Thanks Doug,
Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps?
-Clark
I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug
On 11/13/2012 11:59 AM, Clark Fisher wrote:
Thanks Doug,
Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps?
-Clark
I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though.
On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote:
I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug
On 11/13/2012 11:59 AM, Clark Fisher wrote:
Thanks Doug,
Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps?
-Clark
-- 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: 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.
Hi Clark, hi Doug
fugue has an option that might help here. Here is the relevant excerpt rom calling fugue on the command line (as in fugue of fsl 5.0.1 but I am sure this was also present in fsl 4.1.n): "--unwarpdir specifies direction of warping [x/y/z/x-/y-/z-] (default y)" it seems that this might help if set correctly; Clark maybe you can hack epidewarp.fsl to include an "export option" to supply this information to the script?
best Sebastian
On Nov 13, 2012, at 09:51 , Clark Fisher wrote:
I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though.
On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote:
I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug
On 11/13/2012 11:59 AM, Clark Fisher wrote:
Thanks Doug,
Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps?
-Clark
-- 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: 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.
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I guess it is possible that Siemens is doing something funny with the images. I've never used sagittal before.
On 11/13/2012 12:51 PM, Clark Fisher wrote:
I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though.
On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote:
I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug
On 11/13/2012 11:59 AM, Clark Fisher wrote:
Thanks Doug,
Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps?
-Clark
-- 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: 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.
Hi Doug, All other things being equal, if you switch from AP to RL phase encoding in an axial acquisition, then the PE direction will switch from the y-axis to the x-axis in the images. It doesn't really have anything to do with Siemens, since the images are written out in a standard anatomical orientation, not according to which axis was readout and which was phase encode.
Hope that helps, -MH
Michael Harms, Ph.D.
----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
On 11/13/12 3:46 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I guess it is possible that Siemens is doing something funny with the images. I've never used sagittal before.
On 11/13/2012 12:51 PM, Clark Fisher wrote:
I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though.
On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote:
I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug
On 11/13/2012 11:59 AM, Clark Fisher wrote:
Thanks Doug,
Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps?
-Clark
-- 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: 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Sebastian Moeller