Hi there
Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no transformations have been performed) I get the following snapshot #1.* Clearly, my original labels are aligned with the surface, as they should be since Freesurfer did not alter the space.* So, how can I use mrivol2surf to resample the surface such that the vertices carry the label info? What output format should I use in mrivol2surf? How can I open this output in Freeview?
For instance, when I try a .dat that creates no transformation and save the output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something is going wrong in my mrivol2surf command.
My apologies for the questions Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Thu, Apr 14, 2016 at 12:08 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
will try this, thanks.
In the meantime
After doing some thinking about the command, *I am now confused about why I need to generate a .dat in the first place. here is my thinking:*
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online,* Freesurfer does not change the space of the input volumes?* My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, *shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?* Some clarification would be greatly appreciated!
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Thu, Apr 14, 2016 at 11:33 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Sorry, that is something we put in for version 6 to be able to run under newer versions of mac. Edit the file and remove the following line source $FREESURFER_HOME/sources.csh
On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote:
thanks, Doug. *Unfortunately, I got a different error this time:*
trisanna@kaplan:~$ mni152reg --s icbm-102 /usr/local/freesurfer-5.3//sources.csh: No such file or directory.
What does this mean?
After doing some thinking about the command, *I am now confused about why I need to generate a .dat in the first place. here is my thinking:*
my labels and my icbm volumes are either registered to MNI305 or MNI152 template - i.e. when I painted my voxels to generate my labels, the volumes were already registered to either of these templates when using an in-house software.
So, why do I want to do ANOTHER registration of mni152reg to generate a .dat file that is then needed for mri_vol2surf? Why can't I simply create my surfaces in Freesurfer and then overlay my labels onto those surfaces if, as I have found online,*Freesurfer does not change the space of the input volumes?* My understanding is that it calculates an MNI305 transformation but does not alter the actual input space. Therefore, I do not want to do any further transformations since my labels and volumes are already in sync. If mri_vol2surf really needs a .dat to run, *shouldn't I be creating a registration matrix that does absolutely nothing to ensure my labels don't change?
Some clarification would be greatly appreciated!
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
this is a known bug. Try this version insteadftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
On 04/13/2016 01:06 PM, Trisanna Sprung-Much wrote: > Hi Doug > > So I tried running mni152reg and had the following error: > > mni152reg --s icbm-102_test > > > setenv SUBJECTS_DIR /data-01/trisanna/freesurfer > cd /home/trisanna > /usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test > > > fslregister --mov > /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --s > icbm-102_test --reg >/data-01/trisanna/freesurfer/icbm-102_test/mri/transforms/reg.mni152.2mm.dat
> --dof 12 > mkdir: cannot create directory > ‘/usr/share/fsl/5.0/data/standard/tmp.fslregister.11061’:Permission
> denied > > I spoke with our IT guy and he says that of course I cannot be writing > to fsl/5.0/data. I then did a web search and found that someoneelse
> was having this problem > >https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41276.html
> > How might I fix this? Let me know if I should send the log filethat
> was created. > > best > > Trisanna > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Fri, Apr 8, 2016 at 1:33 PM, Douglas N 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: > > 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 notbe
> 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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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 takesthe
> 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 keepsall
> 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 50volumes,
> 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 tothe
> surfaces of > > your individual 50 subjects? Start by running recon-allon
> 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>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto: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>> > > <mailto: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>>> > > >> <mailto: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>> > > <mailto: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>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto: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 thatI
> 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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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 isintended
> 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> > >> 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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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>> > > <mailto: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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 tel:617-724-2358>
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> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <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> > 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 <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>
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