Re: [Freesurfer] registering to fsaverage

Hi Doug My apologies for the delay - I just returned from vacation. Ok, so when I take a volumetric spam created using minc tools and create an overlay from it using mri_vol2surf, the min and max seems to be between 1 and 255. I am wondering if there is any where to change this into a %? When I

Re: [Freesurfer] registering to fsaverage

Trisanna, has this issue been resolved? doug On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote: > Hi Bruce > > here is the output of my mri_vol2surf for a volumetric spam created in > minc tools. When I then overlay this result in Freeview, it displays a > Min of 127 and a Max of 255. > >

Re: [Freesurfer] registering to fsaverage

Hi Trisanna what does mri_info show about spam_for_label_id_4_blur_minc1.mnc? You said it has the range of values in [0,100]? Or [0,1]? I'm not sure why mri_vol2surf would modify the values - this might have to wait for Doug to get back Bruce On Thu, 30 Jun 2016, Trisanna Sprung-Much

Re: [Freesurfer] registering to fsaverage

Hi Bruce here is the output of my mri_vol2surf for a volumetric spam created in minc tools. When I then overlay this result in Freeview, it displays a Min of 127 and a Max of 255. trisanna@kaplan:~$ mri_vol2surf --mov

Re: [Freesurfer] registering to fsaverage

Hi Bruce I simply use mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader subject --hemi lh --surf pial Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl wrote:

Re: [Freesurfer] registering to fsaverage

how do you create the overlay? On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote: Hi Bruce To create the spam I used minctools:  mincaverage  input.mnc output.mnc  I blurred the spam using mincblur input.mnc output.mnc -fwhm 3  When I open the spams using minc software, the % shown is from

Re: [Freesurfer] registering to fsaverage

Hi Bruce To create the spam I used minctools: mincaverage input.mnc output.mnc I blurred the spam using mincblur input.mnc output.mnc -fwhm 3 When I open the spams using minc software, the % shown is from about 10-40% (i.e. the max overlap). For some reason when I create an overlay from

Re: [Freesurfer] registering to fsaverage

Hi Trisanna what commands did you use to generate the volumetric probability map? Bruce On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote: Hi Bruce So, when I take a probability map formed using linear volumetric registration with minc tools and saved as .mnc and convert it to an

Re: [Freesurfer] registering to fsaverage

Hi Trisanna we need more information if you want us to help you. What does "very odd mean"? If you do it in .mgz do you get a different answer than in .mnc? If so, why not just compute them in .mgz and convert to .mnc at the end? cheers Bruce On Mon, 27 Jun 2016, Trisanna Sprung-Much

Re: [Freesurfer] registering to fsaverage

any ideas? Thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 22, 2016 at 10:22 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > thanks Bruce - I had found that option for my fsaverage maps and it worked. >

Re: [Freesurfer] registering to fsaverage

thanks Bruce - I had found that option for my fsaverage maps and it worked. What about if I am importing probability maps formed as .mnc and creating overlays from them? The percentages seem to be very odd for min and max threshold. Trisanna -- Ph.D. Candidate McGill University Integrated

Re: [Freesurfer] registering to fsaverage

Hi Trisanna if you are using mri_average you can give it -p as the first argument and it will compute a percent at the end Bruce On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote: Hi Bruce Is there is a way to set the probability of an overlay between 0 and 1? Would this have to be done

Re: [Freesurfer] registering to fsaverage

Hi Bruce Is there is a way to set the probability of an overlay between 0 and 1? Would this have to be done when creating the overlay using mri_vol2surf? thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, Jun 20, 2016 at 12:11 PM, Bruce

Re: [Freesurfer] registering to fsaverage

Hi Trisanna the binaries that take mandatory command-line arguments (i.e. without a -- or - in front of them) require all options to be given before the mandatory arguments cheers Bruce On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote: thanks, Bruce. Yes in the end through trial and

Re: [Freesurfer] registering to fsaverage

thanks, Bruce. Yes in the end through trial and error I tried "mri_average -noconform input output" and it worked. I was surprised that I had to put the -noconform first as normally one can put the argument anywhere in the command. Best Trisanna -- Ph.D. Candidate McGill University Integrated

Re: [Freesurfer] registering to fsaverage

yes, your last file on the command line should be the output file (the average) cheers Bruce On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote: As a follow-up, here is the mri_info for one of my overlays in the folder and the output file that mri_average seems to create (if I don't specify an

Re: [Freesurfer] registering to fsaverage

try it with the noconform as the first argument. I think it will ignore it at the end Hi Dr. Fischl I ran the following mri_average and consistently get this message. It seems to be trying to read my output as one of the input volumes. If I don't specify an output it re-writes my last file

Re: [Freesurfer] registering to fsaverage

As a follow-up, here is the mri_info for one of my overlays in the folder and the output file that mri_average seems to create (if I don't specify an output and it re-writes my last file). The dimensions are off: Any ideas? Trisanna Tg

Re: [Freesurfer] registering to fsaverage

Hi Dr. Fischl I ran the following mri_average and consistently get this message. It seems to be trying to read my output as one of the input volumes. If I don't specify an output it re-writes my last file in the input folder and when I try to open this it doesn't work at all. What exactly does

Re: [Freesurfer] registering to fsaverage

no problem. Bruce On Sun, 19 Jun 2016, Trisanna Sprung-Much wrote: thanks Dr. Fischl - I think sometimes my emails don't get sent out on the first try and so I resend - don't mean to spam everyone. Don't know how I missed the mri_average option - I think I need vacation too. thanks and have a

Re: [Freesurfer] registering to fsaverage

thanks Dr. Fischl - I think sometimes my emails don't get sent out on the first try and so I resend - don't mean to spam everyone. Don't know how I missed the mri_average option - I think I need vacation too. thanks and have a lovely Sunday! Trisanna -- Ph.D. Candidate McGill University

Re: [Freesurfer] registering to fsaverage

Hi Trisanna Doug is on vacation and his response time is likely to be pretty slow. If any emails go unanswered you should repost them in a week or two. As for this, if you overlays are mapped to fsaverage you can just use mri_average to average them. cheers Bruce On Sun, 19 Jun 2016,

Re: [Freesurfer] registering to fsaverage

Hi Doug So all of my sulci for each subject have been registered to fsaverage using mri_surf2surf. I am now wondering how I could create an average of a sulcus using these overlays - I understand that mris_make_average_surface is an option but I cannot seem to find whether this works for overlays

Re: [Freesurfer] registering to fsaverage

worked beautifully. Thank you! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve wrote: > Try surf2surf with --mapmethod nnf > > On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote: > >

Re: [Freesurfer] registering to fsaverage

Try surf2surf with --mapmethod nnf On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote: > Hi Doug - yes they do actually, I was quite pleased. I did some trials > with other subjects and the mri_vol2surf all looks good. Very similar > to what I had in our in-house software. > > Would things be

Re: [Freesurfer] registering to fsaverage

Hi Doug - yes they do actually, I was quite pleased. I did some trials with other subjects and the mri_vol2surf all looks good. Very similar to what I had in our in-house software. Would things be better if I were to isolate each sulcus as a .label and then try the mri_label2label? Someone

Re: [Freesurfer] registering to fsaverage

The problem is probably that the vol2surf command did not properly sample the labels onto the surface. Do the labels on subject 00350 surfaces look ok? On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote: > thanks Dr. Fischl > > So the command seems to have worked! I have copied what ran in my

Re: [Freesurfer] registering to fsaverage

Hi Trisanna you would only use those options of if you were transforming a surface Bruce On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote: thanks Dr. Fischl I assume that for surface overlays one cannot specify --sval-xyz and --tval-xyz or the command will treat the input as a surface

Re: [Freesurfer] registering to fsaverage

thanks Dr. Fischl I assume that for surface overlays one cannot specify --sval-xyz and --tval-xyz or the command will treat the input as a surface itself? best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 15, 2016 at 11:11 AM,

Re: [Freesurfer] registering to fsaverage

Hi Trisanna you don't need to inflate the overlays. They can just use the existing surface-based (sphere.reg) registration. cheers Bruce On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote: Hi there So I have sulcal labels from another software (.mnc format) from which I am trying to