Re: [Freesurfer] lobar WM volumes

2012-04-05 Thread Douglas N Greve
You don't need to do 2b if all you want are the lobar wm segmentations. 
2b should just copy the cortical labels into the new seg.

mri_segstats --seg mri/newseg.mgz --sum stats/newseg.stats --pv mri/norm.mgz 
--empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in 
mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv 
--surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolortable --subjectsubject


You can load the newseg.mgz into tkmedit as both a segmentation (-seg) 
and as the aux volume. When you click on a point, you can see the seg 
value associated with the given label.

doug



On 04/04/2012 11:15 PM, Irwin, William wrote:
 Hi Doug-

 I wanted to follow up on this procedure and ask for a bit of clarification. 
 As an extension from Ines' efforts, I believe one can produce a ' 
 lobe+aseg.mgz' lobar volume with both WM and GM for both RH and LH.

 1:
 mri_annotation2label --ssubject   --hemi rh --lobesStrict lobe
 mri_annotation2label --ssubject   --hemi lh --lobesStrict lobe

 2(a):
 mri_aparc2aseg --ssubject   --labelwm --annot lobe

 2(b)
 mri_aparc2aseg --ssubject   --rip-unknown --ctxseg aparc+aseg.mgz --annot 
 lobe
 I'm not sure if this the correct syntax to be analogous to that for WM in 
 2(a).

 What would be the correct syntax to combine 2(a) and 2(b) into one command?

 3:
 Per your suggestion for syntax, this can be found in recon-all.log following 
 that for wmparc (and I have identified that). There is similar syntax for 
 GM/ctx. I'm not sure if the following would need to be slightly modified for 
 my objective:

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz 
 --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in 
 mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv 
 --surf-wm-vol --surf-ctx-vol --totalgray --ctab 
 /usr/local/freesurfer/ASegStatsLUT.txt --subjectsubject

 But, before proceeding with the step 3, how can one determine the lobar label 
 numbers assigned such that a custom LUT can be created. The output of the 
 2(b)  (if the syntax is correct) indicates that 8 entries are read (Frontal, 
 Temporal, Parietal, Occipital for LH and RH?).

 Thanks for your help.

 -Wil

 |-Original Message-
 |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 |Sent: Monday, April 02, 2012 10:39 AM
 |To: freesurfer@nmr.mgh.harvard.edu
 |Subject: Re: [Freesurfer] lobar WM volumes
 |
 |use mri_segstats. You can look in subjid/scripts/recon-all.log for example
 |command lines (look for the one with wmparc). The command will require a
 |color table. The ones in the log file will use the default table,  but this  
 will not
 |have the numbers/names of your lobar regions, so you'll need to create a
 |new color table (or add to the one that is there).
 |doug
 |
 |On 04/02/2012 12:58 PM, Inês Violante wrote:
 |  Dear all,
 |
 |  I need to obtain the white matter volume per lobe for a given numer of
 |subjects.
 |  I started by using the following:
 |
 |  mri_annotation2label --subjectsubjid   --hemi rh --lobesStrict lobe
 |
 |  mri_aparc2aseg --ssubjid   --labelwm --annot lobe
 |
 |  and now I have a lobe+aseg.mgz file.  How can I create a stats file
 |  containing the wm volume for each lobe?
 |
 |  Thank you,
 |
 |  ines
 |
 |  ___
 |  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
 |gr...@nmr.mgh.harvard.edu
 |Phone Number: 617-724-2358
 |Fax: 617-726-7422
 |
 |Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 |FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 |





-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] lobar WM volumes

2012-04-05 Thread Irwin, William
Thanks, Doug.

I actually want lobar both GM and WM. 

So would this be the correct syntax to generate lobar GM and WM labels?

mri_aparc2aseg --ssubject  --labelwm --rip-unknown --ctxseg aparc+aseg.mgz 
--annot lobe

Yes, I started to do as you suggest with tkmedit using FreeView, but I thought 
there might be a less manual way of doing this.

Thanks,
Wil

|-Original Message-
|From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
|Sent: Thursday, April 05, 2012 8:30 AM
|To: Irwin, William
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] lobar WM volumes
|
|You don't need to do 2b if all you want are the lobar wm segmentations.
|2b should just copy the cortical labels into the new seg.
|
|mri_segstats --seg mri/newseg.mgz --sum stats/newseg.stats --pv
|mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --
|subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units
|MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolortable --
|subjectsubject
|
|
|You can load the newseg.mgz into tkmedit as both a segmentation (-seg) and
|as the aux volume. When you click on a point, you can see the seg value
|associated with the given label.
|
|doug
|
|
|
|On 04/04/2012 11:15 PM, Irwin, William wrote:
| Hi Doug-
|
| I wanted to follow up on this procedure and ask for a bit of clarification. 
As
|an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz'
|lobar volume with both WM and GM for both RH and LH.
|
| 1:
| mri_annotation2label --ssubject   --hemi rh --lobesStrict lobe
| mri_annotation2label --ssubject   --hemi lh --lobesStrict lobe
|
| 2(a):
| mri_aparc2aseg --ssubject   --labelwm --annot lobe
|
| 2(b)
| mri_aparc2aseg --ssubject   --rip-unknown --ctxseg aparc+aseg.mgz --
|annot lobe
| I'm not sure if this the correct syntax to be analogous to that for WM in 
2(a).
|
| What would be the correct syntax to combine 2(a) and 2(b) into one
|command?
|
| 3:
| Per your suggestion for syntax, this can be found in recon-all.log following
|that for wmparc (and I have identified that). There is similar syntax for
|GM/ctx. I'm not sure if the following would need to be slightly modified for
|my objective:
|
| mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
| mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent
| --subcortgray --in mri/norm.mgz --in-intensity-name norm
| --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
| --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt
| --subjectsubject
|
| But, before proceeding with the step 3, how can one determine the lobar
|label numbers assigned such that a custom LUT can be created. The output of
|the 2(b)  (if the syntax is correct) indicates that 8 entries are read 
(Frontal,
|Temporal, Parietal, Occipital for LH and RH?).
|
| Thanks for your help.
|
| -Wil
|
| |-Original Message-
| |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
| |Sent: Monday, April 02, 2012 10:39 AM
| |To: freesurfer@nmr.mgh.harvard.edu
| |Subject: Re: [Freesurfer] lobar WM volumes
| |
| |use mri_segstats. You can look in subjid/scripts/recon-all.log for
| |example command lines (look for the one with wmparc). The command
| |will require a color table. The ones in the log file will use the
| |default table,  but this  will not have the numbers/names of your
| |lobar regions, so you'll need to create a new color table (or add to the one
|that is there).
| |doug
| |
| |On 04/02/2012 12:58 PM, Inês Violante wrote:
| |  Dear all,
| |
| |  I need to obtain the white matter volume per lobe for a given
| | numer of
| |subjects.
| |  I started by using the following:
| |
| |  mri_annotation2label --subjectsubjid   --hemi rh --lobesStrict lobe
| |
| |  mri_aparc2aseg --ssubjid   --labelwm --annot lobe
| |
| |  and now I have a lobe+aseg.mgz file.  How can I create a stats
| | file  containing the wm volume for each lobe?
| |
| |  Thank you,
| |
| |  ines
| |
| |  ___
| |  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
| |gr...@nmr.mgh.harvard.edu
| |Phone Number: 617-724-2358
| |Fax: 617-726-7422
| |
| |Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
| |FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
| |
|
|
|
|
|
|--
|Douglas N. Greve, Ph.D.
|MGH-NMR Center
|gr...@nmr.mgh.harvard.edu
|Phone Number: 617-724-2358
|Fax: 617-726-7422
|
|Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
|FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
|
|
|
|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

Re: [Freesurfer] lobar WM volumes

2012-04-05 Thread Douglas N Greve
Yes, that looks right to me
doug

On 04/05/2012 11:50 AM, Irwin, William wrote:
 Thanks, Doug.

 I actually want lobar both GM and WM.

 So would this be the correct syntax to generate lobar GM and WM labels?

 mri_aparc2aseg --ssubject   --labelwm --rip-unknown --ctxseg aparc+aseg.mgz 
 --annot lobe

 Yes, I started to do as you suggest with tkmedit using FreeView, but I 
 thought there might be a less manual way of doing this.

 Thanks,
 Wil

 |-Original Message-
 |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 |Sent: Thursday, April 05, 2012 8:30 AM
 |To: Irwin, William
 |Cc: freesurfer@nmr.mgh.harvard.edu
 |Subject: Re: [Freesurfer] lobar WM volumes
 |
 |You don't need to do 2b if all you want are the lobar wm segmentations.
 |2b should just copy the cortical labels into the new seg.
 |
 |mri_segstats --seg mri/newseg.mgz --sum stats/newseg.stats --pv
 |mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --
 |subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units
 |MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolortable --
 |subjectsubject
 |
 |
 |You can load the newseg.mgz into tkmedit as both a segmentation (-seg) and
 |as the aux volume. When you click on a point, you can see the seg value
 |associated with the given label.
 |
 |doug
 |
 |
 |
 |On 04/04/2012 11:15 PM, Irwin, William wrote:
 |  Hi Doug-
 |
 |  I wanted to follow up on this procedure and ask for a bit of 
 clarification. As
 |an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz'
 |lobar volume with both WM and GM for both RH and LH.
 |
 |  1:
 |  mri_annotation2label --ssubject--hemi rh --lobesStrict lobe
 |  mri_annotation2label --ssubject--hemi lh --lobesStrict lobe
 |
 |  2(a):
 |  mri_aparc2aseg --ssubject--labelwm --annot lobe
 |
 |  2(b)
 |  mri_aparc2aseg --ssubject--rip-unknown --ctxseg aparc+aseg.mgz --
 |annot lobe
 |  I'm not sure if this the correct syntax to be analogous to that for WM in 
 2(a).
 |
 |  What would be the correct syntax to combine 2(a) and 2(b) into one
 |command?
 |
 |  3:
 |  Per your suggestion for syntax, this can be found in recon-all.log 
 following
 |that for wmparc (and I have identified that). There is similar syntax for
 |GM/ctx. I'm not sure if the following would need to be slightly modified for
 |my objective:
 |
 |  mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
 |  mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent
 |  --subcortgray --in mri/norm.mgz --in-intensity-name norm
 |  --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
 |  --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt
 |  --subjectsubject
 |
 |  But, before proceeding with the step 3, how can one determine the lobar
 |label numbers assigned such that a custom LUT can be created. The output of
 |the 2(b)  (if the syntax is correct) indicates that 8 entries are read 
 (Frontal,
 |Temporal, Parietal, Occipital for LH and RH?).
 |
 |  Thanks for your help.
 |
 |  -Wil
 |
 |  |-Original Message-
 |  |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 |  |Sent: Monday, April 02, 2012 10:39 AM
 |  |To: freesurfer@nmr.mgh.harvard.edu
 |  |Subject: Re: [Freesurfer] lobar WM volumes
 |  |
 |  |use mri_segstats. You can look in subjid/scripts/recon-all.log for
 |  |example command lines (look for the one with wmparc). The command
 |  |will require a color table. The ones in the log file will use the
 |  |default table,  but this  will not have the numbers/names of your
 |  |lobar regions, so you'll need to create a new color table (or add to the 
 one
 |that is there).
 |  |doug
 |  |
 |  |On 04/02/2012 12:58 PM, Inês Violante wrote:
 |  |   Dear all,
 |  |
 |  |   I need to obtain the white matter volume per lobe for a given
 |  |  numer of
 |  |subjects.
 |  |   I started by using the following:
 |  |
 |  |   mri_annotation2label --subjectsubjid--hemi rh --lobesStrict 
 lobe
 |  |
 |  |   mri_aparc2aseg --ssubjid--labelwm --annot lobe
 |  |
 |  |   and now I have a lobe+aseg.mgz file.  How can I create a stats
 |  |  file  containing the wm volume for each lobe?
 |  |
 |  |   Thank you,
 |  |
 |  |   ines
 |  |
 |  |   ___
 |  |   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
 |  |gr...@nmr.mgh.harvard.edu
 |  |Phone Number: 617-724-2358
 |  |Fax: 617-726-7422
 |  |
 |  |Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 |  |FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 |  |
 |
 |
 |
 |
 |
 |--
 |Douglas N. Greve, Ph.D.
 |MGH-NMR Center
 |gr...@nmr.mgh.harvard.edu
 |Phone Number: 617-724-2358
 |Fax: 617-726-7422
 |
 |Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 |FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Re: [Freesurfer] lobar WM volumes

2012-04-04 Thread Irwin, William
Hi Doug-

I wanted to follow up on this procedure and ask for a bit of clarification. As 
an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz' 
lobar volume with both WM and GM for both RH and LH.

1:
mri_annotation2label --s subject  --hemi rh --lobesStrict lobe
mri_annotation2label --s subject  --hemi lh --lobesStrict lobe

2(a):
mri_aparc2aseg --s subject  --labelwm --annot lobe

2(b)
mri_aparc2aseg --s subject  --rip-unknown --ctxseg aparc+aseg.mgz --annot lobe
I'm not sure if this the correct syntax to be analogous to that for WM in 2(a).

What would be the correct syntax to combine 2(a) and 2(b) into one command?

3:
Per your suggestion for syntax, this can be found in recon-all.log following 
that for wmparc (and I have identified that). There is similar syntax for 
GM/ctx. I'm not sure if the following would need to be slightly modified for my 
objective:

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz 
--empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in 
mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv 
--surf-wm-vol --surf-ctx-vol --totalgray --ctab 
/usr/local/freesurfer/ASegStatsLUT.txt --subject subject

But, before proceeding with the step 3, how can one determine the lobar label 
numbers assigned such that a custom LUT can be created. The output of the 2(b)  
(if the syntax is correct) indicates that 8 entries are read (Frontal, 
Temporal, Parietal, Occipital for LH and RH?).

Thanks for your help.

-Wil

|-Original Message-
|From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
|Sent: Monday, April 02, 2012 10:39 AM
|To: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] lobar WM volumes
|
|use mri_segstats. You can look in subjid/scripts/recon-all.log for example
|command lines (look for the one with wmparc). The command will require a
|color table. The ones in the log file will use the default table,  but this  
will not
|have the numbers/names of your lobar regions, so you'll need to create a
|new color table (or add to the one that is there).
|doug
|
|On 04/02/2012 12:58 PM, Inês Violante wrote:
| Dear all,
|
| I need to obtain the white matter volume per lobe for a given numer of
|subjects.
| I started by using the following:
|
| mri_annotation2label --subjectsubjid  --hemi rh --lobesStrict lobe
|
| mri_aparc2aseg --ssubjid  --labelwm --annot lobe
|
| and now I have a lobe+aseg.mgz file.  How can I create a stats file
| containing the wm volume for each lobe?
|
| Thank you,
|
| ines
|
| ___
| 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
|gr...@nmr.mgh.harvard.edu
|Phone Number: 617-724-2358
|Fax: 617-726-7422
|
|Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
|FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
|



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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



[Freesurfer] lobar WM volumes

2012-04-02 Thread Inês Violante
Dear all,

I need to obtain the white matter volume per lobe for a given numer of subjects.
I started by using the following:

mri_annotation2label --subject subjid --hemi rh --lobesStrict lobe

mri_aparc2aseg --s subjid --labelwm --annot lobe

and now I have a lobe+aseg.mgz file.  How can I create a stats file
containing the wm volume for each lobe?

Thank you,

ines
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



[Freesurfer] lobar WM volumes

2012-04-02 Thread Inês Violante
Dear all,

I need to obtain the white matter volume per lobe for a given numer of subjects.
I started by using the following:

mri_annotation2label --subject subjid --hemi rh --lobesStrict lobe

mri_aparc2aseg --s subjid --labelwm --annot lobe

and now I have a lobe+aseg.mgz file.  How can I create a stats file
containing the wm volume for each lobe?

Thank you,

ines

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



Re: [Freesurfer] lobar WM volumes

2012-04-02 Thread Douglas N Greve
use mri_segstats. You can look in subjid/scripts/recon-all.log for 
example command lines (look for the one with wmparc). The command will 
require a color table. The ones in the log file will use the default 
table,  but this  will not have the numbers/names of your lobar regions, 
so you'll need to create a new color table (or add to the one that is 
there).
doug

On 04/02/2012 12:58 PM, Inês Violante wrote:
 Dear all,

 I need to obtain the white matter volume per lobe for a given numer of 
 subjects.
 I started by using the following:

 mri_annotation2label --subjectsubjid  --hemi rh --lobesStrict lobe

 mri_aparc2aseg --ssubjid  --labelwm --annot lobe

 and now I have a lobe+aseg.mgz file.  How can I create a stats file
 containing the wm volume for each lobe?

 Thank you,

 ines

 ___
 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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
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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.



Re: [Freesurfer] lobar WM volumes

2012-04-02 Thread Inês Violante
Hi Doug,

Thanks for your reply. However, I was not able to succeed. Can you
give me an extra help?
I created a new color table and I tried the following command:

mri_segstats --seg $SUBJECTS_DIR/Subjid/mri/lobe+aseg.mgz --pv
$SUBJECTS_DIR/Subjid/mri/norm.mgz --excludeid 0 --brain-vol-from-seg
--brainmask $SUBJECTS_DIR/Subjid/mri/brainmask.mgz --in
$SUBJECTS_DIR/Subjid/mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --subject Subjid --surf-wm-vol --ctab
$FREESURFER_HOME/FreeSurferColorLUT_lobe.txt --sum Subjid.aseg.sum

But it only makes calculations for temporal and parietal lobes and
they don't seem like valid numbers.

This is what is shown in the command line:

Loading /home/user/Projects/Freesurfer/AC/mri/lobe+aseg.mgz
Getting Cerebral WM volumes from surface
lh white matter volume 224173
rh white matter volume 229757
Loading /home/user/Projects/Freesurfer/AC/mri/norm.mgz
Loading /home/user/Projects/Freesurfer/AC/mri/norm.mgz
Loading /home/user/Projects/Freesurfer/AC/mri/brainmask.mgz
# nbrainmaskvoxels 1506513
# brainmaskvolume  1506513.0
# nbrainsegvoxels 232396
# brainsegvolume   232396.0
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   7 segmentations
Computing statistics for each segmentation
  1 1  frontal  0
  2 2  cingulate  0
  3 3  occipital  0
  4 4  temporal 3706  3706
  5 5  parietal  247  247
  6 6  insula  0

Reporting on   2 segmentations


Hope you can help. Thank you very much,

ines

On Mon, Apr 2, 2012 at 6:38 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
 use mri_segstats. You can look in subjid/scripts/recon-all.log for
 example command lines (look for the one with wmparc). The command will
 require a color table. The ones in the log file will use the default
 table,  but this  will not have the numbers/names of your lobar regions,
 so you'll need to create a new color table (or add to the one that is
 there).
 doug

 On 04/02/2012 12:58 PM, Inês Violante wrote:
 Dear all,

 I need to obtain the white matter volume per lobe for a given numer of 
 subjects.
 I started by using the following:

 mri_annotation2label --subjectsubjid  --hemi rh --lobesStrict lobe

 mri_aparc2aseg --ssubjid  --labelwm --annot lobe

 and now I have a lobe+aseg.mgz file.  How can I create a stats file
 containing the wm volume for each lobe?

 Thank you,

 ines

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