just another rectangular matrix, but used in a different
way (and with different, more elaborate metadata).

Tim


On Tue, Aug 28, 2018 at 10:55 PM, Xinyang Liu  wrote:

> Dear experts,
>
> Could I ask an additional question following my previous emails about the
> CIFTI data display?
>
> If two surface ROIs of one *.func.gii*  file are displayed in separate
> maps of Connectome Workbench instead of simultaneously shown on one brain
> surface, does it mean the two ROIs are saved separately with two sets of
> global grayordinate coordinates? Thanks.
>
> Best regards,
> Xinyang
>
>
> At 2018-08-27 11:16:42, "Glasser, Matthew"  wrote:
>
> Would have to ask that on the FSL list.
>
> Matt.
>
> From: Xinyang Liu 
> Date: Sunday, August 26, 2018 at 10:14 PM
> To: Matt Glasser 
> Cc: Timothy Coalson , HCP 讨论组 <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] two maximum points using -metric-extrema
>
> Hi, Matt.
> I saw the second ROI on WB as you said then. Thank you so much！
>
> Then another left question is, when I use $FSL/*surf2surf* to change the *
> .func.gii *file (with two ROIs included) to *.asc* format, I only saw the
> coordinates information of one ROI (vertices with 1 values). The
> .func.gii showed vertex number of two ROIs, i.e. 127, 48. But when checking
> the transformed .asc file, I only found the ROI coordinates of the first
> ROI (127 vertices), not the second.
>
> Does it mean the two produced ROIs are saved separately in .func.gii, but
> the "surf2surf "command can only transform one of them to .asc?
>
> Best regards,
> Xinyang
>
>
> At 2018-08-27 01:12:54, "Glasser, Matthew"  wrote:
>
> The other should be in the next map of the ROI file.
>
> Matt.
>
> From: Xinyang Liu 
> Date: Sunday, August 26, 2018 at 2:41 AM
> To: Matt Glasser 
> Cc: Timothy Coalson , HCP 讨论组 <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] two maximum points using -metric-extrema
>
> Hi, Matt.
> Sure. I attached two pictures and two produced GIFTI files here.
>
> In data processing, I first used *-metric-extrema* to find the maximum
> point within a certain fMRI region. The "maximum_IPS.JPG" attached was
> among the condition that two maximum points were found (please see the two
> yellow points in the first attached picture). The corresponding GIFTI file
> is "L.maxima.func.gii".
>
> Then I continued using the "L.maxima.func.gii" and
> *-metric-rois-from-extrema* to draw ROIs, the result only showed one
> created ROI based on one maximum point, as the second picture (IPS_ROI.JPG)
> attached. The "TARGET_ROI_IPS_L.func.gii" file is also attached.
>
> I also used the *-metric-stats* to calculate the vertex number of the
> created ROI, but the result provided two values: 127, 48.
>
> So I am quite confusing about what happened here.
>
> Best regards,
> Xinyang
>
>
>
> At 2018-08-26 13:03:42, "Glasser, Matthew"  wrote:
>
> How about posting some screen captures so we know what is happening?
>
> Matt.
>
> From: Xinyang Liu 
> Date: Saturday, August 25, 2018 at 11:51 PM
> To: Timothy Coalson 
> Cc: Matt Glasser , HCP 讨论组 <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] two maximum points using -metric-extrema
>
> Dear Tim, dear Matt,
>
> Thank you very much for your helpful answers.
>
> Sorry that I may not described very clearly before. As Tim mentioned, we
> used the -metric-extrema to find the maximum point within a certain region
> (produce "maxima.func.gii" file) and then use the -metric-rois-from-extrema
> to draw ROIs (produced "ROI.func.gii" file).
>
> Then there is a contradictory thing emerged. When we used "wb_command
> -metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a
> few results showed  two values, which might indicate two ROIs based on the
> two maximum points. We checked the maxima.func.gii f

Re: [HCP-Users] two maximum points using -metric-extrema

[Xinyang Liu]

Dear experts,


Could I ask an additional question following my previous emails about the CIFTI 
data display? 


If two surface ROIs of one .func.gii  file are displayed in separate maps of 
Connectome Workbench instead of simultaneously shown on one brain surface, does 
it mean the two ROIs are saved separately with two sets of global grayordinate 
coordinates? Thanks.


Best regards,
Xinyang



At 2018-08-27 11:16:42, "Glasser, Matthew"  wrote:

Would have to ask that on the FSL list.


Matt.


From: Xinyang Liu 
Date: Sunday, August 26, 2018 at 10:14 PM
To: Matt Glasser 
Cc: Timothy Coalson , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Hi, Matt.
I saw the second ROI on WB as you said then. Thank you so much！


Then another left question is, when I use $FSL/surf2surf to change the 
.func.gii file (with two ROIs included) to .asc format, I only saw the  
coordinates information of one ROI (vertices with 1 values). The .func.gii 
showed vertex number of two ROIs, i.e. 127, 48. But when checking the 
transformed .asc file, I only found the ROI coordinates of the first ROI (127 
vertices), not the second. 


Does it mean the two produced ROIs are saved separately in .func.gii, but the 
"surf2surf "command can only transform one of them to .asc?



Best regards,
Xinyang



At 2018-08-27 01:12:54, "Glasser, Matthew"  wrote:

The other should be in the next map of the ROI file.


Matt.


From: Xinyang Liu 
Date: Sunday, August 26, 2018 at 2:41 AM
To: Matt Glasser 
Cc: Timothy Coalson , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Hi, Matt.
Sure. I attached two pictures and two produced GIFTI files here. 


In data processing, I first used -metric-extrema to find the maximum point 
within a certain fMRI region. The "maximum_IPS.JPG" attached was among the 
condition that two maximum points were found (please see the two yellow points 
in the first attached picture). The corresponding GIFTI file is 
"L.maxima.func.gii".


Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to 
draw ROIs, the result only showed one created ROI based on one maximum point, 
as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" 
file is also attached.


I also used the -metric-stats to calculate the vertex number of the created 
ROI, but the result provided two values: 127, 48.


So I am quite confusing about what happened here.


Best regards,
Xinyang





At 2018-08-26 13:03:42, "Glasser, Matthew"  wrote:

How about posting some screen captures so we know what is happening?


Matt.


From: Xinyang Liu 
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson 
Cc: Matt Glasser , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Dear Tim, dear Matt,


Thank you very much for your helpful answers.


Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file). 


Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connectome Workbench, we only saw one target ROI drawn on 
the brain surface. This confused us a lot. We don't know whether there were one 
or two ROIs produced. Do you have any suggestions about that? Thanks.


Best regards,
Xinyang





At 2018-08-25 04:16:48, "Timothy Coalson"  wrote:

The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or 
-1 based on if they are a local maximum or minimum.  By default, if there are 
two equal values that are closer than the search range, then *neither* of them 
will be identified as an extrema.  If they are further then the search range, 
then both may be extrema.


The -consolidate-mode acts somewhat differently - if two equal values are 
touching, neither is treated as an initial extrema, but as long as there is at 
least one vertex separating them, they may both be treated as initial extrema.  
After the initial extrema are found, all extrema that are close to other 
extrema are "consolidated" together.  The details are somewhat complicated, and 
it was implemented by request of others, it is not something that we use.


Tim




On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu  wrote:

Hi, Matt. Thank you very much for your reply.


The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum poin

Re: [HCP-Users] two maximum points using -metric-extrema

[Xinyang Liu]

Ok, I will do that. Thanks. :)


Best,
Xinyang


At 2018-08-27 11:16:42, "Glasser, Matthew"  wrote:

Would have to ask that on the FSL list.


Matt.


From: Xinyang Liu 
Date: Sunday, August 26, 2018 at 10:14 PM
To: Matt Glasser 
Cc: Timothy Coalson , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Hi, Matt.
I saw the second ROI on WB as you said then. Thank you so much！


Then another left question is, when I use $FSL/surf2surf to change the 
.func.gii file (with two ROIs included) to .asc format, I only saw the  
coordinates information of one ROI (vertices with 1 values). The .func.gii 
showed vertex number of two ROIs, i.e. 127, 48. But when checking the 
transformed .asc file, I only found the ROI coordinates of the first ROI (127 
vertices), not the second. 


Does it mean the two produced ROIs are saved separately in .func.gii, but the 
"surf2surf "command can only transform one of them to .asc?



Best regards,
Xinyang



At 2018-08-27 01:12:54, "Glasser, Matthew"  wrote:

The other should be in the next map of the ROI file.


Matt.


From: Xinyang Liu 
Date: Sunday, August 26, 2018 at 2:41 AM
To: Matt Glasser 
Cc: Timothy Coalson , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Hi, Matt.
Sure. I attached two pictures and two produced GIFTI files here. 


In data processing, I first used -metric-extrema to find the maximum point 
within a certain fMRI region. The "maximum_IPS.JPG" attached was among the 
condition that two maximum points were found (please see the two yellow points 
in the first attached picture). The corresponding GIFTI file is 
"L.maxima.func.gii".


Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to 
draw ROIs, the result only showed one created ROI based on one maximum point, 
as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" 
file is also attached.


I also used the -metric-stats to calculate the vertex number of the created 
ROI, but the result provided two values: 127, 48.


So I am quite confusing about what happened here.


Best regards,
Xinyang





At 2018-08-26 13:03:42, "Glasser, Matthew"  wrote:

How about posting some screen captures so we know what is happening?


Matt.


From: Xinyang Liu 
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson 
Cc: Matt Glasser , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Dear Tim, dear Matt,


Thank you very much for your helpful answers.


Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file). 


Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connectome Workbench, we only saw one target ROI drawn on 
the brain surface. This confused us a lot. We don't know whether there were one 
or two ROIs produced. Do you have any suggestions about that? Thanks.


Best regards,
Xinyang





At 2018-08-25 04:16:48, "Timothy Coalson"  wrote:

The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or 
-1 based on if they are a local maximum or minimum.  By default, if there are 
two equal values that are closer than the search range, then *neither* of them 
will be identified as an extrema.  If they are further then the search range, 
then both may be extrema.


The -consolidate-mode acts somewhat differently - if two equal values are 
touching, neither is treated as an initial extrema, but as long as there is at 
least one vertex separating them, they may both be treated as initial extrema.  
After the initial extrema are found, all extrema that are close to other 
extrema are "consolidated" together.  The details are somewhat complicated, and 
it was implemented by request of others, it is not something that we use.


Tim




On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu  wrote:

Hi, Matt. Thank you very much for your reply.


The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum points with the same value, they were controlled in a 
limited distance and therefore, the final drawn ROI is a combined region of two 
drawings instead of two separate ones? 


Because the problem is that, when I count the total vertex number for each 
created ROI using -metric-stats, a few results showed two values for one ROI.  
I am wondering w

Re: [HCP-Users] two maximum points using -metric-extrema

[Glasser, Matthew]

Would have to ask that on the FSL list.

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Sunday, August 26, 2018 at 10:14 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>, HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Hi, Matt.
I saw the second ROI on WB as you said then. Thank you so much！

Then another left question is, when I use $FSL/surf2surf to change the 
.func.gii file (with two ROIs included) to .asc format, I only saw the  
coordinates information of one ROI (vertices with 1 values). The .func.gii 
showed vertex number of two ROIs, i.e. 127, 48. But when checking the 
transformed .asc file, I only found the ROI coordinates of the first ROI (127 
vertices), not the second.

Does it mean the two produced ROIs are saved separately in .func.gii, but the 
"surf2surf "command can only transform one of them to .asc?

Best regards,
Xinyang


At 2018-08-27 01:12:54, "Glasser, Matthew" 
mailto:glass...@wustl.edu>> wrote:
The other should be in the next map of the ROI file.

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Sunday, August 26, 2018 at 2:41 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>, HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Hi, Matt.
Sure. I attached two pictures and two produced GIFTI files here.

In data processing, I first used -metric-extrema to find the maximum point 
within a certain fMRI region. The "maximum_IPS.JPG" attached was among the 
condition that two maximum points were found (please see the two yellow points 
in the first attached picture). The corresponding GIFTI file is 
"L.maxima.func.gii".

Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to 
draw ROIs, the result only showed one created ROI based on one maximum point, 
as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" 
file is also attached.

I also used the -metric-stats to calculate the vertex number of the created 
ROI, but the result provided two values: 127, 48.

So I am quite confusing about what happened here.

Best regards,
Xinyang



At 2018-08-26 13:03:42, "Glasser, Matthew" 
mailto:glass...@wustl.edu>> wrote:
How about posting some screen captures so we know what is happening?

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Dear Tim, dear Matt,

Thank you very much for your helpful answers.

Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file).

Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connectome Workbench, we only saw one target ROI drawn on 
the brain surface. This confused us a lot. We don't know whether there were one 
or two ROIs produced. Do you have any suggestions about that? Thanks.

Best regards,
Xinyang



At 2018-08-25 04:16:48, "Timothy Coalson" 
mailto:tsc...@mst.edu>> wrote:
The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or 
-1 based on if they are a local maximum or minimum.  By default, if there are 
two equal values that are closer than the search range, then *neither* of them 
will be identified as an extrema.  If they are further then the search range, 
then both may be extrema.

The -consolidate-mode acts somewhat differently - if two equal values are 
touching, neither is treated as an initial extrema, but as long as there is at 
least one vertex separating them, they may both be treated as initial extrema.  
After the initial extrema are found, all extrema that are close to other 
extrema are "consolidated" together.  The details are somewhat complicated, and 
it was implemented by request of others, it is not something that we use.

Tim


On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu 
mailto:xinyang_ie...@163.com>> wrote:
Hi, Matt. Thank you very much for your reply.

The extreme point was searched in a certain su

Re: [HCP-Users] two maximum points using -metric-extrema

[Xinyang Liu]

Hi, Matt.
I saw the second ROI on WB as you said then. Thank you so much！


Then another left question is, when I use $FSL/surf2surf to change the 
.func.gii file (with two ROIs included) to .asc format, I only saw the  
coordinates information of one ROI (vertices with 1 values). The .func.gii 
showed vertex number of two ROIs, i.e. 127, 48. But when checking the 
transformed .asc file, I only found the ROI coordinates of the first ROI (127 
vertices), not the second. 


Does it mean the two produced ROIs are saved separately in .func.gii, but the 
"surf2surf "command can only transform one of them to .asc?



Best regards,
Xinyang



At 2018-08-27 01:12:54, "Glasser, Matthew"  wrote:

The other should be in the next map of the ROI file.


Matt.


From: Xinyang Liu 
Date: Sunday, August 26, 2018 at 2:41 AM
To: Matt Glasser 
Cc: Timothy Coalson , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Hi, Matt.
Sure. I attached two pictures and two produced GIFTI files here. 


In data processing, I first used -metric-extrema to find the maximum point 
within a certain fMRI region. The "maximum_IPS.JPG" attached was among the 
condition that two maximum points were found (please see the two yellow points 
in the first attached picture). The corresponding GIFTI file is 
"L.maxima.func.gii".


Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to 
draw ROIs, the result only showed one created ROI based on one maximum point, 
as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" 
file is also attached.


I also used the -metric-stats to calculate the vertex number of the created 
ROI, but the result provided two values: 127, 48.


So I am quite confusing about what happened here.


Best regards,
Xinyang





At 2018-08-26 13:03:42, "Glasser, Matthew"  wrote:

How about posting some screen captures so we know what is happening?


Matt.


From: Xinyang Liu 
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson 
Cc: Matt Glasser , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Dear Tim, dear Matt,


Thank you very much for your helpful answers.


Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file). 


Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connectome Workbench, we only saw one target ROI drawn on 
the brain surface. This confused us a lot. We don't know whether there were one 
or two ROIs produced. Do you have any suggestions about that? Thanks.


Best regards,
Xinyang





At 2018-08-25 04:16:48, "Timothy Coalson"  wrote:

The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or 
-1 based on if they are a local maximum or minimum.  By default, if there are 
two equal values that are closer than the search range, then *neither* of them 
will be identified as an extrema.  If they are further then the search range, 
then both may be extrema.


The -consolidate-mode acts somewhat differently - if two equal values are 
touching, neither is treated as an initial extrema, but as long as there is at 
least one vertex separating them, they may both be treated as initial extrema.  
After the initial extrema are found, all extrema that are close to other 
extrema are "consolidated" together.  The details are somewhat complicated, and 
it was implemented by request of others, it is not something that we use.


Tim




On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu  wrote:

Hi, Matt. Thank you very much for your reply.


The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum points with the same value, they were controlled in a 
limited distance and therefore, the final drawn ROI is a combined region of two 
drawings instead of two separate ones? 


Because the problem is that, when I count the total vertex number for each 
created ROI using -metric-stats, a few results showed two values for one ROI.  
I am wondering why this happen and how to deal with that.


Best regards,
Xinyang



At 2018-08-24 19:14:56, "Glasser, Matthew"  wrote:

I believe there is a configurable setting that sets the minimum distance 
between extrema.  It is a local min/max that is found.


Matt.


From:  on behalf of Xinyang Liu 

Date: Friday, August 24, 2018 at 4:21 AM

Re: [HCP-Users] two maximum points using -metric-extrema

[Glasser, Matthew]

The other should be in the next map of the ROI file.

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Sunday, August 26, 2018 at 2:41 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>, HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Hi, Matt.
Sure. I attached two pictures and two produced GIFTI files here.

In data processing, I first used -metric-extrema to find the maximum point 
within a certain fMRI region. The "maximum_IPS.JPG" attached was among the 
condition that two maximum points were found (please see the two yellow points 
in the first attached picture). The corresponding GIFTI file is 
"L.maxima.func.gii".

Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to 
draw ROIs, the result only showed one created ROI based on one maximum point, 
as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" 
file is also attached.

I also used the -metric-stats to calculate the vertex number of the created 
ROI, but the result provided two values: 127, 48.

So I am quite confusing about what happened here.

Best regards,
Xinyang



At 2018-08-26 13:03:42, "Glasser, Matthew" 
mailto:glass...@wustl.edu>> wrote:
How about posting some screen captures so we know what is happening?

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Dear Tim, dear Matt,

Thank you very much for your helpful answers.

Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file).

Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connectome Workbench, we only saw one target ROI drawn on 
the brain surface. This confused us a lot. We don't know whether there were one 
or two ROIs produced. Do you have any suggestions about that? Thanks.

Best regards,
Xinyang



At 2018-08-25 04:16:48, "Timothy Coalson" 
mailto:tsc...@mst.edu>> wrote:
The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or 
-1 based on if they are a local maximum or minimum.  By default, if there are 
two equal values that are closer than the search range, then *neither* of them 
will be identified as an extrema.  If they are further then the search range, 
then both may be extrema.

The -consolidate-mode acts somewhat differently - if two equal values are 
touching, neither is treated as an initial extrema, but as long as there is at 
least one vertex separating them, they may both be treated as initial extrema.  
After the initial extrema are found, all extrema that are close to other 
extrema are "consolidated" together.  The details are somewhat complicated, and 
it was implemented by request of others, it is not something that we use.

Tim


On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu 
mailto:xinyang_ie...@163.com>> wrote:
Hi, Matt. Thank you very much for your reply.

The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum points with the same value, they were controlled in a 
limited distance and therefore, the final drawn ROI is a combined region of two 
drawings instead of two separate ones?

Because the problem is that, when I count the total vertex number for each 
created ROI using -metric-stats, a few results showed two values for one ROI.  
I am wondering why this happen and how to deal with that.

Best regards,
Xinyang


At 2018-08-24 19:14:56, "Glasser, Matthew" 
mailto:glass...@wustl.edu>> wrote:
I believe there is a configurable setting that sets the minimum distance 
between extrema.  It is a local min/max that is found.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Friday, August 24, 2018 at 4:21 AM
To: HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] two maximum points using -metric-extrema

Dear HCP experts,

Hi. When using workbench command "-metric-extrema"

Re: [HCP-Users] two maximum points using -metric-extrema

[Xinyang Liu]

Hi, Matt.
Sure. I attached two pictures and two produced GIFTI files here. 


In data processing, I first used -metric-extrema to find the maximum point 
within a certain fMRI region. The "maximum_IPS.JPG" attached was among the 
condition that two maximum points were found (please see the two yellow points 
in the first attached picture). The corresponding GIFTI file is 
"L.maxima.func.gii".


Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to 
draw ROIs, the result only showed one created ROI based on one maximum point, 
as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" 
file is also attached.


I also used the -metric-stats to calculate the vertex number of the created 
ROI, but the result provided two values: 127, 48.


So I am quite confusing about what happened here.


Best regards,
Xinyang





At 2018-08-26 13:03:42, "Glasser, Matthew"  wrote:

How about posting some screen captures so we know what is happening?


Matt.


From: Xinyang Liu 
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson 
Cc: Matt Glasser , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Dear Tim, dear Matt,


Thank you very much for your helpful answers.


Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file). 


Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connectome Workbench, we only saw one target ROI drawn on 
the brain surface. This confused us a lot. We don't know whether there were one 
or two ROIs produced. Do you have any suggestions about that? Thanks.


Best regards,
Xinyang





At 2018-08-25 04:16:48, "Timothy Coalson"  wrote:

The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or 
-1 based on if they are a local maximum or minimum.  By default, if there are 
two equal values that are closer than the search range, then *neither* of them 
will be identified as an extrema.  If they are further then the search range, 
then both may be extrema.


The -consolidate-mode acts somewhat differently - if two equal values are 
touching, neither is treated as an initial extrema, but as long as there is at 
least one vertex separating them, they may both be treated as initial extrema.  
After the initial extrema are found, all extrema that are close to other 
extrema are "consolidated" together.  The details are somewhat complicated, and 
it was implemented by request of others, it is not something that we use.


Tim




On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu  wrote:

Hi, Matt. Thank you very much for your reply.


The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum points with the same value, they were controlled in a 
limited distance and therefore, the final drawn ROI is a combined region of two 
drawings instead of two separate ones? 


Because the problem is that, when I count the total vertex number for each 
created ROI using -metric-stats, a few results showed two values for one ROI.  
I am wondering why this happen and how to deal with that.


Best regards,
Xinyang



At 2018-08-24 19:14:56, "Glasser, Matthew"  wrote:

I believe there is a configurable setting that sets the minimum distance 
between extrema.  It is a local min/max that is found.


Matt.


From:  on behalf of Xinyang Liu 

Date: Friday, August 24, 2018 at 4:21 AM
To: HCP 讨论组 
Subject: [HCP-Users] two maximum points using -metric-extrema



Dear HCP experts,


Hi. When using workbench command "-metric-extrema" to draw ROI around the 
maximum point of the fMRI surface region, what would happen if there are two 
maximum points? Will the software keep both of them or only keep one? Thanks a 
lot.


Best regards,
Xinyang






 

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HCP-Users mailing list
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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 sende

Re: [HCP-Users] two maximum points using -metric-extrema

[Glasser, Matthew]

How about posting some screen captures so we know what is happening?

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Dear Tim, dear Matt,

Thank you very much for your helpful answers.

Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file).

Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connectome Workbench, we only saw one target ROI drawn on 
the brain surface. This confused us a lot. We don't know whether there were one 
or two ROIs produced. Do you have any suggestions about that? Thanks.

Best regards,
Xinyang



At 2018-08-25 04:16:48, "Timothy Coalson" 
mailto:tsc...@mst.edu>> wrote:
The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or 
-1 based on if they are a local maximum or minimum.  By default, if there are 
two equal values that are closer than the search range, then *neither* of them 
will be identified as an extrema.  If they are further then the search range, 
then both may be extrema.

The -consolidate-mode acts somewhat differently - if two equal values are 
touching, neither is treated as an initial extrema, but as long as there is at 
least one vertex separating them, they may both be treated as initial extrema.  
After the initial extrema are found, all extrema that are close to other 
extrema are "consolidated" together.  The details are somewhat complicated, and 
it was implemented by request of others, it is not something that we use.

Tim


On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu 
mailto:xinyang_ie...@163.com>> wrote:
Hi, Matt. Thank you very much for your reply.

The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum points with the same value, they were controlled in a 
limited distance and therefore, the final drawn ROI is a combined region of two 
drawings instead of two separate ones?

Because the problem is that, when I count the total vertex number for each 
created ROI using -metric-stats, a few results showed two values for one ROI.  
I am wondering why this happen and how to deal with that.

Best regards,
Xinyang


At 2018-08-24 19:14:56, "Glasser, Matthew" 
mailto:glass...@wustl.edu>> wrote:
I believe there is a configurable setting that sets the minimum distance 
between extrema.  It is a local min/max that is found.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Friday, August 24, 2018 at 4:21 AM
To: HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] two maximum points using -metric-extrema

Dear HCP experts,

Hi. When using workbench command "-metric-extrema" to draw ROI around the 
maximum point of the fMRI surface region, what would happen if there are two 
maximum points? Will the software keep both of them or only keep one? Thanks a 
lot.

Best regards,
Xinyang






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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.





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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

Re: [HCP-Users] two maximum points using -metric-extrema

[Xinyang Liu]

Dear Tim, dear Matt,


Thank you very much for your helpful answers.


Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file). 


Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connectome Workbench, we only saw one target ROI drawn on 
the brain surface. This confused us a lot. We don't know whether there were one 
or two ROIs produced. Do you have any suggestions about that? Thanks.


Best regards,
Xinyang





At 2018-08-25 04:16:48, "Timothy Coalson"  wrote:

The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or 
-1 based on if they are a local maximum or minimum.  By default, if there are 
two equal values that are closer than the search range, then *neither* of them 
will be identified as an extrema.  If they are further then the search range, 
then both may be extrema.


The -consolidate-mode acts somewhat differently - if two equal values are 
touching, neither is treated as an initial extrema, but as long as there is at 
least one vertex separating them, they may both be treated as initial extrema.  
After the initial extrema are found, all extrema that are close to other 
extrema are "consolidated" together.  The details are somewhat complicated, and 
it was implemented by request of others, it is not something that we use.


Tim




On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu  wrote:

Hi, Matt. Thank you very much for your reply.


The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum points with the same value, they were controlled in a 
limited distance and therefore, the final drawn ROI is a combined region of two 
drawings instead of two separate ones? 


Because the problem is that, when I count the total vertex number for each 
created ROI using -metric-stats, a few results showed two values for one ROI.  
I am wondering why this happen and how to deal with that.


Best regards,
Xinyang



At 2018-08-24 19:14:56, "Glasser, Matthew"  wrote:

I believe there is a configurable setting that sets the minimum distance 
between extrema.  It is a local min/max that is found.


Matt.


From:  on behalf of Xinyang Liu 

Date: Friday, August 24, 2018 at 4:21 AM
To: HCP 讨论组 
Subject: [HCP-Users] two maximum points using -metric-extrema



Dear HCP experts,


Hi. When using workbench command "-metric-extrema" to draw ROI around the 
maximum point of the fMRI surface region, what would happen if there are two 
maximum points? Will the software keep both of them or only keep one? Thanks a 
lot.


Best regards,
Xinyang






 

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HCP-Users mailing list
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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.





 

___
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HCP-Users@humanconnectome.org
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Re: [HCP-Users] two maximum points using -metric-extrema

[Timothy Coalson]

The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1
or -1 based on if they are a local maximum or minimum.  By default, if
there are two equal values that are closer than the search range, then
*neither* of them will be identified as an extrema.  If they are further
then the search range, then both may be extrema.

The -consolidate-mode acts somewhat differently - if two equal values are
touching, neither is treated as an initial extrema, but as long as there is
at least one vertex separating them, they may both be treated as initial
extrema.  After the initial extrema are found, all extrema that are close
to other extrema are "consolidated" together.  The details are somewhat
complicated, and it was implemented by request of others, it is not
something that we use.

Tim


On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu  wrote:

> Hi, Matt. Thank you very much for your reply.
>
> The extreme point was searched in a certain surface area. Do you mean that
> even there are two maximum points with the same value, they were controlled
> in a limited distance and therefore, the final drawn ROI is a combined
> region of two drawings instead of two separate ones?
>
> Because the problem is that, when I count the total vertex number for each
> created ROI using -metric-stats, a few results showed two values for one
> ROI.  I am wondering why this happen and how to deal with that.
>
> Best regards,
> Xinyang
>
>
> At 2018-08-24 19:14:56, "Glasser, Matthew"  wrote:
>
> I believe there is a configurable setting that sets the minimum distance
> between extrema.  It is a local min/max that is found.
>
> Matt.
>
> From:  on behalf of Xinyang Liu <
> xinyang_ie...@163.com>
> Date: Friday, August 24, 2018 at 4:21 AM
> To: HCP 讨论组 
> Subject: [HCP-Users] two maximum points using -metric-extrema
>
> Dear HCP experts,
>
> Hi. When using workbench command "-metric-extrema" to draw ROI around the
> maximum point of the fMRI surface region, what would happen if there are
> two maximum points? Will the software keep both of them or only keep one?
> Thanks a lot.
>
> Best regards,
> Xinyang
>
>
>
>
>
> ___
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>
> --
>
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> 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.
>
>
>
>
>
> ___
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Re: [HCP-Users] two maximum points using -metric-extrema

[Glasser, Matthew]

I don’t really understand the question, so perhaps with some pictures and the 
command you used it would be clearer.

Matt.

From: Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Friday, August 24, 2018 at 7:11 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] two maximum points using -metric-extrema

Hi, Matt. Thank you very much for your reply.

The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum points with the same value, they were controlled in a 
limited distance and therefore, the final drawn ROI is a combined region of two 
drawings instead of two separate ones?

Because the problem is that, when I count the total vertex number for each 
created ROI using -metric-stats, a few results showed two values for one ROI.  
I am wondering why this happen and how to deal with that.

Best regards,
Xinyang


At 2018-08-24 19:14:56, "Glasser, Matthew" 
mailto:glass...@wustl.edu>> wrote:
I believe there is a configurable setting that sets the minimum distance 
between extrema.  It is a local min/max that is found.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Friday, August 24, 2018 at 4:21 AM
To: HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] two maximum points using -metric-extrema

Dear HCP experts,

Hi. When using workbench command "-metric-extrema" to draw ROI around the 
maximum point of the fMRI surface region, what would happen if there are two 
maximum points? Will the software keep both of them or only keep one? Thanks a 
lot.

Best regards,
Xinyang






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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 
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strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.






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 
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Re: [HCP-Users] two maximum points using -metric-extrema

[Xinyang Liu]

Hi, Matt. Thank you very much for your reply.


The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum points with the same value, they were controlled in a 
limited distance and therefore, the final drawn ROI is a combined region of two 
drawings instead of two separate ones? 


Because the problem is that, when I count the total vertex number for each 
created ROI using -metric-stats, a few results showed two values for one ROI.  
I am wondering why this happen and how to deal with that.


Best regards,
Xinyang



At 2018-08-24 19:14:56, "Glasser, Matthew"  wrote:

I believe there is a configurable setting that sets the minimum distance 
between extrema.  It is a local min/max that is found.


Matt.


From:  on behalf of Xinyang Liu 

Date: Friday, August 24, 2018 at 4:21 AM
To: HCP 讨论组 
Subject: [HCP-Users] two maximum points using -metric-extrema



Dear HCP experts,


Hi. When using workbench command "-metric-extrema" to draw ROI around the 
maximum point of the fMRI surface region, what would happen if there are two 
maximum points? Will the software keep both of them or only keep one? Thanks a 
lot.


Best regards,
Xinyang






 

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Re: [HCP-Users] two maximum points using -metric-extrema

[Glasser, Matthew]

I believe there is a configurable setting that sets the minimum distance 
between extrema.  It is a local min/max that is found.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Friday, August 24, 2018 at 4:21 AM
To: HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] two maximum points using -metric-extrema

Dear HCP experts,

Hi. When using workbench command "-metric-extrema" to draw ROI around the 
maximum point of the fMRI surface region, what would happen if there are two 
maximum points? Will the software keep both of them or only keep one? Thanks a 
lot.

Best regards,
Xinyang






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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 
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