thanks Bruce
I could not find identity.nofile anywhere, when I ran mri_vol2surf I got the following error
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz srcreg = identity.nofile srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): No such file or directory Could not open identity.nofile
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Trisanna
you can give the transformation "file" named identity.nofile and it will assume that the transform is the identity. You can then use mri_vol2label to sample the label onto the surface and visualize it with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers Bruce
On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
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. CandidateMcGill 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. CandidateMcGill 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 instead >ftp://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.d at > > --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 someone else > > 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 file that > > 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 commanddirectly
> > fslregister --mov icbm.nii.gz --s $subject --reg > $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof12
> --lta$SUBJECTS_DIR/subject/transforms/icbm.reg.lta
> > This will use a linear (12 dof) registration whichmight not be
> particularly accurate > > > On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote: > > thanks, Doug. I'll get started on running allbrains 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.edumailto: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-Muchwrote:
> > > thanks, Doug. I am still extremely confused, however. *Am > I meant to > > > run recon-all first? *I was told in aprevious email
that I > > should do > > > this first, however, I thought thatFreesurfer takes the
> volumes and > > > does a linear registration to MNI305template, which
would > not work > > > for my scans that are linearly registered toICBM152
> nonlinear 2006 > > > template... > > run recon-all first, otherwise you won't havesurfaces.
> recon-all > > computes the transform matrix to the mni305but keeps all
> the data in > > the native anatomical space. I think theICBM152 is
the same > as the > > MNI152. Is that right? If so, you can usemni152reg to
> compute the > > registration to 152 space. If not, then we'llhave to
workout > > something > > else. > > > > > > When you have a moment, could you pleaseoutline in
a step > by step > > > manner the steps I should run to take mylabels.mnc
and my > volumes > > > such that I can generate surfaces for those50 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 fromlabels.mnc to the
> surfaces of > > your individual 50 subjects? Start by runningrecon-all on
> the 50. > > > *The idea is that I want to generate somesulcal
> probability maps > > > using surface-based registration, as I canalready
generate > > > probability maps using volumetricregistration quite
easily.* > > > > > > many thanks > > > > > > Trisanna > > > > > > > > > > > > > > > > > > > > > -- > > > Ph.D. Candidate > > > McGill University > > > Integrated Program in Neuroscience > > > Psychology > > > > > > > > > On Wed, Apr 6, 2016 at 2:43 PM, DouglasGreve
> > > <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.edumailto: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 --ssubject, then
> specify > > >$SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or
> .lta) for > > > the argument to --reg. I'll need tofigure out
how to > generate a > > > .dat/.lta for the 305. > > > > > > > > > > > > On 4/6/16 12:50 PM, Trisanna Sprung-Muchwrote:
> > >> 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 thelabels were
> painted in the > > >> MNI305 space (older ones) and themore 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, TrisannaSprung-Much
> > >> wrote: > > >> > > >> > Hi Freesurfer > > >> > > > >> > I have some labels (.mnc)that are
painted > voxels > > >> generated from a Montreal > > >> > Neurological Institutesoftware. I am
trying to > > project > > >> the labels onto the > > >> > surfaces generated fromrecon-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 amsupposed
to be > using? > > >> > > > >> > Many thanks! > > >> > > > >> > Trisanna > > >> > > > >> > -- > > >> > Ph.D. CandidateMcGillUniversity
> > >> > Integrated Program inNeuroscience
> > >> > Psychology > > >> > > > >> > > > >> > > > >> > > > >>
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contact the > > Partners > > >> Compliance HelpLine at > > >> http://www.partners.org/complianceline . Ifthe e-mail
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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.edumailto:greve@nmr.mgh.harvard.edu>
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> > Phone Number:617-724-2358 <tel:617-724-2358><tel:617-724-2358 tel:617-724-2358>
> <tel: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
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<mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>
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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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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