It should actually run all the way through. If your field maps have the same geometry as your fmri volumes, and your fmri runs have correct geometry, then you can run
mri_convert imag_fmap2300.nii imag_fmap2300.geo.nii --in_like fmri.nii Also note that you are just creating a voxel shift map with the epidewarp command, not applying it to the fmri. The application is done in a more complicated way during preproc-sess doug On 05/03/2013 04:10 PM, Corinna Bauer wrote: > hmm. can anything be done to fix it? > > Work the preproc-sess and mkanalysis-sess steps work if I used B0 > corrected images right from the get-go instead of raw fmri runs? > > > On Fri, May 3, 2013 at 4:04 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > yep, it is basically the same error > > > On 05/03/2013 03:57 PM, Corinna Bauer wrote: > > I would imagine so. I tried it with the img files. > > /usr/local/freesurfer/subjects/symmetry/functional/antonio> > epidewarp.fsl --complex > fieldmap/20130409_153340FieldMappings011a001x1.img > fieldmap/20130409_153340FieldMappings011a001x3.img > fieldmap/20130409_153340FieldMappings011a001x2.img > fieldmap/20130409_153340FieldMappings011a001x4.img --tediff > 2.3 --esp 0.59278 --epi bold/005/f.nii --vsm bold/b0dcmap.nii.gz > FSLVersion 5.0.2 > FSLVerMaj 5 > Logfile is bold/b0dcmap.nii.gz.log > FSLOUTPUTTYPE NIFTI_GZ > Extension is nii.gz > nframes = 245, nmidframe = 122 > fslroi > > /usr/local/freesurfer/subjects/symmetry/functional/antonio/bold/005/f.nii > bold/tmp-epidewarp.19423.fsl/exf.nii.gz 122 1 > mri_convert fieldmap/20130409_153340FieldMappings011a001x1.img > bold/tmp-epidewarp.19423.fsl/real1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from fieldmap/20130409_153340FieldMappings011a001x1.img... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x1.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x1.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/real1.nii... > mri_convert fieldmap/20130409_153340FieldMappings011a001x3.img > bold/tmp-epidewarp.19423.fsl/imag1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from fieldmap/20130409_153340FieldMappings011a001x3.img... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x3.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x3.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/imag1.nii... > mri_convert fieldmap/20130409_153340FieldMappings011a001x2.img > bold/tmp-epidewarp.19423.fsl/real2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from fieldmap/20130409_153340FieldMappings011a001x2.img... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x2.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x2.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/real2.nii... > mri_convert fieldmap/20130409_153340FieldMappings011a001x4.img > bold/tmp-epidewarp.19423.fsl/imag2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from fieldmap/20130409_153340FieldMappings011a001x4.img... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x4.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x4.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/imag2.nii... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x1.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x1.mat file > ----------------------------------------------------------------- > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x3.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x3.mat file > ----------------------------------------------------------------- > Saving result to 'bold/tmp-epidewarp.19423.fsl/mag.nii.gz' > (type = nii ) [ ok ] > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > bet bold/tmp-epidewarp.19423.fsl/mag.nii.gz > bold/tmp-epidewarp.19423.fsl/brain.nii.gz > fslmaths bold/tmp-epidewarp.19423.fsl/brain.nii.gz -bin > bold/tmp-epidewarp.19423.fsl/brain.nii.gz > fslmaths bold/tmp-epidewarp.19423.fsl/brain.nii.gz -dilM > bold/tmp-epidewarp.19423.fsl/head.nii.gz > ^C > > > > On Fri, May 3, 2013 at 3:52 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > yes, it should take img files. At some point, the lack of > valid > geometry might mess things up > > > On 05/03/2013 03:47 PM, Corinna Bauer wrote: > > Oh I see. I have the raw par rec files, should I try > converting it again? I used dcm2nii to convert it to > hdr/img > files and then fslchfiletype to get it into nifti. for > some > reason just converting it to nifti right away doesn't > look right. > > Will epidewarp take img files? > > > On Fri, May 3, 2013 at 3:43 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: > > nope, the qform errors mean thatthere is something > going > on with > your data. It means that the geometry is not in > the nifti > file. > > > On 05/03/2013 03:41 PM, Corinna Bauer wrote: > > do they need to be nii.gz? > > > On Fri, May 3, 2013 at 3:38 PM, Corinna Bauer > <corinna...@gmail.com > <mailto:corinna...@gmail.com> <mailto:corinna...@gmail.com > <mailto:corinna...@gmail.com>> > <mailto:corinna...@gmail.com > <mailto:corinna...@gmail.com> <mailto:corinna...@gmail.com > <mailto:corinna...@gmail.com>>> > <mailto:corinna...@gmail.com > <mailto:corinna...@gmail.com> > <mailto:corinna...@gmail.com > <mailto:corinna...@gmail.com>> <mailto:corinna...@gmail.com > <mailto:corinna...@gmail.com> > <mailto:corinna...@gmail.com > <mailto:corinna...@gmail.com>>>>> > > wrote: > > I still get funny warnings about the > nifti-1 qform > or sform > > > /usr/local/freesurfer/subjects/symmetry/functional/antonio> > epidewarp.fsl --complex > fieldmap/real_fmap2300.nii > fieldmap/imag_fmap2300.nii > fieldmap/real_fmap4600.nii > fieldmap/imag_fmap4600.nii --tediff 2.3 --esp > 0.59278 --epi > bold/005/f.nii --vsm bold/b0dcmap.nii.gz > > FSLVersion 5.0.2 > FSLVerMaj 5 > Logfile is bold/b0dcmap.nii.gz.log > FSLOUTPUTTYPE NIFTI_GZ > Extension is nii.gz > nframes = 245, nmidframe = 122 > fslroi > > /usr/local/freesurfer/subjects/symmetry/functional/antonio/bold/005/f.nii > bold/tmp-epidewarp.19137.fsl/exf.nii.gz 122 1 > mri_convert fieldmap/real_fmap2300.nii > bold/tmp-epidewarp.19137.fsl/real1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from fieldmap/real_fmap2300.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > WARNING: it does not appear that there was > sufficient > information > in the input to assign orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/real1.nii... > mri_convert fieldmap/imag_fmap2300.nii > bold/tmp-epidewarp.19137.fsl/imag1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from fieldmap/imag_fmap2300.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > WARNING: it does not appear that there was > sufficient > information > in the input to assign orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/imag1.nii... > mri_convert fieldmap/real_fmap4600.nii > bold/tmp-epidewarp.19137.fsl/real2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from fieldmap/real_fmap4600.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > WARNING: it does not appear that there was > sufficient > information > in the input to assign orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/real2.nii... > mri_convert fieldmap/imag_fmap4600.nii > bold/tmp-epidewarp.19137.fsl/imag2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from fieldmap/imag_fmap4600.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > WARNING: it does not appear that there was > sufficient > information > in the input to assign orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/imag2.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > Saving result to > 'bold/tmp-epidewarp.19137.fsl/mag.nii.gz' > (type = > nii ) [ ok ] > bet bold/tmp-epidewarp.19137.fsl/mag.nii.gz > bold/tmp-epidewarp.19137.fsl/brain.nii.gz > ^C > > > > On Fri, May 3, 2013 at 3:36 PM, Douglas N > Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>>> wrote: > > Actually, it might just be that you > need to > give it > a--exf or > --epi > Can you try that? > > On 05/03/2013 02:59 PM, Corinna Bauer > wrote: > > epidewarp.fsl --complex > fieldmap/real_fmap2300.nii > fieldmap/imag_fmap2300.nii > fieldmap/real_fmap4600.nii > fieldmap/imag_fmap4600.nii > --tediff 2.3 > --esp 0.59278 > --vsm bold/b0dcmap.nii.gz > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> > > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended > only for > the person > to whom it is > addressed. If you believe this e-mail > was sent > to you > in error > and the e-mail > contains patient information, please > contact > the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient > information, please > contact the > sender and properly > dispose of the e-mail. > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- 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
