hi ay, so this is what i did. i flipped the gradient LR intentionally, ran flip4fsl and then dtifit and now the eigenvec 1 looks good, but not if i run dtifit prior to flip4fsl.
but this brings me back to my original point which is that my image and the gradients are (i think) already in proper orientation for fsl tools (since the preflip output in the previous email looks correct) and flip4fsl is making it inappropriate for fsl. also as some additional info: - yes this is the siemens 60 dir scan but that predefined gradient table doesn't take into account the slice orientation - if you use dcm2nii to extract these dicoms, the first two gradients are: 0.996362388134 0.0389195755124 -0.07581084221601 -0.65292024612426 0.00993375014513 -0.75736147165298 this is because dcm2nii, much like DTIPrep takes the image orientation matrix into account when doing the conversion, which mri_convert doesn't. so i think tracula should have an option of not flipping 4 fsl in the scenario where other processes (e.g., my script, dcm2nii) automatically take care of generating an fsl compatible file + gradient info. please let me know if i'm misinterpreting something here. cheers, satra On Tue, Jul 2, 2013 at 8:21 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Satra - What you're showing in the screenshots would be consistent with > a L-R flip of the gradient directions, which is what my comparison of your > gradients to the original Siemens gradients indicated. (Assuming the data > was acquired with the standard Siemens 60 gradient directions.) > > > a.y > > On Tue, 2 Jul 2013, Satrajit Ghosh wrote: > > hi ay, >> i'll look into the orientations a little later tonight, but here is V1 >> overlaid on FA for preflip and postflip execution of dtifit. >> >> cheers, >> >> satra >> >> >> On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What >> flip4fsl will do is convert it to LAS, and perform the same >> conversion on the gradient table that you provide. This of >> course assumes that dwi_orig.nii.gz and your gradient table are >> consistent as they come out of your custom preprocessing. Is >> there any chance that they're not? >> >> Looking at the sample data set that you sent me, I can only see >> what came out of your preprocessing and not what went in. I'm >> assuming that this is from the standard Siemens 60 direction >> sequence, and it has 57 directions b/c 3 of them were thrown out >> by your preprocessing. I don't know which directions were thrown >> out obviously, but the first 2 directions in your gradient table >> are: >> -0.99699027939850948 -0.057720153020443053 0.051758263409041924 >> 0.63287878858184599 0.066164234845749903 0.77141869630019422 >> >> The first two directions in the Siemens 60 direction gradient >> table are: >> 1.0000000000 0.0000000000 0.0000000000 >> 0.5867917880 -0.3765825401 -0.7168409782 >> >> There's not only a small adjustment of the direction but also a >> sign change there. So I'd look into that. >> >> Let me know if any of my assumptions about your original data is >> wrong. >> >> a.y >> >> On Tue, 2 Jul 2013, Satrajit Ghosh wrote: >> >> hi anastasia, >> i'm trying to debug a seg fault that some folks are >> seeing deep into a >> tracula run. >> >> process: >> >> 1. feed dicoms to a script that runs DTIPrep and >> outputs a nifti file, bvec, >> bval >> >> (among checking for many artifacts, this reduces the >> b=0 volumes to a single >> registered mean volume, runs eddy correction, >> discards bad directions, >> reorients the gradients appropriately and generates >> a report of the quality) >> >> 2. run tracula on this nifti file >> >> observation: >> >> when i run fsl/dtifit on the same nifti file + bvec >> + bval, i get the proper >> orientation for eigvec1 lines. however, when i feed >> this into tracula, the >> output of the dtifit step looks terrible - i.e. the >> lines are not oriented >> as how one might expect water to diffuse. >> >> suspicion: >> >> although i have not reached the crash yet, i believe >> it might be related to >> this fact that the gradients are not oriented >> properly relative to the >> volume. >> >> i also suspect that this has something to do with >> the flip4fsl step inside >> tracula, which is possibly unnecessary because fsl >> already likes the input >> files. but it seems this step is encoded quite >> heavily within the trac-all >> scripts. >> >> questions: >> >> a. is there a quick way to turn the flip4fsl step >> off? >> b. alternatively do you have any suggestions for >> what to do here? >> >> the whole point of running through DTIPrep is to >> clean up the data before >> giving it to tracula or other programs, so i would >> really like to keep that >> step. >> >> cheers, >> >> satra >> >> >> >> >> >> 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<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. >> >> >> >>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
