Is this the difference you mean?
[t:D:mri-> grep Cortex ~/tmp/lh.total.stats # Measure Cortex, NumVert, Number of Vertices, 118847, unitless # Measure Cortex, SurfArea, Surface Area, 78090, mm^2
[t:D:mri-> grep Cortex ~/tmp/lh.aparc.stats # Measure Cortex, NumVert, Number of Vertices, 111237, unitless # Measure Cortex, SurfArea, Surface Area, 72998.7, mm^2
If so this is just the difference in the vertices coverted by cortex.label vs aparc
On 03/24/2014 12:49 PM, _andreia_@sapo.pt wrote:
Hi Doug,
I've attached the files. To contextualize a little bit, I'm using Brodmann Areas measures (CT, surface area and volume, thresholded to the correct probability) and I'll be extracting the surface area using pial and white surface. However, I'll be also analyzing whole brain using the aparc stats (again, CT, surface area and volume) - should I use the file that is in agreement with aparc?
I don't understand why total.stats gives different values from cortex.stats since I've created the total.stats file using the command:
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b SUBJ lh white
One more question: is the ?hCortexvol value from aseg that I should use to get the total volume of each hemisphere?
Sorry for so many questions...
Thank you!
Andreia
Quoting Douglas Greve greve@nmr.mgh.harvard.edu:
How much of a difference is there? There should not be much, but there will be some because the aparc does not cover the exact same vertices as cortex.label doug
On 3/24/14 8:04 AM, _andreia_@sapo.pt wrote:
Hello list,
I have a question regarding what stats are more correct to use to get whole hemisphere surface area and mean thickness.
The cortex.label values extracted using the two bottom command lines don't match aparc stats, however they match in the number of vertices between them, and using pial or white surface also results in values that make sense comparing each one (higher surface area using pial, same thickness, same volumes).
In the past I've been using the two first command lines (in which values agree in the same way as cortex.label between them but are also in agreement with aparc.stats), however now I'm having this question: which one is the correct one to use?
And why does this difference exists?
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b SUBJ lh white (matches aparcstats)
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total_pial.stats -b SUBJ lh pial (matches aparcstats)
mris_anatomical_stats -mgz -f ../stats/lh.cortex_pial.stats SUBJ lh pial (does not match aparcstats)
mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats SUBJ lh white (does not match aparcstats)
Thank you in advance, Andreia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
I was also referring to the surface area and thickness (looking at the files originated from white matter, which is also the default for aparc I think):
For surface area aparc= 72998.7 total= 72999 cortex=78090
For CT aparc= 2.422 total= 2.422 cortex= 2.313
And also, which volume measure should I use to get total hemisphere gray volume? Aseg lhCortexVol=196557.55 (is the surface-based estimation?) Aparc (the sum of all labels)=199854 total.stats=199857 cortex= 204048
It seems that the value from total.stats is more approximated to the one from the sum of aparc.
I'm using F.S. 5.0.
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Is this the difference you mean?
[t:D:mri-> grep Cortex ~/tmp/lh.total.stats # Measure Cortex, NumVert, Number of Vertices, 118847, unitless # Measure Cortex, SurfArea, Surface Area, 78090, mm^2
[t:D:mri-> grep Cortex ~/tmp/lh.aparc.stats # Measure Cortex, NumVert, Number of Vertices, 111237, unitless # Measure Cortex, SurfArea, Surface Area, 72998.7, mm^2
If so this is just the difference in the vertices coverted by cortex.label vs aparc
On 03/24/2014 12:49 PM, _andreia_@sapo.pt wrote:
Hi Doug,
I've attached the files. To contextualize a little bit, I'm using Brodmann Areas measures (CT, surface area and volume, thresholded to the correct probability) and I'll be extracting the surface area using pial and white surface. However, I'll be also analyzing whole brain using the aparc stats (again, CT, surface area and volume) - should I use the file that is in agreement with aparc?
I don't understand why total.stats gives different values from cortex.stats since I've created the total.stats file using the command:
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b SUBJ lh white
One more question: is the ?hCortexvol value from aseg that I should use to get the total volume of each hemisphere?
Sorry for so many questions...
Thank you!
Andreia
Quoting Douglas Greve greve@nmr.mgh.harvard.edu:
How much of a difference is there? There should not be much, but there will be some because the aparc does not cover the exact same vertices as cortex.label doug
On 3/24/14 8:04 AM, _andreia_@sapo.pt wrote:
Hello list,
I have a question regarding what stats are more correct to use to get whole hemisphere surface area and mean thickness.
The cortex.label values extracted using the two bottom command lines don't match aparc stats, however they match in the number of vertices between them, and using pial or white surface also results in values that make sense comparing each one (higher surface area using pial, same thickness, same volumes).
In the past I've been using the two first command lines (in which values agree in the same way as cortex.label between them but are also in agreement with aparc.stats), however now I'm having this question: which one is the correct one to use?
And why does this difference exists?
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b SUBJ lh white (matches aparcstats)
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total_pial.stats -b SUBJ lh pial (matches aparcstats)
mris_anatomical_stats -mgz -f ../stats/lh.cortex_pial.stats SUBJ lh pial (does not match aparcstats)
mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats SUBJ lh white (does not match aparcstats)
Thank you in advance, Andreia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- 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
Sorry, what is the difference between total and aparc?
On 03/24/2014 01:29 PM, _andreia_@sapo.pt wrote:
I was also referring to the surface area and thickness (looking at the files originated from white matter, which is also the default for aparc I think):
For surface area aparc= 72998.7 total= 72999 cortex=78090
For CT aparc= 2.422 total= 2.422 cortex= 2.313
And also, which volume measure should I use to get total hemisphere gray volume? Aseg lhCortexVol=196557.55 (is the surface-based estimation?) Aparc (the sum of all labels)=199854 total.stats=199857 cortex= 204048
It seems that the value from total.stats is more approximated to the one from the sum of aparc.
I'm using F.S. 5.0.
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Is this the difference you mean?
[t:D:mri-> grep Cortex ~/tmp/lh.total.stats # Measure Cortex, NumVert, Number of Vertices, 118847, unitless # Measure Cortex, SurfArea, Surface Area, 78090, mm^2
[t:D:mri-> grep Cortex ~/tmp/lh.aparc.stats # Measure Cortex, NumVert, Number of Vertices, 111237, unitless # Measure Cortex, SurfArea, Surface Area, 72998.7, mm^2
If so this is just the difference in the vertices coverted by cortex.label vs aparc
On 03/24/2014 12:49 PM, _andreia_@sapo.pt wrote:
Hi Doug,
I've attached the files. To contextualize a little bit, I'm using Brodmann Areas measures (CT, surface area and volume, thresholded to the correct probability) and I'll be extracting the surface area using pial and white surface. However, I'll be also analyzing whole brain using the aparc stats (again, CT, surface area and volume) - should I use the file that is in agreement with aparc?
I don't understand why total.stats gives different values from cortex.stats since I've created the total.stats file using the command:
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b SUBJ lh white
One more question: is the ?hCortexvol value from aseg that I should use to get the total volume of each hemisphere?
Sorry for so many questions...
Thank you!
Andreia
Quoting Douglas Greve greve@nmr.mgh.harvard.edu:
How much of a difference is there? There should not be much, but there will be some because the aparc does not cover the exact same vertices as cortex.label doug
On 3/24/14 8:04 AM, _andreia_@sapo.pt wrote:
Hello list,
I have a question regarding what stats are more correct to use to get whole hemisphere surface area and mean thickness.
The cortex.label values extracted using the two bottom command lines don't match aparc stats, however they match in the number of vertices between them, and using pial or white surface also results in values that make sense comparing each one (higher surface area using pial, same thickness, same volumes).
In the past I've been using the two first command lines (in which values agree in the same way as cortex.label between them but are also in agreement with aparc.stats), however now I'm having this question: which one is the correct one to use?
And why does this difference exists?
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b SUBJ lh white (matches aparcstats)
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total_pial.stats -b SUBJ lh pial (matches aparcstats)
mris_anatomical_stats -mgz -f ../stats/lh.cortex_pial.stats SUBJ lh pial (does not match aparcstats)
mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats SUBJ lh white (does not match aparcstats)
Thank you in advance, Andreia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
_andreia_＠sapo.pt -
Douglas N Greve