8 Apr
2016
8 Apr
'16
1:33 p.m.
not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
You can always just run the following command directly
fslregister --mov icbm.nii.gz --s $subject --reg $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12 --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta
This will use a linear (12 dof) registration which might not be particularly accurate
On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote:
thanks, Doug. I'll get started on running all brains using recon-all.
The MNI has several ICBM templates now:
ICBM152 linear ICBM152 nonlinear symmetric VI ICBM152 nonlinear 2009
Do you know which one mni152reg is using?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote: > thanks, Doug. I am still extremely confused, however. *Am I meant to > run recon-all first? *I was told in a previous email that I should do > this first, however, I thought that Freesurfer takes the volumes and > does a linear registration to MNI305 template, which would not work > for my scans that are linearly registered to ICBM152 nonlinear 2006 > template... run recon-all first, otherwise you won't have surfaces. recon-all computes the transform matrix to the mni305 but keeps all the data in the native anatomical space. I think the ICBM152 is the same as the MNI152. Is that right? If so, you can use mni152reg to compute the registration to 152 space. If not, then we'll have to workout something else. > > When you have a moment, could you please outline in a step by step > manner the steps I should run to take my labels.mnc and my volumes > such that I can generate surfaces for those 50 volumes, overlay the > labels (for which I thought I was using mri_vol2surf) and then edit > those labels to make them more accurate? so you want to transfer the labels from labels.mnc to the surfaces of your individual 50 subjects? Start by running recon-all on the 50. > *The idea is that I want to generate some sulcal probability maps > using surface-based registration, as I can already generate > probability maps using volumetric registration quite easily.* > > many thanks > > Trisanna > > > > > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > For the 152, you can run mni152reg --s subject, then specify > $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for > the argument to --reg. I'll need to figure out how to generate a > .dat/.lta for the 305. > > > > On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote: >> Any ideas? >> >> Trisanna >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much >> <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca> >> <mailto:trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>>> wrote: >> >> Hi Dr. Fischl >> >> I have a mixture - some of the labels were painted in the >> MNI305 space (older ones) and the more recent ones are >> registered to the ICBM152 nonlinear symmetric VI (2006) template. >> >> Best >> >> Trisanna >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: >> >> Hi Trisanna >> >> what space are your labels in? >> >> cheers >> Bruce >> On Tue, 5 Apr 2016, Trisanna Sprung-Much >> wrote: >> >> > Hi Freesurfer >> > >> > I have some labels (.mnc) that are painted voxels >> generated from a Montreal >> > Neurological Institute software. I am trying to project >> the labels onto the >> > surfaces generated from recon-all that I applied to the >> corresponding MRI >> > volumes. >> > >> > I used mri_vol2surf: >> > >> > mri_vol2surf --src labels.mnc --out test.mgz --srcreg >> talairach.auto.xfm >> > --hemi lh >> > >> > and got the following error: >> > >> > Error reading inplaneres from talairach.auto.xfm >> > >> > >> > Do I need a .dat file? If so, how can I attain it? >> Essentially, what is the >> > registration file that I am supposed to be using? >> > >> > Many thanks! >> > >> > Trisanna >> > >> > -- >> > Ph.D. CandidateMcGill University >> > Integrated Program in Neuroscience >> > Psychology >> > >> > >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto: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. >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto: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> <mailto: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. > > > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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
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--
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/