Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train

can you send us the full command line and screen output of what you ran? On Mon, 5 Aug 2013, Mark Plantz wrote:

For some reason, when I run that command, I get the following output: Input volume  is : seg_mov Output volume is : seg_mov_2

There are no errors, but when I check "mri_info" of the output file, the TR, TE, etc. values are still non-zero. Any ideas what could cause that to happen?

Thanks!

MP

On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: yes, I think so On Mon, 5 Aug 2013, Mark Plantz wrote:

        thank you. Would the command simply be something like this: mri_modify -tr 0 -te 0 -ti 0 -fa 0
        <input.mgz> <output.mgz> ?


        On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
              Hi Mark

              the formatting got messed up so I can't parse your table. You can get around this using
        mri_modify, and just setting
              everything to 0. As for the effects, look at the images and see what you think.

              cheers
              Bruce

              On Thu, 1 Aug 2013, Mark Plantz wrote:

                    Hello freesurfers,
                        I currently have a series of images with various TR,TE,TI,FA values. I
                    would like to use mri_ca_train to create a .gca atlas based on these
                    segmented volumes. Unfortunately, they all have slightly different control
                    parameters (TR,TE,TI,FA). Is there any way around this problem, or would it
                    be best to break the subjects into multiple groups with the same control
                    parameters?

                    Here are the various parameters: [each row is a subject]

                    TR
                    TE
                    TI
                    flip angle
                    9.38
                    3.86
                    450
                    12
                    9.34
                    3.86
                    450
                    12
                    9.38
                    3.86
                    450
                    12
                    9.38
                    3.86
                    450
                    12
                    9.34
                    3.86
                    450
                    12
                    9.44
                    3.87
                    450
                    12
                    9.39
                    3.86
                    450
                    12
                    2065.98
                    7.61
                    886.92
                    90
                    9.45
                    3.89
                    450
                    12
                    9.41
                    3.87
                    450
                    12
                    9.41
                    3.87
                    450
                    12
                    9.42
                    3.91
                    450
                    12
                    9.38
                    3.86
                    450
                    12
                    9.38
                    3.86
                    450
                    12
                    9.44
                    3.86
                    450
                    12
                    9.44
                    3.86
                    450
                    12
                    9.38
                    3.86
                    450
                    12
                    9.38
                    3.86
                    450
                    12
                    9.38
                    3.86
                    450
                    12
                    9.34
                    3.86
                    450
                    12
                    9.34
                    3.86
                    450
                    12
                    9.39
                    3.86
                    450
                    12
                    1900
                    2.6
                    900
                    9
                    1900
                    2.6
                    900
                    9
                    1900
                    2.6
                    900
                    9
                    9.41
                    3.87
                    450
                    12
                    9.41
                    3.87
                    450
                    12
                    9.41
                    3.87
                    450
                    12
                    1900
                    2.6
                    900
                    9
                    9.41
                    3.87
                    450
                    12
                    1900
                    2.6
                    900
                    9
                    1900
                    2.6
                    900
                    9

                    Thank you in advance.

                    -Mark





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