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> 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>> 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
>     >>             >
>     >>             >
>     >>             >
>     >>             >
>     >>  _______________________________________________
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>
>     --
>     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>
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>
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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
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