Re: [Freesurfer] Quantifying volumes

2016-10-17 Thread Josue Luiz Dalboni Da Rocha
-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <gr...@nmr.mgh.harvard.edu> Sent: Friday, October 14, 2016 7:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes How did you create the label ? On 10/14/16 12:43 PM, Josue Luiz Dalboni Da Rocha wrote:

Re: [Freesurfer] Quantifying volumes

2016-10-14 Thread Douglas Greve
Subject:* Re: [Freesurfer] Quantifying volumes please send command lines On 10/14/16 6:36 AM, Damien MARIE wrote: Hi, Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Hes

Re: [Freesurfer] Quantifying volumes

2016-10-14 Thread Josue Luiz Dalboni Da Rocha
edu> on behalf of Douglas Greve <gr...@nmr.mgh.harvard.edu> Sent: Friday, October 14, 2016 5:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes please send command lines On 10/14/16 6:36 AM, Damien MARIE wrote: Hi, Just adding a word about the

Re: [Freesurfer] Quantifying volumes

2016-10-14 Thread Douglas Greve
<http://nmr.mgh.harvard.edu>> Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Quantifying volumes I would binarize the curv file with mri_binarize --i lh.yourcurvfile --abs --min

Re: [Freesurfer] Quantifying volumes

2016-10-14 Thread Damien MARIE
reesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes I would binarize the curv fi

Re: [Freesurfer] Quantifying volumes

2016-10-12 Thread Josue Luiz Dalboni Da Rocha
ay, October 5, 2016 5:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes I would binarize the curv file with mri_binarize --i lh.yourcurvfile --abs --min .001 --o lh.yourcurvfilebin.mgh Then compute the volume with mri_segstats --seg lh.yourcurvfilebin.m

Re: [Freesurfer] Quantifying volumes

2016-10-05 Thread Douglas N Greve
2016 9:41 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Quantifying volumes > > What is the nature of the segmentation? Is it just a binary (1=in, > 0=out) segmentation? And what file format? In general we don't use .w > anymore, but it can be converte

Re: [Freesurfer] Quantifying volumes

2016-10-05 Thread Bruce Fischl
ehalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > Sent: Wednesday, October 5, 2016 3:30 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Quantifying volumes > > Hi Josue > > the *.curv won't help you with the volume. If it is a label file you > s

Re: [Freesurfer] Quantifying volumes

2016-10-05 Thread Josue Luiz Dalboni Da Rocha
er 5, 2016 3:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Quantifying volumes Hi Josue the *.curv won't help you with the volume. If it is a label file you should be able to give it to mris_anatomical_stats with -l to compute the volume cheers Bruce On Wed, 5 Oct 2016, Josue Lui

Re: [Freesurfer] Quantifying volumes

2016-10-05 Thread Bruce Fischl
_ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > Sent: Tuesday, October 4, 2016 9:41 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Fre

Re: [Freesurfer] Quantifying volumes

2016-10-05 Thread Josue Luiz Dalboni Da Rocha
Best regards, Josue From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Tuesday, October 4, 2016 9:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantif

Re: [Freesurfer] Quantifying volumes

2016-10-04 Thread Douglas N Greve
What is the nature of the segmentation? Is it just a binary (1=in, 0=out) segmentation? And what file format? In general we don't use .w anymore, but it can be converted into something else. doug On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote: > > Dear Douglas, > > > I have a

[Freesurfer] Quantifying volumes

2016-10-03 Thread Josue Luiz Dalboni Da Rocha
Dear Douglas, I have a segmented gyrus curvature file (.curv or .w) and I would like to calculate the volume (and other statistics) of this gyrus. I currently only know mris_anatomical_stats to perform that, but requiring a '.label' file. Can I extract statistics directly from the ".curv"