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 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-dmax

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 gr...@nmr.mgh.harvard.edu wrote: don't know what's going on. Can you upload the subject

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

2013-05-30 Thread Douglas N Greve
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 gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu

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

2013-05-30 Thread Gonzalo Rojas Costa
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 gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message

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

2013-05-30 Thread Douglas N Greve
gr...@nmr.mgh.harvard.edu 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-8859-1; format=flowed you will need to run mri_annotation2label and specify the output

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

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

2013-05-28 Thread Douglas N Greve
gr...@nmr.mgh.harvard.edu 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-8859-1; format=flowed you will need to run mri_annotation2label and specify the output

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

2013-05-28 Thread Gonzalo Rojas Costa
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 Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer

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

2013-05-28 Thread Douglas N Greve
] 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-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation

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).