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
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