What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ?
Thanks,
Don
What do you mean by contrast vectors?
On 8/13/14 9:36 AM, Krieger, Donald N. wrote:
What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ?
Thanks,
Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Here is a fragment of the help text for recon-all which pointed me towards this:
WM/GM Contrast (-<no>pctsurfcon)
Computes the vertex-by-vertex percent contrast between white and gray matter. The computation is:
100*(W-G) pct = --------- 0.5*(W+G)
The white matter is sampled 1mm below the white surface. The gray matter is sampled 30% the thickness into the cortex. The volume that is sampled is rawavg.mgz. The output is stored in the surf dir of the given subject as ?h.w-g.pct.mgh. Non-cortical regions (medial wall) are zeroed.
It is this "pct" value along with the coordinates of the vertex that I am interested in.
Regards,
Don
Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Wednesday, August 13, 2014 10:01 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh
What do you mean by contrast vectors? On 8/13/14 9:36 AM, Krieger, Donald N. wrote: What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ?
Thanks,
Don
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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I guess I don't understand what it is you want exactly. the gray/white contrast file is in the surf folder. Do you want to compute a mean over a given set of vertices?
On 8/13/14 10:06 AM, Krieger, Donald N. wrote:
Here is a fragment of the help text for recon-all which pointed me towards this:
WM/GM Contrast (-<no>pctsurfcon)
Computes the vertex-by-vertex percent contrast between white and gray matter.
The computation is:
100*(W-G)pct = ---------
0.5*(W+G)The white matter is sampled 1mm below the white surface. The gray matter is
sampled 30% the thickness into the cortex. The volume that is sampled is
rawavg.mgz. The output is stored in the surf dir of the given subject as
?h.w-g.pct.mgh. Non-cortical regions (medial wall) are zeroed.
It is this "pct" value along with the coordinates of the vertex that I am interested in.
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
Universityof Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Wednesday, August 13, 2014 10:01 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh
What do you mean by contrast vectors?
On 8/13/14 9:36 AM, Krieger, Donald N. wrote:
What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ? Thanks, Don _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
I just want print the list of vertices with their contrast percentages into an ascii file.
Regards,
Don
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Wednesday, August 13, 2014 10:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh
I guess I don't understand what it is you want exactly. the gray/white contrast file is in the surf folder. Do you want to compute a mean over a given set of vertices?
On 8/13/14 10:06 AM, Krieger, Donald N. wrote: Here is a fragment of the help text for recon-all which pointed me towards this:
WM/GM Contrast (-<no>pctsurfcon)
Computes the vertex-by-vertex percent contrast between white and gray matter. The computation is:
100*(W-G) pct = --------- 0.5*(W+G)
The white matter is sampled 1mm below the white surface. The gray matter is sampled 30% the thickness into the cortex. The volume that is sampled is rawavg.mgz. The output is stored in the surf dir of the given subject as ?h.w-g.pct.mgh. Non-cortical regions (medial wall) are zeroed.
It is this "pct" value along with the coordinates of the vertex that I am interested in.
Regards,
Don
Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Wednesday, August 13, 2014 10:01 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh
What do you mean by contrast vectors? On 8/13/14 9:36 AM, Krieger, Donald N. wrote: What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ?
Thanks,
Don
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
use mri_convert with the --ascii flag
--ascii save output as ascii. This will be a data file with a single column of data. The fastest dimension will be col, then row,then slice, then frame.
On 08/13/2014 10:11 AM, Krieger, Donald N. wrote:
I just want print the list of vertices with their contrast percentages into an ascii file.
Regards,
Don
*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Wednesday, August 13, 2014 10:09 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh
I guess I don't understand what it is you want exactly. the gray/white contrast file is in the surf folder. Do you want to compute a mean over a given set of vertices?
On 8/13/14 10:06 AM, Krieger, Donald N. wrote:
Here is a fragment of the help text for recon-all which pointed me towards this: WM/GM Contrast (-<no>pctsurfcon) Computes the vertex-by-vertex percent contrast between white and gray matter. The computation is: 100*(W-G) pct = --------- 0.5*(W+G) The white matter is sampled 1mm below the white surface. The gray matter is sampled 30% the thickness into the cortex. The volume that is sampled is rawavg.mgz. The output is stored in the surf dir of the given subject as ?h.w-g.pct.mgh. Non-cortical regions (medial wall) are zeroed. It is this “pct” value along with the coordinates of the vertex that I am interested in. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text *From:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Wednesday, August 13, 2014 10:01 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh What do you mean by contrast vectors? On 8/13/14 9:36 AM, Krieger, Donald N. wrote: What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ? Thanks, Don _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Thanks.
Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, August 13, 2014 10:51 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh
use mri_convert with the --ascii flag
--ascii save output as ascii. This will be a data file with a single column of data. The fastest dimension will be col, then row,then slice, then frame.
On 08/13/2014 10:11 AM, Krieger, Donald N. wrote:
I just want print the list of vertices with their contrast percentages into an ascii file.
Regards,
Don
*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of
*Douglas
Greve *Sent:* Wednesday, August 13, 2014 10:09 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh
I guess I don't understand what it is you want exactly. the gray/white contrast file is in the surf folder. Do you want to compute a mean over a given set of vertices?
On 8/13/14 10:06 AM, Krieger, Donald N. wrote:
Here is a fragment of the help text for recon-all which pointed me towards this: WM/GM Contrast (-<no>pctsurfcon) Computes the vertex-by-vertex percent contrast between white and gray matter. The computation is: 100*(W-G) pct = --------- 0.5*(W+G) The white matter is sampled 1mm below the white surface. The gray matter is sampled 30% the thickness into the cortex. The volume that is sampled is rawavg.mgz. The output is stored in the surf dir of the given subject as ?h.w-g.pct.mgh. Non-cortical regions (medial wall) are zeroed. It is this "pct" value along with the coordinates of the vertex that I am interested in. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text *From:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Wednesday, August 13, 2014 10:01 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] quick pointer: tool to extract gray/white contrast vectors from [lr]h.w-g.pct.mgh What do you mean by contrast vectors? On 8/13/14 9:36 AM, Krieger, Donald N. wrote: What is the tool to extract the contrast vectors from surf/[ lr]h.w-g.pct.mgh ? Thanks, Don _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/
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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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Krieger, Donald N.