Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] epi correction of fmri data
by Douglas N Greve 03 May '13

03 May '13

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 > <greve(a)nmr.mgh.harvard.edu <mailto:greve@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 > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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 > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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 > <corinnab83(a)gmail.com > <mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>> <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@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 > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 greve(a)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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Re: [Freesurfer] epi correction of fmri data
by Douglas N Greve 03 May '13

03 May '13

What is your cmd line? Can you run it with --debug as the first arg, capture the output, and send it to me? eg, dewarp.fsl --debug ... |& tee dng.log On 05/03/2013 01:43 PM, Corinna Bauer wrote: > I get this: > > FSLVersion 5.0.2 > FSLVerMaj 5 > FSL Version is 5.0.2, must be 3.X or 4.X > > > > On Fri, May 3, 2013 at 1:42 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > What is going wrong when you run FSL 5? > > > On 05/03/2013 01:38 PM, Corinna Bauer wrote: > > oh great. Is there a way to get this to work with FSL 5? > > > On Fri, May 3, 2013 at 1:11 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > It needs to be 0 to 4095, see below > > --ph phasevolid > > Phase volume from the B0 fieldmap (if the phases from > Echo1, Echo2 are > available instead of their difference). These are assumed > to be scaled > between 0 to 4095 for -pi to pi. Eg, ph.ext, where ext is > either nii, > nii.gz, or img. Not with --complex or with --dph. > > This is made to work with the default Siemens field map. > Note that > you can also use complex inputs instead of mag and phase > > doug > > > > > > On 05/03/2013 01:05 PM, Corinna Bauer wrote: > > Should the phase image be in rads? and does the magnitude > image need to be skull-stripped first? > > > On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer > <corinnab83(a)gmail.com <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>>>> > > wrote: > > thanks Doug, I will give that a try. > > > On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > Create the B0 voxel shift map. Call it > b0dcmap.nii.gz > and put > it in > the bold folder, eg: > > epidewarp.fsl \ > --mag mag.nii.gz \ > --dph dphase.nii.gz \ > --tediff YOUR_TE_DIFF --esp YOUR_ESP \ > --vsm bold/b0dcmap.nii.gz > > When you run mkanalysis-sess and preproc-sess, add > "-b0dc" to the > command lines. > > doug > > > On 05/03/2013 12:16 PM, Corinna Bauer wrote: > > Yes, I am using FSFAST. > > > On Fri, May 3, 2013 at 12:08 PM, Douglas N > Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > Hi Corinna, are you using FSFAST? If > not, are you > still going to the > surface? > doug > > On 05/03/2013 11:07 AM, Corinna Bauer > wrote: > > Is there a way to correct fmri data > for epi > distortions in > freesurfer? > > Or does the data need to be first fun > through FSL's > B0 unwarping? > > > > Corinna > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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/ > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > 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. 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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 greve(a)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/

2 4

Re: [Freesurfer] epi correction of fmri data
by Douglas N Greve 03 May '13

03 May '13

Create the B0 voxel shift map. Call it b0dcmap.nii.gz and put it in the bold folder, eg: epidewarp.fsl \ --mag mag.nii.gz \ --dph dphase.nii.gz \ --tediff YOUR_TE_DIFF --esp YOUR_ESP \ --vsm bold/b0dcmap.nii.gz When you run mkanalysis-sess and preproc-sess, add "-b0dc" to the command lines. doug On 05/03/2013 12:16 PM, Corinna Bauer wrote: > Yes, I am using FSFAST. > > > On Fri, May 3, 2013 at 12:08 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Corinna, are you using FSFAST? If not, are you still going to the > surface? > doug > > On 05/03/2013 11:07 AM, Corinna Bauer wrote: > > Is there a way to correct fmri data for epi distortions in > freesurfer? > > Or does the data need to be first fun through FSL's B0 unwarping? > > > > Corinna > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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. 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 greve(a)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/

2 5

determine the peak vertex
by limengsecret 03 May '13

03 May '13

Hi freesurfer, I have a label and each vertex in this label has a probability value. My problem is that how to determine the peak vertex (or the center of gravity) of this label and get the coordinates. And I also want to know, in the tksurfer interface, whether the vertex index has a correspondence to the vertex RAS. Thanks a lot! Best wishes, Meng

2 1

Issues with Cluster generation
by Joshua deSouza 03 May '13

03 May '13

Hello all, I am facing a problem whereby after running GLMfit and cluserwise correction for multiple comparisons using the monte-carlo method, I was unable to generate any clusters. I do have significant images produced for the glmfit. All procedures were done according to the tutorial to match the effects under FSGD. There are no clusters available even when I set the cwpvalthresh to .999 which is supposed to show all clusters. What is the cluster generation dependent upon? As my glmfit does show significant areas. Please advise

2 1

epi correction of fmri data
by Corinna Bauer 03 May '13

03 May '13

Is there a way to correct fmri data for epi distortions in freesurfer? Or does the data need to be first fun through FSL's B0 unwarping? Corinna

3 2

Re: [Freesurfer] Longitudinal analysis of one timepoint
by Sarah Whittle 03 May '13

03 May '13

Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah .... Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote: > Hi Freesurfer experts, > > > > This week a read the article of Bernal-Rusiel et al. titled > “Statistical analysis of longitudinal neuroimage data with Linear > Mixed Effects models”. In this article you described the submission of > single time-point scans to the longitudinal pipeline of Freesurfer. > I’m very interested in how to do this. Your help will be appreciated. > > > > Thanks in advance, > > > > Henk-Jan > > > > ______________________________________________________________________ > > De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de > afzender direct te informeren door het bericht te retourneren. Het > Universitair Medisch Centrum Utrecht is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van > Koophandel voor Midden-Nederland onder nr. 30244197. > > Denk s.v.p aan het milieu voor u deze e-mail afdrukt. > > > ______________________________________________________________________ > > This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the sender > immediately by return e-mail. University Medical Center Utrecht is a > legal person by public law and is registered at the Chamber of > Commerce for Midden-Nederland under no. 30244197. > > Please consider the environment before printing this e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

4 12

Question
by Jerskey, Beth 03 May '13

03 May '13

What effect, if any, would the implantation of a Vagus Nerve Stimulator have on registration? Thank you, Beth

2 1

tracula FS 5.2
by Antonenko, Daria 03 May '13

03 May '13

Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013 I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria

4 6

Flattening a specific surface parcellation or a group of spatially adjacent parcellations
by Bilal Ahmed 02 May '13

02 May '13

Hi, I was wondering if there is a simple way to flatten specific surface parcellations without manually specifying cuts. For example if I want a flattened patch pertaining to the left temporal pole for fsaverage, I would have to manually specify the cut points and then extract and flatten it. As we already know the boundary for this parcellation can we use this information to automatically extract the patch and then flatten it, by providing the boundary points as the cut points? thanks,

3 3

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