Sorry, I'll have to defer to Bruce, who wrote the code. doug
On 12/17/2012 11:24 AM, Gabriel Gonzalez Escamilla wrote:
OK the Doug,
I know which are the voxels contained into a ROI. From all of them I know the norm.mgz and the brainmask.mgz values, because I'm assuming that FS always work with the brainmask.mgz to know the actual voxel intensity, as indicated when running mri_segstats.
I can easily calculate the mean of the norm voxel intensities, do I need anything else?
Could you tell me the formula to compute the PV?
Kind Regards, Gabriel.
El 17/12/12, *Douglas N Greve * greve@nmr.mgh.harvard.edu escribió:
The PV is done based on intensities. For each voxel an the boundary of an ROI, the voxel intensity is assumed to be a weighted summation of the the average intensities in each ROI. Knowing the average intensities in the ROIs and the actual intensity of the voxel, the PV can be computed. doug
On 12/17/2012 09:59 AM, Gabriel Gonzalez Escamilla wrote:
Thanks Doug,
In my case I did as you said but as Bruce recommend use the wmparc, so the voxels less than 4000, and = 5001 were left , and more than or equal to 4000, and =5002 were right.
So different approach but I think would be the same, isn't it?
Can you explain to me how FS makes the PV correction on the output volumes in aseg.stats?
Best Regards, Gabriel.
El 13/12/12, *Douglas N Greve * greve@nmr.mgh.harvard.edu escribió:
Gabriel, the way I've done it is to just assign WMSA to left or right based on the column number of the WMSA voxel. If it is less than 128, then it is right (78) if it is greater than 128 it is left (79). It's not perfect, but it is correct in the vast majority of cases. doug
On 12/12/2012 01:56 PM, Gabriel Gonzalez Escamilla wrote:
Thanks Bruce,
The problem is that for this set of subjects I only have the T1s,
anyways I would like to give a try onto the tools for WMSA, since I have T2 from some subjects.
On the other hand, If I'm right the way to do the assignment on
matlab, would be something like opening the mgz, finding their positions and look which are the neighbors right?
If so, I would like to not assign just the neighbor voxel, as this
might bias the assignment, I'm guessing that something like the assignment done during the aparc+aseg.mgz creation (using GM parcelation to map GM labels to the wm voxels - mri_aparc2aseg) should be a correct way to do so. Can you point me to an article or explain to me how this works indeed, and how the decision to the belonging voxel is made, I think I know the basis, but not enough to make my own script.
If I do not understand bad, is something like, you take a voxel a
look to some contiguous voxels till you get into a point where all the contiguous voxels are too far from the seed, and are surrounded by lots of voxels belonging to other areas. I'm not quite sure about the decision about when to stop the search. I really think that the method like the implemented in the mri_apar2aseg is the perfect
solution.
Regards, Gabriel
El 12/12/12, *Bruce Fischl * fischl@nmr.mgh.harvard.edu escribió:
then I would either use TRACULA (if you have DWI) or the wmparc to
generate ROIs. I meant that you could count whether there are more lh or rh wm labels neighboring each one to figure out which hemi they
are in
cheers Bruce
On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote:
>Yes I did loo at the total WH-hypointensities(77), and substract
them without a problem.
> >What do you mean with lateralize them based on neighboring labels?
How can I perform such thing on FS?
> >Actually I'm interested in knowing to wich specific label o region
they are.
> >Bests, >Gabriel > > >El 12/12/12, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió: > Hi Gabriel > > we don't lateralize them by default, so look for
WM_hypointensities (77) instead. It would be pretty easy to
> lateralize them based on neighboring labels. > > cheers > Bruce > > > On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: > > > > >Dear Freesurfers, > > > >I'm looking for a way to compute the left and right
WM-hypointensities, as volume values or images. They always
> appear empty in > >the aseg.stats, and the corresponding segs No 78 & 79 do
not appear in the aseg.mgz, and I'm a bit lost with it.
> > > >Can any one help me? > > > >Best Regards, > >Gabriel. > > > > > > > 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. > > >-- >-------------------------- >PhD. student Gabriel González-Escamilla >Laboratory of Functional Neuroscience >Department of Physiology, Anatomy, and Cell Biology >University Pablo de Olavide >Ctra. de Utrera, Km.1 >41013 - Seville >- Spain - > >Email: ggonesc@upo.es >http://www.upo.es/neuroaging/es/ >
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
-- 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 Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
-- 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 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
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
Hi Gabriel
we find the mean of the label intensity in a region around the voxel in question using voxels that don't border another label, then do the same for the most common neighboring label that is different from the one in question and compute the volume fraction assuming a linear mixing between those two means.
cheers Bruce
On Mon, 17 Dec 2012, Douglas N Greve wrote:
Sorry, I'll have to defer to Bruce, who wrote the code. doug
On 12/17/2012 11:24 AM, Gabriel Gonzalez Escamilla wrote:
OK the Doug,
I know which are the voxels contained into a ROI. From all of them I know the norm.mgz and the brainmask.mgz values, because I'm assuming that FS always work with the brainmask.mgz to know the actual voxel intensity, as indicated when running mri_segstats.
I can easily calculate the mean of the norm voxel intensities, do I need anything else?
Could you tell me the formula to compute the PV?
Kind Regards, Gabriel.
El 17/12/12, *Douglas N Greve * greve@nmr.mgh.harvard.edu escribió:
The PV is done based on intensities. For each voxel an the boundary of an ROI, the voxel intensity is assumed to be a weighted summation of the the average intensities in each ROI. Knowing the average intensities in the ROIs and the actual intensity of the voxel, the PV can be computed. doug
On 12/17/2012 09:59 AM, Gabriel Gonzalez Escamilla wrote:
Thanks Doug,
In my case I did as you said but as Bruce recommend use the wmparc, so the voxels less than 4000, and = 5001 were left , and more than or equal to 4000, and =5002 were right.
So different approach but I think would be the same, isn't it?
Can you explain to me how FS makes the PV correction on the output volumes in aseg.stats?
Best Regards, Gabriel.
El 13/12/12, *Douglas N Greve * greve@nmr.mgh.harvard.edu escribió:
Gabriel, the way I've done it is to just assign WMSA to left or right based on the column number of the WMSA voxel. If it is less than 128, then it is right (78) if it is greater than 128 it is left (79). It's not perfect, but it is correct in the vast majority of cases. doug
On 12/12/2012 01:56 PM, Gabriel Gonzalez Escamilla wrote:
Thanks Bruce,
The problem is that for this set of subjects I only have the T1s,
anyways I would like to give a try onto the tools for WMSA, since I have T2 from some subjects.
On the other hand, If I'm right the way to do the assignment on
matlab, would be something like opening the mgz, finding their positions and look which are the neighbors right?
If so, I would like to not assign just the neighbor voxel, as this
might bias the assignment, I'm guessing that something like the assignment done during the aparc+aseg.mgz creation (using GM parcelation to map GM labels to the wm voxels - mri_aparc2aseg) should be a correct way to do so. Can you point me to an article or explain to me how this works indeed, and how the decision to the belonging voxel is made, I think I know the basis, but not enough to make my own script.
If I do not understand bad, is something like, you take a voxel a
look to some contiguous voxels till you get into a point where all the contiguous voxels are too far from the seed, and are surrounded by lots of voxels belonging to other areas. I'm not quite sure about the decision about when to stop the search. I really think that the method like the implemented in the mri_apar2aseg is the perfect
solution.
Regards, Gabriel
El 12/12/12, *Bruce Fischl * fischl@nmr.mgh.harvard.edu escribió: > then I would either use TRACULA (if you have DWI) or the wmparc to
generate ROIs. I meant that you could count whether there are more lh or rh wm labels neighboring each one to figure out which hemi they
are in
> > cheers > Bruce > > > On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: > >> Yes I did loo at the total WH-hypointensities(77), and substract
them without a problem.
>> >> What do you mean with lateralize them based on neighboring labels?
How can I perform such thing on FS?
>> >> Actually I'm interested in knowing to wich specific label o region
they are.
>> >> Bests, >> Gabriel >> >> >> El 12/12/12, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió: >> Hi Gabriel >> >> we don't lateralize them by default, so look for
WM_hypointensities (77) instead. It would be pretty easy to
>> lateralize them based on neighboring labels. >> >> cheers >> Bruce >> >> >> On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: >> >> > >> >Dear Freesurfers, >> > >> >I'm looking for a way to compute the left and right
WM-hypointensities, as volume values or images. They always
>> appear empty in >> >the aseg.stats, and the corresponding segs No 78 & 79 do
not appear in the aseg.mgz, and I'm a bit lost with it.
>> > >> >Can any one help me? >> > >> >Best Regards, >> >Gabriel. >> > >> > >> >> >> 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. >> >> >> -- >> -------------------------- >> PhD. student Gabriel González-Escamilla >> Laboratory of Functional Neuroscience >> Department of Physiology, Anatomy, and Cell Biology >> University Pablo de Olavide >> Ctra. de Utrera, Km.1 >> 41013 - Seville >> - Spain - >> >> Email: ggonesc@upo.es >> http://www.upo.es/neuroaging/es/ >>
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
-- 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 Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
-- 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 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
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Gabriel Gonzalez Escamilla