On Fri, May 3, 2013 at 4:30 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

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/

--
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/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/