Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

yes, I have it On Tue, 19 Mar 2013, Longchuan Li wrote: Hi, Bruce The command line I used is:  mris_fill -r 1 -c rh.white rh.white.nii.gz I attached the rh.white in my previous mail. Could you see it in the attachment? Thank you! Longchuan

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

can you send your mris_fill command line? And maybe the lh.white surface you are trying to fill? Bruce On Tue, 19 Mar 2013, Longchuan Li wrote: Hi, Bruce This is the lh.white that gives me the empty volume when I use mris_fill to sample it to the volume space. Could you help diagnose what is

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

Hi, Bruce The command line I used is:  mris_fill -r 1 -c rh.white rh.white.nii.gz I attached the rh.white in my previous mail. Could you see it in the attachment? Thank you! Longchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

We use the MNI305through the (affine) talairach.xfm transform. doug On 03/17/2013 11:47 AM, Bruce Fischl wrote: Hi Longchuan I'm not sure what space the volume average is constructed in - Doug would know. Probably talairach, in which case it won't match the surfaces well. Can you send along

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

Hi, Bruce Thank you for the information. I tried all possible combinations of mris_fill command line and none of them worked. Also, I loaded my ?h.white in tksurfer and confirmed that the surface is there. Do you want me to send you the surface file? One example I used is this: mris_fill

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

Hi Longchuan I'm not sure what space the volume average is constructed in - Doug would know. Probably talairach, in which case it won't match the surfaces well. Can you send along your mris_fill command line? It shouldn't produce an empty volume. There's no reason to look at the inflated

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

For many non-human primate species, volume templates already exist. I would recommend using them and aligning your surface templates to them to aid in the ability to compare studies across laboratories in the same space. For rhesus, see the 112RM-SL atlas. Best Regards, Donald McLaren

[Freesurfer] make a volume template from the surface-based template for non-human primates

Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

Hi Longchuan what kind of volume template do you mean? Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

Hi, Bruce Sorry for the late reply as I was trying to figure it out by myself. I mean the average of the subjects in the volume space that were used for generating the surface template. Actually I kind of found a volume average in the mri folder named as T1.mgz that seems to correspond to the