Should also add that I can import the cortical surface into matlab without any issues using read_surf.m what I would like to have is the ICA overlay also imported into matlab as corresponding colors for each face on the cortical mesh. Thanks.
From: andrewzhao@live.com.au To: greve@nmr.mgh.harvard.edu Date: Tue, 11 Mar 2014 11:54:10 +1100 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
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: greve@nmr.mgh.harvard.edu To: andrewzhao@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: greve@nmr.mgh.harvard.edu To: andrewzhao@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: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> To: andrewzhao@live.com.au <mailto:andrewzhao@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: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > To: andrewzhao@live.com.au <mailto:andrewzhao@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: greve@nmr.mgh.harvard.edu <mailto:greve@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 > > > greve@nmr.mgh.harvard.edu <mailto:greve@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 > greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@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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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.