Regarding matlab: Currently, I have in freesurfer the surface extracted via recon-all. I also have the overlay from running mri_vol2surf on the ICA components.
I would like to export the pial surface + overlay into matlab together as a single object. Is there a matlab script for this, or do I need to do some further processing? Thanks. > Date: Mon, 10 Mar 2014 11:25:23 -0400 > From: gr...@nmr.mgh.harvard.edu > To: andrewz...@live.com.au > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > On 03/09/2014 09:12 AM, Xuelong Zhao wrote: > > Hi Doug, > > > > To clarify my previous question: > > > > There is definitely some fuzziness when comparing with the mov, > > whereas the target comparison looks very pristine. I was just > > wondering if this is expected. The mov, as I scroll through the layers > > seem to be also slightly offset in certain regions, I guess this again > > may be due to the fuzziness of the mov fmri data. > Yes this is somewhat expected. The target is the data the surface was > generated from, so it should look perfect. > > > > Regarding my second q: > > > > I've got this working now- the segfault was due to me naively loading > > the surface image as a surface, instead of using it as an overlay, I > > can now successfully scroll through the various frames. However, I > > noticed that in the documentation to load into matlab, say the left > > pial surface (with the ICA components on it), I have to save it as a > > mgz file and then use MRI_read. However, freeview doesn't seem to > > offer this option once I load the pial surface and the the ICA components? > > Sorry, what has to be mgz? What matlab command? What instructions? > doug > > > > > > > ------------------------------------------------------------------------ > > Date: Thu, 6 Mar 2014 10:19:25 -0500 > > From: gr...@nmr.mgh.harvard.edu > > To: andrewz...@live.com.au > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > On 3/6/14 6:39 AM, Xuelong Zhao wrote: > > > > Hi Doug, > > > > A follow-up. I've gone back and re-done the registration using > > nifti file with the ICA20 maps. I noticed in tkregister2 that when > > I press on the TARGET tab there is extremely good alignment ( i > > think it is to 'orig.mgz' in the mri folder of my subject which I > > had processed using recon-all. While, when I switch to the > > 'moveable' tab the green line seems to be slightly offset, but the > > underlying image is very fuzzy too. Is this an issue? > > > > I don't know without seeing it. The mov is often lower resolution, so > > some fuzziness is expected. > > > > > > Also, when I load the surface image in freeview produced by > > mri_vol2surf nothing seems to show up, even when I use the > > registration file. In fact, if I have other volumes loaded it > > causes freeview to segfault. When I do manage to load it > > successfully with the anatomical template in talairach space, it > > doesn't really show up and it seems that the anatomical template > > is really small and I have to zoom in a lot. Maybe I didn't > > process/register? > > > > Can you be more specific? What are your vol2surf and fv command lines? > > Have you tried it in tksurfer? > > > > > > Thanks again. > > > > ------------------------------------------------------------------------ > > Date: Tue, 4 Mar 2014 22:52:38 -0500 > > From: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > To: andrewz...@live.com.au <mailto:andrewz...@live.com.au> > > CC: freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > On 3/4/14 7:18 PM, Xuelong Zhao wrote: > > > > Dear Doug, > > > > I've managed to get functional information onto the cortical > > surface following your instructions. > > But, there's a few issues that are still not resolved: > > > > 1/ wrt to registration I believe the supplied anatomical > > template (in tailarach coords) is already aligned with the ica > > maps (which come from one individual). However, when I run > > mri_vol2surf I need a registration.dat file so in such a > > situation is the registration data from the anatomical > > template sufficient? > > > > If the ica maps are in voxel-for-voxel alignment with the template > > then yes (i,e they must have the same dimension and voxel size) > > > > > > 2/ the nifti file for functional data actually contains 20 ICA > > components. After I ran mri_vol2surf how do I view each > > component independently? Currently it seems to only show one > > particular ICA component in freeview. > > > > Bring up the overlay configuration window. You can control the > > frame/time point from there. > > > > > > 3/ using mri_vol2surf if I want .nii output do I specify thus: > > '--out_type nii' ? (i did this and it seemed to have worked, > > but just wanted to double check). > > > > You can just specify the output file with a .nii extension > > doug > > > > > > > > Thanks! > > > > > Date: Tue, 4 Mar 2014 10:37:19 -0500 > > > From: gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > > To: andrewz...@live.com.au <mailto:andrewz...@live.com.au>; > > freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Resting State Networks on Cortical > > Surface > > > > > > > > > On 03/03/2014 11:25 PM, Xuelong Zhao wrote: > > > > Hi Doug, thanks for the quick reply. I've been playing > > around with the > > > > commands you suggested and managed to get what seemed like > > a good > > > > registration by inspecting the green lines in tkregister. > > > > > > > > However, I wasn't actually sure if I put the correct input: > > > > > > > > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg > > > > > > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat > > --t1 > > > > --init-header > > > > > > > > after the '--mov' option should i be using the anatomical > > template or > > > > the .nii file containing the 20 ICA components (4D)? I > > tried both > > > > (changing the between the --t1 and --bold options) and the > > anatomical > > > > template came out much better, but I thought the movable > > (--mov) is > > > > meant to be the functional image? > > > It should be a functional image. If the ica maps come from an > > > individual, then use the mean functional for that subject or > > whatever > > > you used for fMRI motion correction (which should be aligned > > with the > > > ica maps). If it is in a group space, then use the > > registration target > > > (that is exactly the same size as your maps). > > > > > > > > Also, wrt to mri_vol2surf, what should the --src_type, > > --projfrac > > > > options be set to in my case? > > > > Also for --out_type, if I want an easy format to port to > > matlab? > > > For projfrac we usually use .5. You can ignore src_type. For > > output > > > type, you can use nii (nifti) and then use MRIread.m > > > doug > > > > > > > > Thanks! > > > > > > > > > Date: Mon, 3 Mar 2014 14:20:55 -0500 > > > > > From: gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > > > > To: freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > Subject: Re: [Freesurfer] Resting State Networks on > > Cortical Surface > > > > > > > > > > > > > > > you will need to create a registration between your > > volume (maps) and > > > > > the anatomical. You can do this with bbregister. Then > > use mri_vol2surf > > > > > to map your ICs to the surface > > > > > doug > > > > > > > > > > > > > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote: > > > > > > > > > > > > Hi, > > > > > > > > > > > > I am trying to display the 20 ICA components in this > > nifti file > > > > > > > > > > > > http://brainmap.org/icns/maps.zip > > > > > > > > > > > > onto anatomical template they've provided here > > > > > > > > > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii > > > > > > > > > > > > My question is: > > > > > > > > > > > > How do I extract only the cortical surface from the > > anatomical > > > > > > template and overlay > > > > > > it with only parts of each ICA component that > > intersects with the > > > > surface? > > > > > > > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > The information in this e-mail is intended only for the > > person to > > > > whom it is > > > > > addressed. If you believe this e-mail was sent to you in > > error and > > > > the e-mail > > > > > contains patient information, please contact the > > Partners Compliance > > > > HelpLine at > > > > > http://www.partners.org/complianceline . If the e-mail > > was sent to > > > > you in error > > > > > but does not contain patient information, please contact > > the sender > > > > and properly > > > > > dispose of the e-mail. > > > > > > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ Freesurfer mailing > > list Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The > > information in this e-mail is intended only for the person to whom > > it is addressed. If you believe this e-mail was sent to you in > > error and the e-mail contains patient information, please contact > > the Partners Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error but does not contain patient information, please > > contact the sender and properly dispose of the e-mail. > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >
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