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> 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.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 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>> 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 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>
>     <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 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>>
>     >     <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>>>> 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>>>> 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
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>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
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>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
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>     >     >>     Freesurfer mailing list
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>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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>     <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
>     >     >
>     >     >
>     >     >  _______________________________________________
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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>>
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>     <tel:617-726-7422>>
>     >
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>     >
>     >
>     >
>     > _______________________________________________
>     > 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
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> 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
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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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer