<BODY>1) We are first time users of LDDMM and and are encountering a problem when we use the single channel registration: "file not found: process.md5". <BR><BR>Is DiffeoMap on a network disk instead of on your local disk? <BR><BR><BR>Xin<BR><BR>----- Original Message -----<BR>From: Usha Sinha <usinha@mail.sdsu.edu><BR>Date: Sunday, March 17, 2013 3:52 pm<BR>Subject: Re: [Mristudio-users] Fwd: loading DSI dataset into DTIStudio<BR>To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users@mristudio.org>, susumu@mri.jhu.edu<BR>Cc: Vadim Malis <vadmalis@gmail.com><BR><BR><BR>> Hi Susumu<BR>> I apologize for using your direct mail but I had some problems <BR>> logging into<BR>> the forum.<BR>> I have the following questions:<BR>> <BR>> <BR>> *LDDMM*<BR>> <BR>
> 1) We are first time users of LDDMM and and are encountering a problem<BR>> when we use the single channel registration: "file not found:<BR>> process.md5". Further, we are using the LDDMM to correct for distortions<BR>> in muscle DTI images, these images are acquired rather anisotropically<BR>> (1.4mm in plane and 5 mm thickness), so the requirement for isotropic <BR>> voxel<BR>> in LDDMM is a stretch. Is there a LDDMM algorithm as a 2D version<BR>> available where we correct on slice by slice basis as the maximum<BR>> distortions are along the in-plane phase encode. Our T2 and b0 <BR>> slices are<BR>> matched acquisitions. If a 2D version is not available, would it be <BR>> OK to<BR>> reslice the T2 and DTI volumes to be isotropic despite a highly anisotropic<BR>> acquisition?<BR>> *Fiber Tracking*<BR>
> <BR>> 1) When performing tracking in DTIStudio, is there a way to obtain a <BR>> track<BR>> through a selected voxel. The reason I ask is that when selecting <BR>> even a<BR>> single voxel ROI, the number of tracks through it more than one; this <BR>> is<BR>> from the brute force aspect of the algorithm, I guess. We are trying <BR>> to<BR>> get muscle fiber pennation angles using seed points starting near the<BR>> aponeurosis. It will help us in trying to get the fiber that originates<BR>> from the seed point rather than the ROI at that seed point (or is <BR>> there a<BR>> non-brute force available).<BR>> <BR>> 2) This feature (getting the fiber coordinates from a seed voxel) is <BR>> also<BR>> important for our brain fiber atlases where we are trying to evaluate <BR>> the<BR>
> quality of tracking in atlases generated by different methods. One method<BR>> suggested is the sum of distances of equally spaced points along the <BR>> fiber<BR>> tract starting from the seed point in atlas and subjects. The other method<BR>> to compare is the track end point divergence. When several tracks go<BR>> through a single voxel ROI, it makes comparisons difficult.<BR>> <BR>> <BR>> Thanks<BR>> <BR>> Usha<BR>> <BR>> <BR>> <BR>> <BR>> <BR>> On Fri, Mar 15, 2013 at 4:27 PM, susumu mori <susumu@mri.jhu.edu> wrote:<BR>> <BR>> > OK, Deepa,<BR>> ><BR>> > I believe you did a typical DSI study. Because it would be of <BR>> interest for<BR>> > many DtiStudio users, allow me to share my response to you, <BR>> together with<BR>
> > your images.<BR>> ><BR>> > There are two important differences between DTI and DSI.<BR>> > First, of course, DSI requires many more gradient orientations. In <BR>> your<BR>> > case, you used 257 directions. In general, 100 orientation measurement<BR>> > takes more than 10 min. So, 257 orientations would take about 30 <BR>> min. You<BR>> > repeated it twice. So, it must take 1 hour, if I'm not mistaken.<BR>> > I once asked Van Wedeen about how many orientations would be preferable.<BR>> > He said, "even 300 is very sparse, if you map them on the surface <BR>> of a<BR>> > sphere. So, the more the better" was his reply.<BR>> > On the other hand, if you use a model like spherical decomvolution, <BR>> there<BR>> > are papers demonstrating directions as few as 60 would give you decent<BR>
> > estimation of crossing fibers. I don't have an answer to it.<BR>> ><BR>> > Second, high-angular resolution imaging like DSI requires higher b<BR>> > values. This actually have more profound effects on your experiment <BR>> design<BR>> > and image quality. DTI typically uses b = 700-1,000. The higher you <BR>> go, the<BR>> > more signal you loose, more motion artifacts you get, and more eddy <BR>> current<BR>> > distortion you suffer. On top of it, because each image is so noisy,<BR>> > detection and correction of artifacts become more difficult. DSI <BR>> requires b<BR>> > = 3,000 - 30,000, which is much higher than DTI.<BR>> ><BR>> > Some people believe DSI data naturally includes DTI data. <BR>> Therefore, once<BR>> > you get DSI data, you wouldn't loose anything. However, that is not <BR>> the<BR>
> > case, because you suffer from SNR loss and more artifacts. This is <BR>> why it<BR>> > is difficult to adopt DSI protocols for routine research and clinical<BR>> > studies.<BR>> ><BR>> > I attached a nice paper by Derek discussing this issue.<BR>> ><BR>> > Now, let's go back to your images. The b0 looks good. The DWIs are <BR>> what<BR>> > you would expect from high b-value DWIs. Your images look very <BR>> similar to<BR>> > Fig. 3 in Derek's paper with b=2,000-3,000. So your data are fine. <BR>> They<BR>> > don't look like typical DTI data because I bet that the b-values <BR>> you used<BR>> > are b = 2,000-3,000.<BR>> ><BR>> > You have slight ghosting in the background, but it seems <BR>> calibration error<BR>> > for your EPI phase correction; not a major problem, I think.<BR>
> ><BR>> > So, the bottom line is, your DICOM files were correctly read. The<BR>> > appearance of DWIs should be different between DSI and DTI <BR>> protocols and<BR>> > your images are what you expect.<BR>> ><BR>> > Hope this will help.<BR>> ><BR>> > Susumu<BR>> ><BR>> > On Fri, Mar 15, 2013 at 6:31 PM, Deepa Krishnaswamy <<BR>> > deepa.krishnaswamy1@gmail.com> wrote:<BR>> ><BR>> >> Hi,<BR>> >> I have attached a power point with a few images.<BR>> >> Yes I did read the data as Mosaic. There are 515 gradient <BR>> directions in<BR>> >> total, which is comprised of repeated 257 directions plus 1 b0.<BR>> >> I do know that DTIStudio does not support DSI data analysis, but <BR>> isn't it<BR>
> >> still possible to fit the DTI model to DSI data?<BR>> >> I also just wanted to run through the LDDMM pipeline to get our data<BR>> >> registered to the same space as the JHU MNI WM atlas, and then use <BR>> our own<BR>> >> tractography algorithms.<BR>> >> I hope this is possible, thanks.<BR>> >><BR>> >> Deepa<BR>> >><BR>> >> On Thu, Mar 14, 2013 at 10:20 AM, susumu mori <susumu@mri.jhu.edu> <BR>> wrote:<BR>> >><BR>> >>> Hi Deepa,<BR>> >>><BR>> >>> Did you read the data as Mosaic?<BR>> >>> Please send me the actual images in PowerPoint.<BR>> >>><BR>> >>> If you are using non off-the-shelf image protocol, it is possible <BR>> that<BR>
> >>> DtiStudio can't read the user-defined data format.<BR>> >>> If you get a custom data acquisition method from somebody, I encourage<BR>> >>> you to talk with them about how to read the data. DtiStudio <BR>> doesn't support<BR>> >>> DSI data analysis anyway.<BR>> >>><BR>> >>> Susumu<BR>> >>><BR>> >>> On Tue, Mar 12, 2013 at 9:50 PM, Deepa Krishnaswamy <<BR>> >>> deepa.krishnaswamy1@gmail.com> wrote:<BR>> >>><BR>> >>>> Hi,<BR>> >>>> I have a DSI dataset in MOSAIC format, along with the <BR>> corresponding b<BR>> >>>> btable. I noticed that after loading in the data, some of it appears<BR>> >>>> extremely blurry/shifted. I know that the data actually does not <BR>> look like<BR>
> >>>> this, as I have used other programs to view the raw data. Has <BR>> anybody else<BR>> >>>> encountered this problem?<BR>> >>>> Thanks,<BR>> >>>><BR>> >>>> Deepa<BR>> >>>><BR>> >>>> _______________________________________________<BR>> >>>> mristudio-users mailing list<BR>> >>>> mristudio-users@mristudio.org<BR>> >>>> <BR>> >>>> Unsubscribe, send a blank email to:<BR>> >>>> mristudio-users-unsubscribe@mristudio.org<BR>> >>>><BR>> >>>><BR>> >>><BR>> >><BR>> ><BR>> > _______________________________________________<BR>> > mristudio-users mailing list<BR>> > mristudio-users@mristudio.org<BR>
> > <BR>> > Unsubscribe, send a blank email to:<BR>> > mristudio-users-unsubscribe@mristudio.org<BR>> ><BR>> > <BR>> _______________________________________________<BR>> mristudio-users mailing list<BR>> mristudio-users@mristudio.org<BR>> <BR>> Unsubscribe, send a blank email to: mristudio-users-unsubscribe@mristudio.org <BR></BODY>