Hi Folks,
I am trying to create an entorhinal cortex volume from ?h.entorhinal_exvivo.label using mri_label2vol
I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is:
*mri_label2vol --label label/lh.entorhinal_exvivo.label --temp mri/nu.mgz --identity --o mri/lh-new-erc.mgz *
I took the sum of the voxels in this new mask i created (lh-new-erc.mgz) and it is 215;
I looked at the volume provided in lh.entorhinal_exvivo.stats and it is 925; (from the log file I believe this is created using the command:
mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label bert lh white)
I was expecting the numbers to match or at-least be close; I am guessing I am using mri_label2vol incorrectly ?
Could someone help me with this issue ?
Thanks
Mehul
not necessarily. That is a very small structure, and getting a few edge voxels wrong will mess things up a lot. Can you load lh-new-erc.mgz in tkmedit and load the surfaces too and see how good it did? doug
On 06/26/2013 06:49 PM, Mehul Sampat wrote:
Hi Folks,
I am trying to create an entorhinal cortex volume from ?h.entorhinal_exvivo.label using mri_label2vol
I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is:
*mri_label2vol --label label/lh.entorhinal_exvivo.label --temp mri/nu.mgz --identity --o mri/lh-new-erc.mgz*
I took the sum of the voxels in this new mask i created (lh-new-erc.mgz) and it is 215; I looked at the volume provided inlh.entorhinal_exvivo.stats and it is 925; (from the log file I believe this is created using the command:
mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label bert lh white)
I was expecting the numbers to match orat-leastbe close; I am guessing I am using mri_label2vol incorrectly ?
Could someone help me with this issue ?
Thanks
Mehul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
won't the anatomical_stats one multiply thickness by surface area, where the label2vol will only fill voxels on the gray/white boundary, not all the way through the ribbon? Mehul: if you visualize the one from label2vol does it fill the ribbon or just hug the white boundary?
On Wed, 26 Jun 2013, Douglas N Greve wrote:
not necessarily. That is a very small structure, and getting a few edge voxels wrong will mess things up a lot. Can you load lh-new-erc.mgz in tkmedit and load the surfaces too and see how good it did? doug
On 06/26/2013 06:49 PM, Mehul Sampat wrote:
Hi Folks,
I am trying to create an entorhinal cortex volume from ?h.entorhinal_exvivo.label using mri_label2vol
I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is:
*mri_label2vol --label label/lh.entorhinal_exvivo.label --temp
mri/nu.mgz --identity --o mri/lh-new-erc.mgz*
I took the sum of the voxels in this new mask i created (lh-new-erc.mgz) and it is 215; I looked at the volume provided inlh.entorhinal_exvivo.stats and it is 925; (from the log file I believe this is created using the command:
mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label bert lh white)
I was expecting the numbers to match orat-leastbe close; I am guessing I am using mri_label2vol incorrectly ?
Could someone help me with this issue ?
Thanks
Mehul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Oh, right. Mehul, you'll need to tell it to fill the ribbon with something like --proj frac 0 1 .1 doug
On 06/26/2013 06:55 PM, Bruce Fischl wrote:
won't the anatomical_stats one multiply thickness by surface area, where the label2vol will only fill voxels on the gray/white boundary, not all the way through the ribbon? Mehul: if you visualize the one from label2vol does it fill the ribbon or just hug the white boundary?
On Wed, 26 Jun 2013, Douglas N Greve wrote:
not necessarily. That is a very small structure, and getting a few edge voxels wrong will mess things up a lot. Can you load lh-new-erc.mgz in tkmedit and load the surfaces too and see how good it did? doug
On 06/26/2013 06:49 PM, Mehul Sampat wrote:
Hi Folks,
I am trying to create an entorhinal cortex volume from ?h.entorhinal_exvivo.label using mri_label2vol
I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is:
*mri_label2vol --label label/lh.entorhinal_exvivo.label --temp
mri/nu.mgz --identity --o mri/lh-new-erc.mgz*
I took the sum of the voxels in this new mask i created (lh-new-erc.mgz) and it is 215; I looked at the volume provided inlh.entorhinal_exvivo.stats and it is 925; (from the log file I believe this is created using the command:
mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label bert lh white)
I was expecting the numbers to match orat-leastbe close; I am guessing I am using mri_label2vol incorrectly ?
Could someone help me with this issue ?
Thanks
Mehul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, Yes, the one from label2vol "just hugs the white boundary" Doug, I will try with the --proj frac 0 1 .1 option and let you all know. Thanks Mehul
On Wed, Jun 26, 2013 at 3:58 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Oh, right. Mehul, you'll need to tell it to fill the ribbon with something like --proj frac 0 1 .1 doug
On 06/26/2013 06:55 PM, Bruce Fischl wrote:
won't the anatomical_stats one multiply thickness by surface area, where the label2vol will only fill voxels on the gray/white boundary, not all the way through the ribbon? Mehul: if you visualize the one from label2vol does it fill the ribbon or just hug the white boundary?
On Wed, 26 Jun 2013, Douglas N Greve wrote:
not necessarily. That is a very small structure, and getting a few edge voxels wrong will mess things up a lot. Can you load lh-new-erc.mgz in tkmedit and load the surfaces too and see how good it did? doug
On 06/26/2013 06:49 PM, Mehul Sampat wrote:
Hi Folks,
I am trying to create an entorhinal cortex volume from ?h.entorhinal_exvivo.label using mri_label2vol
I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is:
*mri_label2vol --label label/lh.entorhinal_exvivo.label --temp
mri/nu.mgz --identity --o mri/lh-new-erc.mgz*
I took the sum of the voxels in this new mask i created (lh-new-erc.mgz) and it is 215; I looked at the volume provided inlh.entorhinal_exvivo.stats and it is 925; (from the log file I believe this is created using the command:
mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label bert lh white)
I was expecting the numbers to match orat-leastbe close; I am guessing I am using mri_label2vol incorrectly ?
Could someone help me with this issue ?
Thanks
Mehul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Hi Doug and Bruce,
Adding the option "-proj frac 0 1 .0 " to mri_label2vol helps a lot;
Just in case anyone needs it, the full command is :
mri_label2vol --label label/lh.entorhinal_exvivo.label --temp mri/nu.mgz --identity --o mri/lh-new-erc-filled-0.4.mgz --proj frac 0 1 .1 --subject bert --hemi lh
I attached images of slices of the masks created with and without this option; The sum of the voxels in the mask i created is 1016 and is much closer to the volume
the volume provided in lh.entorhinal_exvivo.stats (which is 925). I am curious why they are different? are there other advanced options in mri_label2vol I can try out ?
Thanks
Mehul
On Wed, Jun 26, 2013 at 4:11 PM, Mehul Sampat mpsampat@gmail.com wrote:
Hi Bruce, Yes, the one from label2vol "just hugs the white boundary" Doug, I will try with the --proj frac 0 1 .1 option and let you all know. Thanks Mehul
On Wed, Jun 26, 2013 at 3:58 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Oh, right. Mehul, you'll need to tell it to fill the ribbon with something like --proj frac 0 1 .1 doug
On 06/26/2013 06:55 PM, Bruce Fischl wrote:
won't the anatomical_stats one multiply thickness by surface area, where the label2vol will only fill voxels on the gray/white boundary, not all the way through the ribbon? Mehul: if you visualize the one from label2vol does it fill the ribbon or just hug the white boundary?
On Wed, 26 Jun 2013, Douglas N Greve wrote:
not necessarily. That is a very small structure, and getting a few edge voxels wrong will mess things up a lot. Can you load lh-new-erc.mgz in tkmedit and load the surfaces too and see how good it did? doug
On 06/26/2013 06:49 PM, Mehul Sampat wrote:
Hi Folks,
I am trying to create an entorhinal cortex volume from ?h.entorhinal_exvivo.label using mri_label2vol
I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is:
*mri_label2vol --label label/lh.entorhinal_exvivo.label --temp
mri/nu.mgz --identity --o mri/lh-new-erc.mgz*
I took the sum of the voxels in this new mask i created (lh-new-erc.mgz) and it is 215; I looked at the volume provided inlh.entorhinal_exvivo.stats and it is 925; (from the log file I believe this is created using the
command:
mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label bert lh white)
I was expecting the numbers to match orat-leastbe close; I am guessing I am using mri_label2vol incorrectly ?
Could someone help me with this issue ?
Thanks
Mehul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Hi Mehul
the surfaces don't follow voxel boundaries and mris_anatomical_stats is computed from them so they won't necessarily match
cheers Bruce On Wed, 26 Jun 2013, Mehul Sampat wrote:
Hi Doug and Bruce,
Adding the option "-proj frac 0 1 .0 " to mri_label2vol helps a lot;
Just in case anyone needs it, the full command is :
mri_label2vol --label label/lh.entorhinal_exvivo.label --temp mri/nu.mgz - -identity --o mri/lh-new-erc-filled-0.4.mgz --proj frac 0 1 .1 --subject ber t --hemi lh
I attached images of slices of the masks created with and without this optio n; The sum of the voxels in the mask i created is 1016 and is much closer to the volume
the volume provided in lh.entorhinal_exvivo.stats (which is 925). I am curio us why they are different? are there other advanced options in mri_label2vol I can try out ?
Thanks
Mehul
On Wed, Jun 26, 2013 at 4:11 PM, Mehul Sampat mpsampat@gmail.com wrote: Hi Bruce, Yes, the one from label2vol "just hugs the white boundary" Doug, I will try with the --proj frac 0 1 .1 option and let you all know. Thanks Mehul
On Wed, Jun 26, 2013 at 3:58 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Oh, right. Mehul, you'll need to tell it to fill the ribbon with something like --proj frac 0 1 .1 doug
On 06/26/2013 06:55 PM, Bruce Fischl wrote: > won't the anatomical_stats one multiply thickness by surface area, > where the label2vol will only fill voxels on the gray/white boundary, > not all the way through the ribbon? Mehul: if you visualize the one > from label2vol does it fill the ribbon or just hug the white boundary? > > On Wed, 26 Jun 2013, Douglas N Greve wrote: > >> not necessarily. That is a very small structure, and getting a few edge >> voxels wrong will mess things up a lot. Can you load lh-new-erc.mgz in >> tkmedit and load the surfaces too and see how good it did? >> doug >> >> On 06/26/2013 06:49 PM, Mehul Sampat wrote: >>> Hi Folks, >>> >>> >>> I am trying to create an entorhinal cortex volume from >>> ?h.entorhinal_exvivo.label using mri_label2vol >>> >>> >>> I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is: >>> >>> >>> *mri_label2vol --label label/lh.entorhinal_exvivo.label --temp > mri/nu.mgz --identity --o mri/lh-new-erc.mgz* >>> >>> >>> >>> >>> >>> I took the sum of the voxels in this new mask i created >>> (lh-new-erc.mgz) and it is 215; >>> I looked at the volume provided inlh.entorhinal_exvivo.stats and it >>> is 925; (from the log file I believe this is created using the command: >>> >>> >>> mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b >>> -l ./lh.entorhinal_exvivo.label bert lh white) >>> >>> >>> >>> >>> >>> I was expecting the numbers to match orat-leastbe close; I am >>> guessing I am using mri_label2vol incorrectly ? >>> >>> >>> Could someone help me with this issue ? >>> >>> >>> Thanks >>> >>> >>> Mehul >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Mehul Sampat