Try this:
First, compute the registration between the bold and the 152 mri_matrix_multiply -im bold/register.dat -iim mri/transforms/reg.mni152.2mm.dat -om bold-to-mni152.reg.dat
Check the reg tkregister2 --mov bold.bhdr --reg bold-to-mni152.reg.dat --targ /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz
Resample the t maps mri_vol2vol --mov t.bhdr --reg bold-to-mni152.reg.dat --targ /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz --o t-in-mni152.nii
doug
On 07/31/2014 11:05 AM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Doug,
Ideally, I am trying to take subject tstat maps from FsFast (stable3 environment) and register these native structural space maps to the MNI152_2mm standard brain.
The t_000.bfloat file is what was generated relative to my contrast that was set up in FsFast stable3. There are a series of these files ranging from t_000.bfloat to t_029.bfloat and there are also these same named files with a .hdr extension. t_000.bfloat is the file I designate when I select an overlay within tkmedit.
Your help sorting out this registration is very appreciated.
Thank you, Jacob
I'm not sure what you are trying to do, but that command line looks
like
things are not set up properly. What is t_000.bfloat? (And why are you
using bfloats?)
doug On 7/17/14 1:14 PM, JacobML@nmr.mgh.harvard.edu wrote:
Hello again Doug, Thank you for sending the updated version of mri152reg. It ran without
error and generated the reg.mni152.2mm.dat registration matrix. Unfortunately though, when I tried to apply the transformation to the same
subject's t_000.bfloat, the registration is not correct (command
below). mri_vol2vol --inv --targ /.../t_000.bfloat --mov
$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg
/.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat On a positive note, I was able to load the output image and
MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to
be shifted too far anterior.
With my next attempt, I used mri_convert to make the t_000.bfloat into
a .mgz and than ran mri_vol2vol, but the same misalignment occurred (see attached photo).
Using tkmedit, I have confirmed that this file aligns properly on this
subject's native structural image, so I am not quite sure why the registration matrix may be off. Given that the reg.mni152.2mm.dat file reflects the transformation of the native struc to MNI, I wonder if I need
to account for the reg file between the func data and the native
struc?
Can you please let me know what I may be doing incorrectly? As always, your help is very appreciated. Jacob
Yea, i fixed this problem. I've attached a new version with the fix.
doug
On 07/17/2014 10:35 AM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Freesurfer Experts, I am trying to view stats generated with FsFast in fslview/MNIspace,
and
in doing so I have run mni152reg to generate the registration
matrix.
That said, mni152reg did not complete correctly and below I have
pasted
the terminal output:
Thu Jul 17 09:58:10 EDT 2014 setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
/usr/local/freesurfer/stable5_3_0/bin/mni152reg --s
CD_cerv_pat4_sess1_recon Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
UTC
2014 x86_64 x86_64 x86_64 GNU/Linux fslregister --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
--s CD_cerv_pat4_sess1_recon --reg
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
--dof 12
mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833':
Permission denied
Log file is /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log
Thu Jul 17 09:58:11 EDT 2014
--mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
--s CD_cerv_pat4_sess1_recon --reg
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
--dof 12
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ purkinje Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
UTC
2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1
/autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
mri_convert
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
mri_convert
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
niiWrite(): error opening file
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz...
TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00
i_ras = (-1, 0, 0) j_ras = (-0, -0, -1) k_ras = (0, 1, 0) writing to /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii...
ERROR: failure writing
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
I tried to run the fslregister command from within the subject's
directory
(in hopes to possible correct what may be a permissions issue), but
this
produces the same final error, "ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii."
Lastly, probably to no surprise, the
/.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any
ideas how I may be able to correct these errors?
Thank you for the help! Jacob _______________________________________________ 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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