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Thank you all for your responses. My problem is that, as I was new to Siemens, on the Contrast tab of the sequence parameters, there is a Reconstruction setting with options to output Magnitude, Phase, or Magn./Phase. I initially (unknowingly) had this set to output only the Phase (I have since corrected the sequence to output both Magn./Phase). So I only have Phase data; is there a way to use the Fieldmap toolbox (or another EPI distortion correction algorithm) without the Magnitude images, or a way to reconstruct the Magnitude from the Phase? Much appreciated, -Julie On Wed, Aug 22, 2012 at 11:11 AM, xiaoying fan <[log in to unmask]> wrote: > Hi Julie, > > We use Siemens TrioTim and get the same 3 files ( two mags with short and > long TE, one phase) as Glad mentioned. Also you can use Osirix to view the > images directly showing TR and TE values on the images. > > Good Luck, > > Xiaoying > > > On Wed, Aug 22, 2012 at 9:55 AM, Glad Mihai <[log in to unmask]>wrote: > >> The magnitude image is the one I mentioned before, mind you I gave you >> the names of the images in nifti format which were converted from DICOM >> with SPM. You can use either the first or the second, it makes no >> difference. >> >> To make sure you get the right image, use an image viewer like MRICRON. >> Then go to Window > Information > Optional (Tab) > Notes (field). There you >> should see TR and TE length. For my images the short TE is 4.92ms and the >> long is 7.38ms. >> >> >> I hope this helps. >> >> Glad >> >> >> On 22.08.2012 15:41, Julie McEntee wrote: >> >> Sorry- by time points, I mean I have longitudinal data. >> >> I was pretty sure that the field map had to come from the same >> pt/position/scan session; like I said, it was suggested, so I threw it out >> there. >> >> What is the magnitude image used for in the Fieldmap toolbox? I was >> thinking I could substitute it with another image (acquired with same pt >> during same scan session) or mask. >> >> Thanks, >> >> -Julie >> >> On Wed, Aug 22, 2012 at 8:23 AM, Glad Mihai <[log in to unmask]>wrote: >> >>> Hi Julie, >>> >>> I don't quite understand what you mean with time point 1, 2, 3, etc. You >>> set one subject in the scanner, then started measuring the field map, after >>> which you measured your first trial, then you measured the field map again, >>> then the next trial? >>> >>> Basically every time a new person or a new position is being scanned you >>> will have to record a field map. Also, if you have different sequences, for >>> example one with a resolution of 2x2x2 mm³ and one with a resolution of >>> 3x3x3 mm³, you will have to record a field map corresponding to each of >>> those sequences, even though you scanned the same person without him or her >>> leaving the scanner. >>> >>> Regards, >>> Glad >>> >>> >>> On 22.08.2012 13:26, Julie McEntee wrote: >>> >>> Thanks, Glad. >>> >>> I am now acquiring the field map sequence as you describe. >>> >>> However, initially I did not have parameter set to output both mag & >>> phase- it was set to output phase only. >>> >>> So, I only have phase change image for the first time point. >>> >>> I do have all 3 outputs (2 mags & 1 phase) for time point 2 (& 3 in some >>> cased)- it was suggested that I use the mag images from time point 2 with >>> the phase from time point 1 (from same subject). Any input on this approach >>> would be appreciated. >>> >>> Thank you, >>> >>> -Julie >>> >>> sent via DROID by Verizon >>> On Aug 22, 2012 3:24 AM, "Glad Mihai" <[log in to unmask]> wrote: >>> >>>> Hey Julie, >>>> >>>> How many files did you get from the field mapping sequence? The Siemens >>>> Verio at our site gives three files using the gre_field_mapping sequence: 2 >>>> magnitude images (one with a short TE and one with a long TE) and a phase >>>> change image. They look something like this: >>>> >>>> magnitude images: >>>> s000*-0002-*-*-01.hdr >>>> s000*-0002-*-*-01.img >>>> s000*-0002-*-*-02.hdr >>>> s000*-0002-*-*-02.img >>>> >>>> phase change image: >>>> s000*-0003-*-*-02.hdr >>>> s000*-0003-*-*-02.img >>>> >>>> If you use the Fieldmap toolbox, you would only need to load one >>>> magnitude image (won't matter which) and the one phase change image, and >>>> provide it with the two TE values. >>>> >>>> I hope this helps. >>>> >>>> Glad >>>> >>>> Hello, >>>>> >>>>> I have phase-only data from a Siemens Verio gre_field_mapping sequence >>>>> (new to Siemens & didn't know to check that I wanted magnitude & phase >>>>> images). >>>>> >>>>> Is there any way I can use the Fieldmap toolbox with these phase-only >>>>> field maps to correct my EPI data for distortion? I have almost every other >>>>> image type- MPRage/T1, T2, FLAIR, SWI, DTI. >>>>> >>>>> Thank you in advance, >>>>> >>>>> -Julie >>>>> >>>>> -- >>>>> Julie E. McEntee, MA, CCRP >>>>> Image Processing Technologist >>>>> Center for Neuroscience & Regenerative Medicine, NIH/USUHS >>>>> The Henry M. Jackson Foundation for the Advancement of Military >>>>> Medicine >>>>> >>>>> NIH Clinical Center >>>>> Building 10, Room 1C370 >>>>> 301-919-4273 (cell)* >>>>> 301-451-5175 (office) >>>>> [log in to unmask] >>>>> >>>> >>>> -- >>>> Glad MIHAI, M.Sc. Biomedical Physics >>>> Funktionelle Bildgebung >>>> Uni-Klinikum Greifswald >>>> Walther-Rathenau-Straße 46 >>>> 17489 Greifswald >>>> www.baltic-imaging-center.de >>>> >>>> >>> -- >>> Glad MIHAI, M.Sc. Biomedical Physics >>> Funktionelle Bildgebung >>> Uni-Klinikum Greifswald >>> Walther-Rathenau-Straße 46 >>> 17489 Greifswald www.baltic-imaging-center.de >>> >>> >> >> >> -- >> Julie E. McEntee, MA, CCRP >> Image Processing Technologist >> Center for Neuroscience & Regenerative Medicine, NIH/USUHS >> The Henry M. Jackson Foundation for the Advancement of Military Medicine >> >> NIH Clinical Center >> Building 10, Room 1C370 >> 301-919-4273 (cell)* >> 301-451-5175 (office) >> [log in to unmask] >> >> >> -- >> Glad MIHAI, M.Sc. Biomedical Physics >> Funktionelle Bildgebung >> Uni-Klinikum Greifswald >> Walther-Rathenau-Straße 46 >> 17489 Greifswald www.baltic-imaging-center.de >> >> > -- Julie E. McEntee, MA, CCRP Image Processing Technologist Center for Neuroscience & Regenerative Medicine, NIH/USUHS The Henry M. Jackson Foundation for the Advancement of Military Medicine NIH Clinical Center Building 10, Room 1C370 301-919-4273 (cell)* 301-451-5175 (office) [log in to unmask]