Re: [Freesurfer] white matter volume per lobe...

2013-06-10 Thread Douglas N Greve
Hi Gonzalo, the segmentation that you are seeing is paired with the insula parcellation. doug On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote: > Hi Doug: > >The command is: > > mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown > --volmask --o mri/lobulitos.mgz --annot

Re: [Freesurfer] white matter volume per lobe...

2013-05-31 Thread Gonzalo Rojas Costa
Hi Douglas: The file is the OAS1_0001_MR1 case of OASIS-BRAINS database that I re-processed using freesurfer 5.2.0... Sincerely, Gonzalo Rojas Costa On Fri, May 31, 2013 at 12:12 PM, Douglas N Greve wrote: > don't know what's going on. Can you upload the subject to our file drop? > doug >

Re: [Freesurfer] white matter volume per lobe...

2013-05-31 Thread Douglas N Greve
don't know what's going on. Can you upload the subject to our file drop? doug On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote: > Hi Doug: > >The command is: > > mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown > --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-d

Re: [Freesurfer] white matter volume per lobe...

2013-05-30 Thread Gonzalo Rojas Costa
Hi Doug: The command is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200 and the terminal output is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos_2.mgz

Re: [Freesurfer] white matter volume per lobe...

2013-05-30 Thread Douglas N Greve
>>> neuroanatomical area is ?... >>> >>> Sincerely, >>> >>> >>> Gonzalo Rojas Costa >>> >>> >>>> Message: 15 >>>> Date: Mon, 27 May 2013 22:41:41 -0400 >>>> From: Douglas Greve >>

Re: [Freesurfer] white matter volume per lobe...

2013-05-30 Thread Gonzalo Rojas Costa
r per >> each lobule... But, I got the grey colored region (red arrow)... Which >> neuroanatomical area is ?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >>> Message: 15 >>> Date: Mon, 27 May 2013 22:41:41 -

Re: [Freesurfer] white matter volume per lobe...

2013-05-30 Thread Douglas N Greve
t, I got the grey colored region (red arrow)... Which > neuroanatomical area is ?... > >Sincerely, > > > Gonzalo Rojas Costa > > >> Message: 15 >> Date: Mon, 27 May 2013 22:41:41 -0400 >> From: Douglas Greve >> Subject: Re: [Freesurfer] white mat

Re: [Freesurfer] white matter volume per lobe...

2013-05-28 Thread Douglas N Greve
> Gonzalo Rojas Costa >>> >>> >>>> Message: 15 >>>> Date: Mon, 27 May 2013 22:41:41 -0400 >>>> From: Douglas Greve >>>> Subject: Re: [Freesurfer] white matter volume per lobe... >>>> To: freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] white matter volume per lobe...

2013-05-28 Thread Gonzalo Rojas Costa
the instructions that you told me... But, why I get the gray >> colored region (red arrow) ?... >> >>Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >>> Message: 15 >>> Date: Mon, 27 May 2013 22:41:41 -0400 >>> From: Douglas

Re: [Freesurfer] white matter volume per lobe...

2013-05-28 Thread Douglas N Greve
gt;> Date: Mon, 27 May 2013 22:41:41 -0400 >> From: Douglas Greve >> Subject: Re: [Freesurfer] white matter volume per lobe... >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: <51a41965.6050...@nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=ISO-8859

Re: [Freesurfer] white matter volume per lobe...

2013-05-27 Thread Douglas Greve
you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then

[Freesurfer] white matter volume per lobe...

2013-05-27 Thread Gonzalo Rojas Costa
Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_an