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 >> <[email protected]> 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 >> <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 >> <[email protected]> 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 >> <[email protected]> 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 >> <[email protected]> >> 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 >> <[email protected]> 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 >> >> >> >> >> >> 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. >> >> >> >> >> >> >> >> >> >> >> <example1a.png> >> >> <example1b.png> >> >> <example2a.png> >> >> <example2b.png> >> >> <example3a.png> >> >> <example3b.png> >> >> >> >> >> >> > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
