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 --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

are you sure you have the right numbers in the color table? You can load the segmentation as both a segmentation and as a simple volume, something like this: tkmedit subject orig.mgz -aux yourseg.mgz -seg yourseg.mgz yourcolortable.txt when you click on a point, it will show you the value in the Aux field and you can make sure that you have all the numbers there doug

On 4/2/12 4:04 PM, Inês Violante wrote:

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 greve@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 --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

-- 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: 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.

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 --subject<subject>

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 --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:greve@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 --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 |> |> | |-- |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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html |

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 --s<subject> --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:greve@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 -- |subject<subject> | | |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 --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:greve@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 --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 |> |> |> |> |> | |> |-- |> |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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html |> | |> |> |> |> | |-- |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: 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 not contain patient information, please contact the |sender and properly dispose of the e-mail.