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@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@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@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@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@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@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@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@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@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/
It did run all the way through using the .img files.
Should I try that mri_convert on all 4 real/imaginary files?
On Fri, May 3, 2013 at 4:30 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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@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@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.** harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ 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<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@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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><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 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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<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<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 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
-
Corinna Bauer -
Douglas N Greve