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 <mpsam...@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
<gr...@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
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
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.
