[Freesurfer] Cortical volume from masked region
Hi all, I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command. The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe. I have run: mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum This has output a text file with a value of 495563 mm3 in the last row. I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done - so any tips would be greatly appreciated. Many thanks Eli ___ 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] Cortical volume from masked region
Hi Doug, Thanks a lot for your help! I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be? Many thanks! Eli Douglas N Grevegreve at nmr.mgh.harvard.edu <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E> Wed Jan 18 15:30:45 EST 2017 * Previous message: [Freesurfer] Cortical volume from masked region <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html> * Next message: [Freesurfer] installation fail :( <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html> * Messages sorted by: [ date ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559> [ thread ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559> [ subject ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559> [ author ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559> I would probably map the mask to the surface,eg, mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz The run mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats From: Eli Johnson Sent: Tuesday, 17 January 2017 4:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Cortical volume from masked region Hi all, I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command. The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe. I have run: mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum This has output a text file with a value of 495563 mm3 in the last row. I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done - so any tips would be greatly appreciated. Many thanks Eli ___ 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] Cortical volume from masked region
Hi Doug, Thank you - I have uploaded the files for you. Eli From: Eli Johnson Sent: Friday, 20 January 2017 5:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Cortical volume from masked region Hi Doug, Thanks a lot for your help! I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be? Many thanks! Eli Douglas N Grevegreve at nmr.mgh.harvard.edu <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E> Wed Jan 18 15:30:45 EST 2017 * Previous message: [Freesurfer] Cortical volume from masked region <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html> * Next message: [Freesurfer] installation fail :( <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html> * Messages sorted by: [ date ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559> [ thread ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559> [ subject ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559> [ author ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559> I would probably map the mask to the surface,eg, mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz The run mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats From: Eli Johnson Sent: Tuesday, 17 January 2017 4:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Cortical volume from masked region Hi all, I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command. The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe. I have run: mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum This has output a text file with a value of 495563 mm3 in the last row. I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done - so any tips would be greatly appreciated. Many thanks Eli ___ 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] Cortical volume from masked region
Yes, I think I got the correct email. Attached is the notification I received upon upload. Thanks Eli You recently uploaded the following files to the Martinos Center FileDrop: + 20001-013-1_std.zip (251.3 MiB) Here are the people you sent these files to: + gr...@nmr.mgh.harvard.edu In case you'd like to modify some of the above information, please use the link below: http://gate.nmr.mgh.harvard.edu/filedrop2/?g=ahht5qz16h5 Cheers, The Martinos Center Web Team From: Eli Johnson Sent: Wednesday, 25 January 2017 9:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Cortical volume from masked region Hi Doug, Thank you - I have uploaded the files for you. Eli From: Eli Johnson Sent: Friday, 20 January 2017 5:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Cortical volume from masked region Hi Doug, Thanks a lot for your help! I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be? Many thanks! Eli Douglas N Grevegreve at nmr.mgh.harvard.edu <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E> Wed Jan 18 15:30:45 EST 2017 * Previous message: [Freesurfer] Cortical volume from masked region <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html> * Next message: [Freesurfer] installation fail :( <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html> * Messages sorted by: [ date ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559> [ thread ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559> [ subject ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559> [ author ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559> I would probably map the mask to the surface,eg, mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz The run mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats From: Eli Johnson Sent: Tuesday, 17 January 2017 4:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Cortical volume from masked region Hi all, I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command. The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe. I have run: mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum This has output a text file with a value of 495563 mm3 in the last row. I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done - so any tips would be greatly appreciated. Many thanks Eli ___ 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] Cortical volume from masked region
Sent from my iPhone > On 26 Jan 2017, at 18:11, Douglas N Greve wrote: > > In looking at your mask, it covers only half (or less) of the brain. > This would explain why the total volume you get from the mask is much > lesss than the total gm volume reported in aseg.stats. > > >> On 01/20/2017 12:08 PM, Eli Johnson wrote: >> >> *Hi Doug,* >> >> * >> * >> >> *Thanks a lot for your help!* >> >> * >> * >> >> *I have run these commands and they complete with no problems. I can >> also view the region overlaid on a surface and this looks ok, however >> the volumes that are extracted from mri_segstats are much lower than >> expected - around half the volume expected, and they don't seem in >> line with the volumes automatically extracted (i.e. total cortical gm >> volume from the aseg.stats file). Any thoughts on why this might be?* >> >> * >> * >> >> *Many thanks!* >> >> *Eli >> * >> >> * >> * >> >> * >> * >> >> * >> * >> >> *Douglas N Greve*greve at nmr.mgh.harvard.edu >> <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E> >> /Wed Jan 18 15:30:45 EST 2017/ >> >> * Previous message: [Freesurfer] Cortical volume from masked region >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html> >> * Next message: [Freesurfer] installation fail :( >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html> >> * *Messages sorted by:* [ date ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559> >>[ thread ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559> >>[ subject ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559> >>[ author ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559> >> >> >> >> I would probably map the mask to the surface,eg, >> >> mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i >> scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz >> >> The run >> >> mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o >> lh.vol.stats >> >> >> >> *From:* Eli Johnson >> *Sent:* Tuesday, 17 January 2017 4:24 PM >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Cortical volume from masked region >> >> Hi all, >> >> >> I am trying to extract the volume from a FreeSurfer segmented scan >> within a pre-registered mask region, but only within the cortex, and >> wanted to check my command. >> >> >> The mask is a binary mask (value of 1 across the mask) and is in the >> same space as the orig.mgz file. It covers part of the frontal lobe. >> >> >> I have run: >> >> mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i >> ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum >> >> >> This has output a text file with a value of 495563 mm3 in the last row. >> >> >> I wanted to check whether this is the correct command to extract only >> cortical GM within this mask. If this is correct, should be adding >> other flags (e.g. -pv). I have searched the mailing list and the >> options for mri_segstats, but I'm not 100% confident in what I've done >> - so any tips would be greatly appreciated. >> >> >> Many thanks >> Eli >> >> >> >> ___ >> 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: 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/ > > ___ > 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical volume from masked region
Hi Doug, Yes, I have a series of masks that I have created to cover the whole cortex, but I want to examine the regions separately. Each region outputs a volume much smaller than I would expect given the volumes from aseg stats for the whole cortex. That is to say, when I combine the volume from each region although I would expect it to be different to the volume from aseg stats (aseg stats is of course highly optimized), it's a lot smaller than expected - around half the size. Sorry for not being more clear! Thanks > On 26 Jan 2017, at 18:11,y Douglas N Greve wrote: > > In looking at your mask, it covers only half (or less) of the brain. > This would explain why the total volume you get from the mask is much > lesss than the total gm volume reported in aseg.stats. > > >> On 01/20/2017 12:08 PM, Eli Johnson wrote: >> >> *Hi Doug,* >> >> * >> * >> >> *Thanks a lot for your help!* >> >> * >> * >> >> *I have run these commands and they complete with no problems. I can >> also view the region overlaid on a surface and this looks ok, however >> the volumes that are extracted from mri_segstats are much lower than >> expected - around half the volume expected, and they don't seem in >> line with the volumes automatically extracted (i.e. total cortical gm >> volume from the aseg.stats file). Any thoughts on why this might be?* >> >> * >> * >> >> *Many thanks!* >> >> *Eli >> * >> >> * >> * >> >> * >> * >> >> * >> * >> >> *Douglas N Greve*greve at nmr.mgh.harvard.edu >> <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E> >> /Wed Jan 18 15:30:45 EST 2017/ >> >> * Previous message: [Freesurfer] Cortical volume from masked region >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html> >> * Next message: [Freesurfer] installation fail :( >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html> >> * *Messages sorted by:* [ date ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559> >>[ thread ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559> >>[ subject ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559> >>[ author ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559> >> >> >> >> I would probably map the mask to the surface,eg, >> >> mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i >> scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz >> >> The run >> >> mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o >> lh.vol.stats >> >> >> >> *From:* Eli Johnson >> *Sent:* Tuesday, 17 January 2017 4:24 PM >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Cortical volume from masked region >> >> Hi all, >> >> >> I am trying to extract the volume from a FreeSurfer segmented scan >> within a pre-registered mask region, but only within the cortex, and >> wanted to check my command. >> >> >> The mask is a binary mask (value of 1 across the mask) and is in the >> same space as the orig.mgz file. It covers part of the frontal lobe. >> >> >> I have run: >> >> mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i >> ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum >> >> >> This has output a text file with a value of 495563 mm3 in the last row. >> >> >> I wanted to check whether this is the correct command to extract only >> cortical GM within this mask. If this is correct, should be adding >> other flags (e.g. -pv). I have searched the mailing list and the >> options for mri_segstats, but I'm not 100% confident in what I've done >> - so any tips would be greatly appreciated. >> >> >> Many thanks >> Eli >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.n
Re: [Freesurfer] Cortical volume from masked region
Ok sure, I will do it tomorrow as I don't have access to the stats file right now Many thanks! From: Eli Johnson Sent: Thursday, 26 January 2017 6:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region Hi Doug, Yes, I have a series of masks that I have created to cover the whole cortex, but I want to examine the regions separately. Each region outputs a volume much smaller than I would expect given the volumes from aseg stats for the whole cortex. That is to say, when I combine the volume from each region although I would expect it to be different to the volume from aseg stats (aseg stats is of course highly optimized), it's a lot smaller than expected - around half the size. Sorry for not being more clear! Thanks > On 26 Jan 2017, at 18:11,y Douglas N Greve wrote: > > In looking at your mask, it covers only half (or less) of the brain. > This would explain why the total volume you get from the mask is much > lesss than the total gm volume reported in aseg.stats. > > >> On 01/20/2017 12:08 PM, Eli Johnson wrote: >> >> *Hi Doug,* >> >> * >> * >> >> *Thanks a lot for your help!* >> >> * >> * >> >> *I have run these commands and they complete with no problems. I can >> also view the region overlaid on a surface and this looks ok, however >> the volumes that are extracted from mri_segstats are much lower than >> expected - around half the volume expected, and they don't seem in >> line with the volumes automatically extracted (i.e. total cortical gm >> volume from the aseg.stats file). Any thoughts on why this might be?* >> >> * >> * >> >> *Many thanks!* >> >> *Eli >> * >> >> * >> * >> >> * >> * >> >> * >> * >> >> *Douglas N Greve*greve at nmr.mgh.harvard.edu >> <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E> >> /Wed Jan 18 15:30:45 EST 2017/ >> >> * Previous message: [Freesurfer] Cortical volume from masked region >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html> >> * Next message: [Freesurfer] installation fail :( >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html> >> * *Messages sorted by:* [ date ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559> >>[ thread ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559> >>[ subject ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559> >>[ author ] >> >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559> >> >> >> >> I would probably map the mask to the surface,eg, >> >> mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i >> scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz >> >> The run >> >> mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o >> lh.vol.stats >> >> >> >> *From:* Eli Johnson >> *Sent:* Tuesday, 17 January 2017 4:24 PM >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Cortical volume from masked region >> >> Hi all, >> >> >> I am trying to extract the volume from a FreeSurfer segmented scan >> within a pre-registered mask region, but only within the cortex, and >> wanted to check my command. >> >> >> The mask is a binary mask (value of 1 across the mask) and is in the >> same space as the orig.mgz file. It covers part of the frontal lobe. >> >> >> I have run: >> >> mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i >> ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum >> >> >> This has output a text file with a value of 495563 mm3 in the last row. >> >> >> I wanted to check whether this is the correct command to extract only >> cortical GM within this mask. If this is correct, should be adding >> other flags (e.g. -pv). I have searched the mailing list and the >> options for mri_segstats, but I'm not 100% confident in what I've done >> - so any tips would be greatly appreciated. >
Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
I have re-uploaded the file (see bottom of this email for info):
Along with the default FS output, there are 5 masks, corresponding to frontal,
temporal, parietal, occipital and insula regions (e.g.
20001-013-1_std/mri/20001_MNI_lobes_1-in-fs.mgz).
There are 10 surfs corresponding to lh & rh frontal,lh & rh temporal, lh & rh
parietal,lh & rh occipital and lh & rh insula (e.g.
20001-013-1_std/surf/20001_MNI_lobes_1-in-fs_surfrh.mgz).
I ran the commands:
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region1.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region2.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region3.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region4.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region5.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region1.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region2.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region3.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region4.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region5.stats
to extract volumes from the 10 regions. The stats files are located as
described in the command.
Also, in the ./20001-013-1_std/stats/ folder are the default FS lobular volumes
for comparison.
Thanks again for all of your help, do let me know if I've missed anything
again!!
Eli
You recently uploaded the following files to the Martinos Center FileDrop:
+ 20001-013-1_std.tar.gz (252.1 MiB)
Here are the people you sent these files to:
+ gr...@nmr.mgh.harvard.edu
In case you'd like to modify some of the above information, please use the link
below:
http://gate.nmr.mgh.harvard.edu/filedrop2/?g=7z2xk77v3ue
Cheers,
The Martinos Center Web Team
________
From: Eli Johnson
Sent: Thursday, 26 January 2017 7:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Ok sure, I will do it tomorrow as I don't have access to the stats file right
now
Many thanks!
________
From: Eli Johnson
Sent: Thursday, 26 January 2017 6:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
Yes, I have a series of masks that I have created to cover the whole cortex,
but I want to examine the regions separately. Each region outputs a volume much
smaller than I would expect given the volumes from aseg stats for the whole
cortex. That is to say, when I combine the volume from each region although I
would expect it to be different to the volume from aseg stats (aseg stats is of
course highly optimized), it's a lot smaller than expected - around half the
size.
Sorry for not being more clear!
Thanks
> On 26 Jan 2017, at 18:11,y Douglas N Greve wrote:
>
> In looking at your mask, it covers only half (or less) of the brain.
> This would explain why the total volume you get from the mask is much
> lesss than the total gm volume reported in aseg.stats.
>
>
>> On 01/20/2017 12:08 PM, Eli Johnson wrote:
>>
>> *Hi Doug,*
>>
>> *
>> *
>>
>> *Thanks a lot for your help!*
>>
>> *
>> *
>>
>> *I have run these commands and they complete with no problems. I can
>> also view the region overlaid on a surface and this looks ok, however
>> the volumes that are extracted from mri_segstats are much lower than
>> expected - around half the volume expected, and they don't seem in
>> line with the volumes automatically extracted (i.e. total cortical gm
>> volume from the aseg.stats file). Any thoughts on why this might be?*
>>
>> *
>> *
>>
>> *Many thanks!*
>>
>> *Eli
>> *
Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
I was reading the fourth column in the stats files as the volumes (highlighted
in yellow), as that seems to correspond to the volume_mm3 label when the
columns are lined up. Also, when I run asegstats2file with the
'rh.vol_region1.stats' file specified alongside 'volume' as the measure, the
output is the fourth(highlighted) number in the stats files.
region 1 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 4988549885.0 Seg0001 88695.1094 1.1755 0.
19.499419.4994
region 2 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 2076120761.0 Seg0001 29523.0742 0.9522 0.
11.554711.5547
region 3 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 3599535995.0 Seg0001 57553.2656 1.0586 0.
10.954010.9540
region 4 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 2706027060.0 Seg0001 56422.7969 1.5332 0.
22.944622.9446
region 5 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 2873 2873.0 Seg0001 5976.5181 1.4734 0.0424
11.541211.4987
If it's simply a case of me misinterpreting the stats file, and column 6 being
the volume then I agree - there is no problem (and sorry for wasting so much
time!). In that case, what does the fourth/highlighted column represent?
Many thanks
Eli
____________
From: Eli Johnson
Sent: Friday, 27 January 2017 10:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
I have re-uploaded the file (see bottom of this email for info):
Along with the default FS output, there are 5 masks, corresponding to frontal,
temporal, parietal, occipital and insula regions (e.g.
20001-013-1_std/mri/20001_MNI_lobes_1-in-fs.mgz).
There are 10 surfs corresponding to lh & rh frontal,lh & rh temporal, lh & rh
parietal,lh & rh occipital and lh & rh insula (e.g.
20001-013-1_std/surf/20001_MNI_lobes_1-in-fs_surfrh.mgz).
I ran the commands:
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region1.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region2.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region3.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region4.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region5.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region1.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region2.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region3.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region4.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region5.stats
to extract volumes from the 10 regions. The stats files are located as
described in the command.
Also, in the ./20001-013-1_std/stats/ folder are the default FS lobular volumes
for comparison.
Thanks again for all of your help, do let me know if I've missed anything
again!!
Eli
You recently uploaded the following files to the Martinos Center FileDrop:
+ 20001-013-1_std.tar.gz (252.1 MiB)
Here are the people you sent these files to:
+ gr...@nmr.mgh.harvard.edu
In case you'd like to modify some of the above information, please use the link
below:
http://gate.nmr.mgh.harvard.edu/filedrop2/?g=7z2xk77v3ue
Cheers,
The Martinos Center Web Team
From: Eli Johnson
Sent: Thursday, 26 January 2017 7:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Ok sure, I will do it tomorrow as I don't have access to the stats file rig
Re: [Freesurfer] Cortical volume from masked region
Great - that makes sense!
Thanks again for your help in resolving this.
Eli
From: Eli Johnson
Sent: Friday, 27 January 2017 4:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
I was reading the fourth column in the stats files as the volumes (highlighted
in yellow), as that seems to correspond to the volume_mm3 label when the
columns are lined up. Also, when I run asegstats2file with the
'rh.vol_region1.stats' file specified alongside 'volume' as the measure, the
output is the fourth(highlighted) number in the stats files.
region 1 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 4988549885.0 Seg0001 88695.1094 1.1755 0.
19.499419.4994
region 2 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 2076120761.0 Seg0001 29523.0742 0.9522 0.
11.554711.5547
region 3 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 3599535995.0 Seg0001 57553.2656 1.0586 0.
10.954010.9540
region 4 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 2706027060.0 Seg0001 56422.7969 1.5332 0.
22.944622.9446
region 5 rh:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
1 1 2873 2873.0 Seg0001 5976.5181 1.4734 0.0424
11.541211.4987
If it's simply a case of me misinterpreting the stats file, and column 6 being
the volume then I agree - there is no problem (and sorry for wasting so much
time!). In that case, what does the fourth/highlighted column represent?
Many thanks
Eli
____________
From: Eli Johnson
Sent: Friday, 27 January 2017 10:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
I have re-uploaded the file (see bottom of this email for info):
Along with the default FS output, there are 5 masks, corresponding to frontal,
temporal, parietal, occipital and insula regions (e.g.
20001-013-1_std/mri/20001_MNI_lobes_1-in-fs.mgz).
There are 10 surfs corresponding to lh & rh frontal,lh & rh temporal, lh & rh
parietal,lh & rh occipital and lh & rh insula (e.g.
20001-013-1_std/surf/20001_MNI_lobes_1-in-fs_surfrh.mgz).
I ran the commands:
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region1.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region2.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region3.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region4.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surfrh.mgz --id
1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum
./${i}-013-1_std/rh.vol_region5.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region1.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region2.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region3.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region4.stats
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surf.mgz --id 1
--accumulate --i ./${i}-013-1_std/surf/lh.volume --sum
./${i}-013-1_std/lh.vol_region5.stats
to extract volumes from the 10 regions. The stats files are located as
described in the command.
Also, in the ./20001-013-1_std/stats/ folder are the default FS lobular volumes
for comparison.
Thanks again for all of your help, do let me know if I've missed anything
again!!
Eli
You recently uploaded the following files to the Martinos Center FileDrop:
+ 20001-013-1_std.tar.gz (252.1 MiB)
Here are the people you sent these files to:
+ gr...@nmr.mgh.harvard.edu
In case you'd like to modify some of the above information, please use the link
below:
http://gate.nmr.mgh.harvard.edu/filedrop2/?g=7z2xk77v3ue
Cheers,
The Martinos Center Web Team
_
