Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012

Desimone Lab, McGovern Institute for Brain Research

MIT Archery Club

Alpha Kappa Psi Colony at MIT

On Wed, Aug 10, 2011 at 2:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

One thing you can try is to look at the current orientation with
mri_info --orientation f.img
This will print out a 3-letter string like LPS or LSA. Create a new string by replacing the A with a P or P with an A. then
mri_convert f.img --in_orientation NewString f.new.nii
where NewString is the 3-letter string you created.
Try loading this into tkmedit or freeview to make sure that it is oriented correctly.
But, like Bruce says, you won't be able to tell left from right (unless you have fiducials).
doug

Bruce Fischl wrote:

Hi Chris,

that won't work for us. We assume it's in an ras coordinate system. I think you can do it with mri_convert, Doug probably knows how, but if you can't tell left from right it's going to be a problem forever. It's not worth running it through recon-all until the .img files comes up with the appropriate directions in freeview or tkmedit. Try looking at the mri_convert help

cheers
Bruce

On Wed, 10 Aug 2011, Christopher Luna wrote:

Hi Bruce,
We tried to reverse A/P by reversing it the Talairach transform since recon-all wasn't able to do it automatically. I'm actually not sure how to
reverse it in the IMG and HDR files.

Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT

On Wed, Aug 10, 2011 at 2:19 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Chris,

when I bring that one up in freeview it looks like the a/p axis is still reversed (i.e. 'P' is at the front of the head)

Bruce
On Wed, 10 Aug 2011, Christopher Luna wrote:

Okay, I've uploaded them as cdluna_whitematter_002.img and *.hdr.
Thanks,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT

On Tue, Aug 9, 2011 at 11:02 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Eek, that looks awful! Can you upload this subject so we can figure out what is going on?

On Aug 9, 2011, at 4:09 PM, Christopher Luna <cdluna@mit.edu> wrote:

Hello,
On this topic again, we tried fixing the coordinate system (we flipped A/P) as much as we could until we heard back from our
colleagues.

And we also altered the white matter thresholds from mri_segment in case the missing white matter was due to some strange qualities
in the original IMG files.

Unfortunately, this didn't work. I've attached some example pictures of what we end up with even after tinkering with the white
threshold.

Are we going to have to add in this missing white matter by hand?

Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT

On Mon, Aug 1, 2011 at 3:04 PM, Christopher Luna <cdluna@mit.edu> wrote:
Hi Bruce,
Thank you very much! We'll get in contact with them.

Best,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT

On Mon, Aug 1, 2011 at 2:52 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Chris,

they are front/back reversed (a/p), which is why everything fails. I don't know how you are ever going to know left
from right though. You should talk to whoever got you this data and see if they have some way to tell.

cheers
Bruce

On Mon, 1 Aug 2011, Christopher Luna wrote:

I've uploaded the IMG and HDR files, they are named after my email address.
Thank you kindly,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT

On Mon, Aug 1, 2011 at 12:40 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange?highlight=%28ftp%29
On Mon, 1 Aug 2011, Christopher Luna wrote:

Ah, I forgot about the left/right orientation. Where should I upload these
files?
Thanks,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab, McGovern
Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT

On Mon, Aug 1, 2011 at 12:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
how do you know left/right is correct? In any case, if you
upload the subject we'll take a look. Things very rarely fail
that badly

On Mon, 1 Aug 2011, Christopher Luna wrote:

Hi Bruce,
The orientations are correct - they weren't at first so I
had to do a lot of work in tkregister2 to get the
orientations correct. Unfortunately I only have access to
the
*.IMG and sometimes the *.HDR file for each subject.

Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab,
McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT

On Mon, Aug 1, 2011 at 12:16 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
Hi Christopher,

are you sure that the orientations are correct? That is,
when you bring the orig.mgz up in tkmedit does the coronal view
actually show the brain coronally? Img
is a dangerous format to use as it doesn't contain
orientation info. Do you have access to the data in some other
format before it was convered to img?

Bruce

On Mon, 1 Aug 2011, Christopher Luna wrote:

Hello Freesurfers,
I'm putting *.IMG files into the program and after correcting
talaraich transformations for them, I notice that when the
reconstructions have completed, that
there are
entire lobes of white matter absent from the surfaces detected
and from the wm.mgz file. I went through my hand at first to
manually fill in the missing white
matter for
the first case, but after seeing how many were affected, I
figured there was some setting I may be missing or some contrast
level that may be off.

I had tried using control points, but after following the WIKI
instructions on regenerating surfaces after placing them, I
found no significant difference in
white matter
detection.

How do I ensure all of the white matter in my converted IMGs is
identified?

Thank you kindly,
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012Desimone Lab,
McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT

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