How can I permanently change the orientation of an I-Phone MOV file.

I'm trying to burn DVDs for family members from some wedding videos I  took with my I-Phone.  Because I held the I-Phone in an upright, or  "portrait" position, the normal playback comes through in a "landscape"  orientation with the images laying sideways.  Within QuickTime Pro, I'm  able to rotate the viewing angle by 90 degrees to be viewed properly,  but when I save the adjusted settings, the original file remains  unchanged in its "un-rotated" format.  How can I change the actual,  native file format so that the orientation is correct for a DVD playback  that does not have the benefit of QuickTime functionality?

The "normal" size of the source video is 1920 pixels wide x 1080 pixels high.  My goal is to crop some of both the top and bottom of the display area so as to reduce the size of the pillar box effect when I export the file in the 90-degree rotated position.  Within Photoshop I made as many as 12 different variations of masks using the same 1920x1080 dimensions.  But when I apply the masks, the resulting views I get are bottom left, bottom right, bottom middle, etc., but none of the masks will display any portion of the top half of my source video?
Maybe it would be easier to run through the entire strategy here. First of all you have determine your workflow.
1) First of all you have to decide if you are making a data DVD (one that plays on a computer) or a normal DVD that is to be played on a commercial DVD player. Based on your previous comments, I had assumed you wanted the latter.
2) The next step is to decide which DVD standard you need for the DVD player. Am assuming you are creating an NTSC DVD here which means your final encode matrix will be 720x480.
3) The next step is to decide whether you are creating a widescreen or a full screen DVD. I.e., you need to decide whether you need to mask or crop your content to a 16:9 or 4:3 aspect ratio.
4) At this point I would decide upon a specific workflow strategy—i.e., whether to crop or mask the content. Since you mention the creation of masks, I assume this is your preference.
5) Having answered the above questions, I would now open the rotated file in QT 7 Pro as a 1080x1920 display file.
6) At this point I would probably scale the display dimensions as needed to most easily work at your preferred target aspect ratio. By this I mean your maximum width is 1080 which works well at a 4:3 aspect (1080x810) but not so well as 16:9 aspect (1080x607.5) mask. Obviously in the latter case dimensions something like 960x540 would be easier to work with and I would likely "scale" the display width to 960 in the "Keep Aspect" mode and allow QT 7 Pro to scale the verticle dimension as it pleases.
7) Now is the time to create the white mask background at the same dimensions as your scaled or unscaled display screen as currently open in QT 7 Pro.
8) To create the actual mask, you now black out the area (e.g., 1080x810 within a 1080x1920 screen or 960x540 within your "scaled" display screen) you want to display in your final DVD. This area can be centered or offset high or low to center the focus of attention in your final DVD.
9) Once you have finished step 8, you can export your properly oriented and masked content to any compression formats compatible with your DVD authoring application which will properly scale, convert, and author the content for DVD burning according to the proper widescreen or full screen settings selected by you.

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