Thank you for the heads up Bruce. > Hi Jacob > > Doug is on vacation for a couple of weeks, so you should probably repost > in early August. > > cheers > Bruce > On Mon, 21 Jul 2014, jaco...@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, jaco...@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, jaco...@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 >>>>>> gr...@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/ >> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> 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 >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> 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 >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
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