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, [email protected] 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, [email protected] 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 >>>> [email protected] >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> [email protected] >>> 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 >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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