Hi All,
I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n.
Thanks, Josh
OK, I think I can take the output of binarize and then use FSL's fslroi tool to split up on my plane, the find the volume of that final mask...that will work as long as the output of binarize is in the same space as its input.?.
On Wed, Nov 23, 2011 at 8:12 AM, Joshua Lee jkilee@ucdavis.edu wrote:
Hi All,
I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n.
Thanks, Josh
If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/FreeSurferColorLUT.txt doug
Joshua Lee wrote:
Hi All,
I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n.
Thanks, Josh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hey Doug, THanks. That looks simpler. I'll probably use that.
Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats?
Josh
On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/**FreeSurferColorLUT.txt doug
Joshua Lee wrote:
Hi All,
I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n.
Thanks, Josh
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/**compliancelinehttp://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.
probably not, as the aseg.stats calculation uses partial volume estimates.
cheers Bruce On Wed, 30 Nov 2011, Joshua Lee wrote:
Hey Doug, THanks. That looks simpler. I'll probably use that.
Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats?
Josh
On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/FreeSurferColorLUT.txt doug
Joshua Lee wrote:Hi All,
I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n.
Thanks, Josh
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
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.
Hi Bruce,
I'll see if I can phrase this right
In aseg.mgz each region has essentially been given a unique number (e.g. 17 for left hippocampus, for example). ROI taken from aseg.mgz volumes are non-probabilistic, yes-no affairs already. MRI_binarize just pulls this out when we want to look at particular regions, say left hipp???
Josh
On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
probably not, as the aseg.stats calculation uses partial volume estimates.
cheers Bruce
On Wed, 30 Nov 2011, Joshua Lee wrote:
Hey Doug, THanks. That looks simpler. I'll probably use that.
Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats?
Josh
On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/**FreeSurferColorLUT.txt doug
Joshua Lee wrote:Hi All,
I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n.
Thanks, Josh
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/**compliancelinehttp://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.
yes, that's all true, but the #s reported in the aseg.mgz use a partial volume estimation to correct for border voxels using the image intensities in the norm.mgz
cheers Bruce On Wed, 30 Nov 2011, Joshua Lee wrote:
Hi Bruce,
I'll see if I can phrase this right
In aseg.mgz each region has essentially been given a unique number (e.g. 17 for left hippocampus, for example). ROI taken from aseg.mgz volumes are non-probabilistic, yes-no affairs already. MRI_binarize just pulls this out when we want to look at particular regions, say left hipp???
Josh
On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: probably not, as the aseg.stats calculation uses partial volume estimates.
cheers BruceOn Wed, 30 Nov 2011, Joshua Lee wrote:
Hey Doug, THanks. That looks simpler. I'll probably use that. Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats? Josh On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/FreeSurferColorLUT.txt doug Joshua Lee wrote: Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh ------------------------------------------------------------------------ _______________________________________________ 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 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.
oops, I meant the aseg.stats, not the aseg.mgz On Wed, 30 Nov 2011, Joshua Lee wrote:
Hi Bruce,
I'll see if I can phrase this right
In aseg.mgz each region has essentially been given a unique number (e.g. 17 for left hippocampus, for example). ROI taken from aseg.mgz volumes are non-probabilistic, yes-no affairs already. MRI_binarize just pulls this out when we want to look at particular regions, say left hipp???
Josh
On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: probably not, as the aseg.stats calculation uses partial volume estimates.
cheers BruceOn Wed, 30 Nov 2011, Joshua Lee wrote:
Hey Doug, THanks. That looks simpler. I'll probably use that. Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats? Josh On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/FreeSurferColorLUT.txt doug Joshua Lee wrote: Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh ------------------------------------------------------------------------ _______________________________________________ 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 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.
I'm glad you caught that because I suddenly got really confused! Thank Bruce for all your hard work! Josh -
On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
oops, I meant the aseg.stats, not the aseg.mgz
On Wed, 30 Nov 2011, Joshua Lee wrote:
Hi Bruce,
I'll see if I can phrase this right
In aseg.mgz each region has essentially been given a unique number (e.g. 17 for left hippocampus, for example). ROI taken from aseg.mgz volumes are non-probabilistic, yes-no affairs already. MRI_binarize just pulls this out when we want to look at particular regions, say left hipp???
Josh
On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: probably not, as the aseg.stats calculation uses partial volume estimates.
cheers BruceOn Wed, 30 Nov 2011, Joshua Lee wrote:
Hey Doug, THanks. That looks simpler. I'll probably use that. Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats? Josh On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/**FreeSurferColorLUT.txt doug Joshua Lee wrote: Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh ------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://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<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.
Actually, I have one last-last question. If I use mri_binarize on my aseg.mgz file, does it remain in the same 'space'? Meaning, if I identify a z-coordinate of interest in aseg.mgz, will that z -coordinate still be valid in nifti file i'd have mri-Binarize create?
Josh
On Wed, Nov 30, 2011 at 2:32 PM, Joshua Lee jkilee@ucdavis.edu wrote:
I'm glad you caught that because I suddenly got really confused! Thank Bruce for all your hard work! Josh
On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
oops, I meant the aseg.stats, not the aseg.mgz
On Wed, 30 Nov 2011, Joshua Lee wrote:
Hi Bruce,
I'll see if I can phrase this right
In aseg.mgz each region has essentially been given a unique number (e.g. 17 for left hippocampus, for example). ROI taken from aseg.mgz volumes are non-probabilistic, yes-no affairs already. MRI_binarize just pulls this out when we want to look at particular regions, say left hipp???
Josh
On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: probably not, as the aseg.stats calculation uses partial volume estimates.
cheers BruceOn Wed, 30 Nov 2011, Joshua Lee wrote:
Hey Doug, THanks. That looks simpler. I'll probably use that. Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats? Josh On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/**FreeSurferColorLUT.txt doug Joshua Lee wrote: Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh ------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://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<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.
yes On Wed, 30 Nov 2011, Joshua Lee wrote:
Actually, I have one last-last question. If I use mri_binarize on my aseg.mgz file, does it remain in the same 'space'? Meaning, if I identify a z-coordinate of interest in aseg.mgz, will that z -coordinate still be valid in nifti file i'd have mri-Binarize create?
Josh
On Wed, Nov 30, 2011 at 2:32 PM, Joshua Lee jkilee@ucdavis.edu wrote: I'm glad you caught that because I suddenly got really confused! Thank Bruce for all your hard work! Josh -
On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: oops, I meant the aseg.stats, not the aseg.mgz
On Wed, 30 Nov 2011, Joshua Lee wrote:
Hi Bruce, I'll see if I can phrase this right In aseg.mgz each region has essentially been given a unique number (e.g. 17 for left hippocampus, for example). ROI taken from aseg.mgz volumes are non-probabilistic, yes-no affairs already. MRI_binarize just pulls this out when we want to look at particular regions, say left hipp??? Josh On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: probably not, as the aseg.stats calculation uses partial volume estimates. cheers Bruce On Wed, 30 Nov 2011, Joshua Lee wrote: Hey Doug, THanks. That looks simpler. I'll probably use that. Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats? Josh On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/FreeSurferColorLUT.txt doug Joshua Lee wrote: Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh ------------------------------------------------------------------------ _______________________________________________ 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 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.
Since it has be reiterated many times that aseg.stats is calulated using estimates of partial volumes that increase accuracy over obtaining volumes from binarized masks, I wonder whether I might still incorporate this advanced procedure while still bisecting a previous segmentation by some arbitrary plane, say z=27.
I propose the following procedure as an example for splitting the left amygdala (for example) and still using the partial volume estimation:
1. Make copies of aseg.mgz, one each for the partial segmentation you want to create (e.g. aseg_anterior.mgz and aseg_posterior.mgz, to split the amygdala by the plane z =27 on some particular brain, by some particular protocol). 2. Edit aseg_posterior.mgz (e.g. by tkmedit) to remove all amygdala anterior to z = 27. Similarly edit aseg_anterior.mgz to remove posterior segments. 3. Run the stats on these edited segmentations, and record the data in aseg_posterior.stats and aseg_anterior.stats
Does this sound reasonable and wise procedure? If so, is there a quick way to remove the unwanted segmentations without manually using a brush, slice by slice in tkmedit? Loading it into Matlab, like Doug suggests, would allow the edits I think, but then I'd have to rewrite the file from matlab.. I think.
Josh
On Wed, Nov 30, 2011 at 2:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
yes
On Wed, 30 Nov 2011, Joshua Lee wrote:
Actually, I have one last-last question.
If I use mri_binarize on my aseg.mgz file, does it remain in the same 'space'? Meaning, if I identify a z-coordinate of interest in aseg.mgz, will that z -coordinate still be valid in nifti file i'd have mri-Binarize create?
Josh
On Wed, Nov 30, 2011 at 2:32 PM, Joshua Lee jkilee@ucdavis.edu wrote: I'm glad you caught that because I suddenly got really confused! Thank Bruce for all your hard work! Josh -
On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: oops, I meant the aseg.stats, not the aseg.mgz
On Wed, 30 Nov 2011, Joshua Lee wrote:
Hi Bruce, I'll see if I can phrase this right In aseg.mgz each region has essentially been given a unique number (e.g. 17 for left hippocampus, for example). ROI taken from aseg.mgz volumes are non-probabilistic, yes-no affairs already. MRI_binarize just pulls this out when we want to look at particular regions, say left hipp??? Josh On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: probably not, as the aseg.stats calculation uses partial volume estimates. cheers Bruce On Wed, 30 Nov 2011, Joshua Lee wrote: Hey Doug, THanks. That looks simpler. I'll probably use that. Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats? Josh On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/**FreeSurferColorLUT.txt doug Joshua Lee wrote: Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh -----------------------------**------------------------------**
_____________________________**__________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.**edu<Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://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<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.
Forgive me, I hadn't realize that tkmedit had a fill a function. I can do what I propsed easily. Thanks again! - Joshua
On Thu, Dec 1, 2011 at 11:15 AM, Joshua Lee jkilee@ucdavis.edu wrote:
Since it has be reiterated many times that aseg.stats is calulated using estimates of partial volumes that increase accuracy over obtaining volumes from binarized masks, I wonder whether I might still incorporate this advanced procedure while still bisecting a previous segmentation by some arbitrary plane, say z=27.
I propose the following procedure as an example for splitting the left amygdala (for example) and still using the partial volume estimation:
- Make copies of aseg.mgz, one each for the partial segmentation you
want to create (e.g. aseg_anterior.mgz and aseg_posterior.mgz, to split the amygdala by the plane z =27 on some particular brain, by some particular protocol). 2. Edit aseg_posterior.mgz (e.g. by tkmedit) to remove all amygdala anterior to z = 27. Similarly edit aseg_anterior.mgz to remove posterior segments. 3. Run the stats on these edited segmentations, and record the data in aseg_posterior.stats and aseg_anterior.stats
Does this sound reasonable and wise procedure? If so, is there a quick way to remove the unwanted segmentations without manually using a brush, slice by slice in tkmedit? Loading it into Matlab, like Doug suggests, would allow the edits I think, but then I'd have to rewrite the file from matlab.. I think.
Josh
On Wed, Nov 30, 2011 at 2:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
yes
On Wed, 30 Nov 2011, Joshua Lee wrote:
Actually, I have one last-last question.
If I use mri_binarize on my aseg.mgz file, does it remain in the same 'space'? Meaning, if I identify a z-coordinate of interest in aseg.mgz, will that z -coordinate still be valid in nifti file i'd have mri-Binarize create?
Josh
On Wed, Nov 30, 2011 at 2:32 PM, Joshua Lee jkilee@ucdavis.edu wrote: I'm glad you caught that because I suddenly got really confused! Thank Bruce for all your hard work! Josh -
On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: oops, I meant the aseg.stats, not the aseg.mgz
On Wed, 30 Nov 2011, Joshua Lee wrote:
Hi Bruce, I'll see if I can phrase this right In aseg.mgz each region has essentially been given a unique number (e.g. 17 for left hippocampus, for example). ROI taken from aseg.mgz volumes are non-probabilistic, yes-no affairs already. MRI_binarize just pulls this out when we want to look at particular regions, say left hipp??? Josh On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: probably not, as the aseg.stats calculation uses partial volume estimates. cheers Bruce On Wed, 30 Nov 2011, Joshua Lee wrote: Hey Doug, THanks. That looks simpler. I'll probably use that. Question: Will the total volume of a ROI taken from aseg.mgz correspond to the volume given in aseg.stats? Josh On Wed, Nov 30, 2011 at 9:55 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: If you have matlab, you can load the aseg into matlab, like aseg = MRIread('aseg.mgz'); vol = length(aseg.vol(:,:,n:256) == ID); where ID is the code number for the ROI you want as found in $FREESURFER_HOME/**FreeSurferColorLUT.txt doug Joshua Lee wrote: Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh -----------------------------**------------------------------**
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