The mask sort of covers the whole brain (see attached). It may be due to the display thresholding, when I viewed the path.pd.nii.gz using fslview, the tract actually has been recovered as compared to the previous one (old_path.png).
However, the path.pd still does seem normal, i.e. with quite a few extraordinary high intensity (probability, yellow)? Thanks. ping On Wed, Oct 19, 2011 at 2:52 PM, Anastasia Yendiki <[email protected]> wrote: > > Hi Ping - Do the corresponding brain masks in diffusion space > (dlabel/diff/aparc+aseg_mask.bbr.nii.gz and aparc+aseg_mask.flt.nii.gz) now > cover the entire brain well, after the aparc+aseg fixes? > > a.y > > On Tue, 18 Oct 2011, Ping-Hong Yeh wrote: > >> Hi Anastasia, >> >> I got fixed of the aparc+aseg (see aparc+aseg.png) in one of >> problematic data and re-ran the trac-all following your suggestions. >> However, the segmented forceps major using "FLIRT" still not getting >> good result (see flt.png) though "BBR" one is OK (see bbr.png). >> Similarly the segmented L CST using BBR looks weird, but the ones >> using FLIRT seem OK. >> It appear the problems are not simply due to the poor segmentation >> from the T1 recon-all. >> >> Any further suggestions? >> >> BR, >> Ping >> >> On Fri, Oct 14, 2011 at 11:04 AM, Anastasia Yendiki >> <[email protected]> wrote: >>> >>> Hi Ping-Hong, >>> >>> Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask >>> will be extracted from the DWI data by the bet tool, instead of using the >>> aparc+aseg. >>> >>> But, and this is a big but, TRACULA uses the aparc+aseg to constrain the >>> tractography solutions, i.e. the aparc+aseg is where the UnderLying >>> Anatomy >>> in TRACULA comes from. So the quality of the trac-all results depend on >>> the >>> quality of the aparc+aseg regardless of where your mask came from. >>> >>> a.y >>> >>> On Fri, 14 Oct 2011, Ping-Hong Yeh wrote: >>> >>>> Hi Anastasia, >>>> >>>> Can trac-all just use the mask in diffusion native space (by setting >>>> "usemaskanat = 0"? ) so I get around the T1 segmentation problem from >>>> FS recon? >>>> >>>> It seems that there is no quick answer on fixing the aparc+aseg? >>>> >>>> Thank you, >>>> p >>>> >>>> >>>> >>>> >>>> On Tue, Oct 11, 2011 at 10:35 PM, Anastasia Yendiki >>>> <[email protected]> wrote: >>>>> >>>>> I'll have to refer you back to the freesurfer list for that one. There >>>>> are >>>>> people with much more expertise than me on troubleshooting the >>>>> recon-all >>>>> stream. >>>>> >>>>> Once you get your recons fixed, you'll have to rerun all trac-all steps >>>>> except 1.1 (image corrections). >>>>> >>>>> On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: >>>>> >>>>>> The original aparc+aseg are not good, at least for these two cases. So >>>>>> which parameters in recon-all should be tweaked? >>>>>> >>>>>> On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki >>>>>> <[email protected]> wrote: >>>>>>> >>>>>>> Is the original aparc+aseg from the freesurfer recon not good either >>>>>>> (from >>>>>>> mri/aparc+aseg.mgz)? Or is it messed up only after registration into >>>>>>> diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz, >>>>>>> dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the >>>>>>> freesurfer >>>>>>> recon needs to be fixed or if the registration needs to fixed. >>>>>>> >>>>>>> On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: >>>>>>> >>>>>>>> yeap, the aparc+aseg_masks are not good. >>>>>>>> Any way to fix this? Thanks. >>>>>>>> >>>>>>>> On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki >>>>>>>> <[email protected]> wrote: >>>>>>>>> >>>>>>>>> I see, the mask may be the answer to the initialization failures! >>>>>>>>> It >>>>>>>>> seems >>>>>>>>> like the fmajor you sent me also has its endings masked out? That'd >>>>>>>>> cause >>>>>>>>> it >>>>>>>>> to fail. I wish I'd thought of this earlier! >>>>>>>>> >>>>>>>>> With usemaskanat = 1, the mask that's used is a slightly dilated >>>>>>>>> version >>>>>>>>> of >>>>>>>>> the aparc+aseg from the FS recon, mapped to diffusion space. So if >>>>>>>>> the >>>>>>>>> aparc+aseg has those parts missing, or if the diffusion-anatomical >>>>>>>>> registration is not good, parts will be masked out that shouldn't. >>>>>>>>> The >>>>>>>>> anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if >>>>>>>>> you've >>>>>>>>> run >>>>>>>>> both flirt and bbregister registrations, there'll be 2 of them). >>>>>>>>> Does >>>>>>>>> this >>>>>>>>> mask look like something went wrong? >>>>>>>>> >>>>>>>>> On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: >>>>>>>>> >>>>>>>>>> I used the default, i.e. set usemaskanat =1, but it looks that >>>>>>>>>> tracts >>>>>>>>>> were not reconstructed at the place where it was masked out (see >>>>>>>>>> the >>>>>>>>>> cross-bar at L_unc.png). >>>>>>>>>> >>>>>>>>>> I still have no luck in fixing the initialization issue (see >>>>>>>>>> fmajor.png for example). >>>>>>>>>> >>>>>>>>>> Thanks. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki >>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>> >>>>>>>>>>> Hi Ping - If you're using the anatomical brain as a mask (set >>>>>>>>>>> usemaskanat >>>>>>>>>>> = >>>>>>>>>>> 1, which is the default), then the diffusion-based mask won't >>>>>>>>>>> have >>>>>>>>>>> an >>>>>>>>>>> effect >>>>>>>>>>> on your outputs. >>>>>>>>>>> >>>>>>>>>>> BTW, have you had any luck with your initialization issues? Sorry >>>>>>>>>>> I >>>>>>>>>>> haven't >>>>>>>>>>> had another chance to look at your data since we last emailed, I >>>>>>>>>>> got >>>>>>>>>>> bogged >>>>>>>>>>> down with some other stuff. >>>>>>>>>>> >>>>>>>>>>> a.y >>>>>>>>>>> >>>>>>>>>>> On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Anastasia, >>>>>>>>>>>> >>>>>>>>>>>> I'd like to lower the bet threshold value by "set thrbet = 0.01" >>>>>>>>>>>> for >>>>>>>>>>>> skull-stripping because some of the brains have been cut, but it >>>>>>>>>>>> does >>>>>>>>>>>> not seem to make any changes (see attached). >>>>>>>>>>>> >>>>>>>>>>>> Any suggestion? Thank you, >>>>>>>>>>>> >>>>>>>>>>>> Ping >>>>>>>>>>>> >>>>>>>>>>>> On Fri, Sep 30, 2011 at 12:09 PM, Anastasia Yendiki >>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> Yes! Please add the "set reinit = 1" to the file that you pass >>>>>>>>>>>>> with >>>>>>>>>>>>> -c. >>>>>>>>>>>>> >>>>>>>>>>>>> On Fri, 30 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> so I should pass with the -c argument instead? >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Fri, Sep 30, 2011 at 12:04 PM, Anastasia Yendiki >>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> That file gets overwritten by whatever is in the file that >>>>>>>>>>>>>>> you >>>>>>>>>>>>>>> pass >>>>>>>>>>>>>>> with >>>>>>>>>>>>>>> the >>>>>>>>>>>>>>> -c argument to trac-all. Sorry for the confusion. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Fri, 30 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I edited the file under scripts/dmrirc.local >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Fri, Sep 30, 2011 at 12:00 PM, Anastasia Yendiki >>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Ping - Thanks for trying that. When you say in the >>>>>>>>>>>>>>>>> dmrirc.local, >>>>>>>>>>>>>>>>> do >>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>> mean that you edit the file under scripts/dmrirc.local, or >>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>> that >>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>> pass to trac-all as "-c dmrirc"? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> a.y >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Fri, 30 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Anastasia, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I've rerun NCNC0047, the one I sent you, and another one, >>>>>>>>>>>>>>>>>> but >>>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>>> does >>>>>>>>>>>>>>>>>> not help fixing the tracts. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I redone trac-all -prior with "set reinit =1" in the >>>>>>>>>>>>>>>>>> dmrirc.local >>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>> and then trac-all -path >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Any further suggestions? Thanks. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ping >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Thu, Sep 29, 2011 at 5:58 PM, Anastasia Yendiki >>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I wonder if the problem is with the replacement >>>>>>>>>>>>>>>>>>> executables >>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>> snow >>>>>>>>>>>>>>>>>>> leopard. They should not have a time stamp of April 14th, >>>>>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>>>>> don't >>>>>>>>>>>>>>>>>>> know >>>>>>>>>>>>>>>>>>> how >>>>>>>>>>>>>>>>>>> that could've happened. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Can you please try copying the version that I'm attaching >>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>> running >>>>>>>>>>>>>>>>>>> first >>>>>>>>>>>>>>>>>>> trac-all -prior and then trac-all -path with it? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If this version works, I'll have to reupload it and let >>>>>>>>>>>>>>>>>>> everyone >>>>>>>>>>>>>>>>>>> on >>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>> list >>>>>>>>>>>>>>>>>>> know. Thanks! >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Thu, 29 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The dmri_* files in the $freesurfer/bin are all after >>>>>>>>>>>>>>>>>>>> May, >>>>>>>>>>>>>>>>>>>> 2011 >>>>>>>>>>>>>>>>>>>> (see >>>>>>>>>>>>>>>>>>>> attached). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I think the one version, which failed on the MAC, has >>>>>>>>>>>>>>>>>>>> been >>>>>>>>>>>>>>>>>>>> replaced >>>>>>>>>>>>>>>>>>>> by >>>>>>>>>>>>>>>>>>>> the newer version. Is there a way to make sure the old >>>>>>>>>>>>>>>>>>>> version >>>>>>>>>>>>>>>>>>>> has >>>>>>>>>>>>>>>>>>>> been deleted? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Thu, Sep 29, 2011 at 4:28 PM, Anastasia Yendiki >>>>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The problem would be if the programs that trac-all runs >>>>>>>>>>>>>>>>>>>>> (dmri_*) >>>>>>>>>>>>>>>>>>>>> were >>>>>>>>>>>>>>>>>>>>> from a >>>>>>>>>>>>>>>>>>>>> version earlier than the stable 5.1 release, which was >>>>>>>>>>>>>>>>>>>>> made >>>>>>>>>>>>>>>>>>>>> public >>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>> late >>>>>>>>>>>>>>>>>>>>> May. Do you think you might have a different version on >>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>> machine >>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>> whatever reason? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Thu, 29 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks, Anastasia, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Most of the T1 segmentation results were done on >>>>>>>>>>>>>>>>>>>>>> another >>>>>>>>>>>>>>>>>>>>>> machine >>>>>>>>>>>>>>>>>>>>>> using >>>>>>>>>>>>>>>>>>>>>> V4.4.0, but the one running trac-all is on the machine >>>>>>>>>>>>>>>>>>>>>> with >>>>>>>>>>>>>>>>>>>>>> "freesurfer-i686-apple-darwin9.8.0-stable5-20110525". >>>>>>>>>>>>>>>>>>>>>> Can >>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>> cause >>>>>>>>>>>>>>>>>>>>>> the problem? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> p >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 29, 2011 at 1:43 PM, Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks, Ping, I got the files. The Apr 14th build >>>>>>>>>>>>>>>>>>>>>>> time >>>>>>>>>>>>>>>>>>>>>>> stamp >>>>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>>>> suspicious, >>>>>>>>>>>>>>>>>>>>>>> since the official 5.1 release was a month later, and >>>>>>>>>>>>>>>>>>>>>>> these >>>>>>>>>>>>>>>>>>>>>>> initialization >>>>>>>>>>>>>>>>>>>>>>> issues were mostly what I was debugging during that >>>>>>>>>>>>>>>>>>>>>>> month. >>>>>>>>>>>>>>>>>>>>>>> When >>>>>>>>>>>>>>>>>>>>>>> was >>>>>>>>>>>>>>>>>>>>>>> your >>>>>>>>>>>>>>>>>>>>>>> version of freesurfer installed? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Thu, 29 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Anastasia, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I followed the instruction on >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> see if you can find the file there. Indeed I've >>>>>>>>>>>>>>>>>>>>>>>> re-run >>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>> one >>>>>>>>>>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>>>>>>>>>> sent >>>>>>>>>>>>>>>>>>>>>>>> you last night, now it seems OK for that particular >>>>>>>>>>>>>>>>>>>>>>>> case. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I've loaded another one to the >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>>>>>>>>>>>>>>>> (still >>>>>>>>>>>>>>>>>>>>>>>> loading while writing this email), which has severe >>>>>>>>>>>>>>>>>>>>>>>> ventricular >>>>>>>>>>>>>>>>>>>>>>>> dilatation and the result of right anterior thalamic >>>>>>>>>>>>>>>>>>>>>>>> radiation >>>>>>>>>>>>>>>>>>>>>>>> path >>>>>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>>>>> not right. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I've attached the picture of another case failed at >>>>>>>>>>>>>>>>>>>>>>>> forceps >>>>>>>>>>>>>>>>>>>>>>>> major >>>>>>>>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>>>>>>>> the first attempt, and the snapshot after manually >>>>>>>>>>>>>>>>>>>>>>>> picking >>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>> initial >>>>>>>>>>>>>>>>>>>>>>>> points. The gray scale intensity is still not right, >>>>>>>>>>>>>>>>>>>>>>>> i.e. >>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>> initial >>>>>>>>>>>>>>>>>>>>>>>> path is very high (yellow), the others are >>>>>>>>>>>>>>>>>>>>>>>> significantly >>>>>>>>>>>>>>>>>>>>>>>> low, >>>>>>>>>>>>>>>>>>>>>>>> which >>>>>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>>>>> not I've usually seen. Does the gray scale still >>>>>>>>>>>>>>>>>>>>>>>> represent >>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>> likelihood (probability) of path or something else >>>>>>>>>>>>>>>>>>>>>>>> now? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Here is the output of dmri_train --all-info: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ProgramName: dmri_train ProgramArguments: >>>>>>>>>>>>>>>>>>>>>>>> --all-info >>>>>>>>>>>>>>>>>>>>>>>> ProgramVersion: >>>>>>>>>>>>>>>>>>>>>>>> $Name: $ TimeStamp: 2011/09/29-16:41:32-GMT >>>>>>>>>>>>>>>>>>>>>>>> BuildTimeStamp: >>>>>>>>>>>>>>>>>>>>>>>> Apr >>>>>>>>>>>>>>>>>>>>>>>> 14 >>>>>>>>>>>>>>>>>>>>>>>> 2011 15:35:19 CVS: User: twbrkmp2 Machine: >>>>>>>>>>>>>>>>>>>>>>>> twbrkmp2s-Mac-Pro-5.local Platform: Darwin >>>>>>>>>>>>>>>>>>>>>>>> PlatformVersion: >>>>>>>>>>>>>>>>>>>>>>>> 10.8.0 >>>>>>>>>>>>>>>>>>>>>>>> CompilerName: GCC CompilerVersion: 40200 >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Ping >>>>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 29, 2011 at 11:37 AM, Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Ping - Did you try to attach it to your email? I >>>>>>>>>>>>>>>>>>>>>>>>> didn't >>>>>>>>>>>>>>>>>>>>>>>>> get >>>>>>>>>>>>>>>>>>>>>>>>> anything. >>>>>>>>>>>>>>>>>>>>>>>>> Please try our file drop site: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> a.y >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Wed, 28 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Anastasia, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I've loaded the file, pingforAY.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>> This example data set failed in forceps major in >>>>>>>>>>>>>>>>>>>>>>>>>> flt >>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>> L >>>>>>>>>>>>>>>>>>>>>>>>>> slfp >>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>> bbr. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you very much. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Ping >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Sep 28, 2011 at 6:17 PM, Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Ping - You can upload your data if you want me >>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>> take >>>>>>>>>>>>>>>>>>>>>>>>>>> a >>>>>>>>>>>>>>>>>>>>>>>>>>> look >>>>>>>>>>>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>>>>>>>>>>> it. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 1. The initial points ideally should be along the >>>>>>>>>>>>>>>>>>>>>>>>>>> midline >>>>>>>>>>>>>>>>>>>>>>>>>>> of >>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>> pathway, >>>>>>>>>>>>>>>>>>>>>>>>>>> starting from one end region of the pathway and >>>>>>>>>>>>>>>>>>>>>>>>>>> going >>>>>>>>>>>>>>>>>>>>>>>>>>> all >>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>> way >>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>> other end region. (The default number is 5 >>>>>>>>>>>>>>>>>>>>>>>>>>> control >>>>>>>>>>>>>>>>>>>>>>>>>>> points >>>>>>>>>>>>>>>>>>>>>>>>>>> but >>>>>>>>>>>>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>> "set >>>>>>>>>>>>>>>>>>>>>>>>>>> ncpts = ..." in your dmrirc to change that.) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 2. You can look in >>>>>>>>>>>>>>>>>>>>>>>>>>> $FREESURFER_HOME/bin/dmrirc.example >>>>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>>>> how >>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>> specify >>>>>>>>>>>>>>>>>>>>>>>>>>> the field map inputs. They don't need to have the >>>>>>>>>>>>>>>>>>>>>>>>>>> same >>>>>>>>>>>>>>>>>>>>>>>>>>> matrix >>>>>>>>>>>>>>>>>>>>>>>>>>> size >>>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>>> resolution as the DWIs. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 3a. If it's the initialization that's failed, the >>>>>>>>>>>>>>>>>>>>>>>>>>> output >>>>>>>>>>>>>>>>>>>>>>>>>>> will >>>>>>>>>>>>>>>>>>>>>>>>>>> just >>>>>>>>>>>>>>>>>>>>>>>>>>> be >>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>> initial path and nothing else (which is I think >>>>>>>>>>>>>>>>>>>>>>>>>>> what >>>>>>>>>>>>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>>>>>>>>>>>> mean >>>>>>>>>>>>>>>>>>>>>>>>>>> by >>>>>>>>>>>>>>>>>>>>>>>>>>> "fewer >>>>>>>>>>>>>>>>>>>>>>>>>>> voxels"). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 3b. The diffusion model used here is the same as >>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>> ball-and-stick >>>>>>>>>>>>>>>>>>>>>>>>>>> model >>>>>>>>>>>>>>>>>>>>>>>>>>> that FSL uses. If the threshold you're referring >>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>> minimum >>>>>>>>>>>>>>>>>>>>>>>>>>> volume >>>>>>>>>>>>>>>>>>>>>>>>>>> fraction for the anisotropic compartments of that >>>>>>>>>>>>>>>>>>>>>>>>>>> model, >>>>>>>>>>>>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>> "set >>>>>>>>>>>>>>>>>>>>>>>>>>> fmin = >>>>>>>>>>>>>>>>>>>>>>>>>>> ..." in your dmrirc to choose one. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this helps a bit! >>>>>>>>>>>>>>>>>>>>>>>>>>> a.y >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, 28 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Anastasia, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I've tried both options, the choice 1 fixed some >>>>>>>>>>>>>>>>>>>>>>>>>>>> of >>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>> cases, >>>>>>>>>>>>>>>>>>>>>>>>>>>> but >>>>>>>>>>>>>>>>>>>>>>>>>>>> not all; and the choice 2 did not work at all. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Maybe >>>>>>>>>>>>>>>>>>>>>>>>>>>> I've >>>>>>>>>>>>>>>>>>>>>>>>>>>> missed >>>>>>>>>>>>>>>>>>>>>>>>>>>> something here. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Few more questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 1. Will the initial points have to include the >>>>>>>>>>>>>>>>>>>>>>>>>>>> points >>>>>>>>>>>>>>>>>>>>>>>>>>>> around >>>>>>>>>>>>>>>>>>>>>>>>>>>> start, >>>>>>>>>>>>>>>>>>>>>>>>>>>> way, and end points of the tracts need to be >>>>>>>>>>>>>>>>>>>>>>>>>>>> segmented? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Can >>>>>>>>>>>>>>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>>>>>>>>>>>>>> just >>>>>>>>>>>>>>>>>>>>>>>>>>>> enter the points in the main stem of tracts? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 2. Will EPI distortion correction, like using >>>>>>>>>>>>>>>>>>>>>>>>>>>> field >>>>>>>>>>>>>>>>>>>>>>>>>>>> map, >>>>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>> preprocessing steps help co-registration and >>>>>>>>>>>>>>>>>>>>>>>>>>>> thus >>>>>>>>>>>>>>>>>>>>>>>>>>>> improving >>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>> labeling? So far more than 80% (4 out of 5 data >>>>>>>>>>>>>>>>>>>>>>>>>>>> sets) >>>>>>>>>>>>>>>>>>>>>>>>>>>> of >>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>> data >>>>>>>>>>>>>>>>>>>>>>>>>>>> have at least one suboptimal tract, either in >>>>>>>>>>>>>>>>>>>>>>>>>>>> flt >>>>>>>>>>>>>>>>>>>>>>>>>>>> or >>>>>>>>>>>>>>>>>>>>>>>>>>>> bbr. >>>>>>>>>>>>>>>>>>>>>>>>>>>> (BTW, >>>>>>>>>>>>>>>>>>>>>>>>>>>> which >>>>>>>>>>>>>>>>>>>>>>>>>>>> flag will call B0 fieldmaps (or phase and >>>>>>>>>>>>>>>>>>>>>>>>>>>> magnitude >>>>>>>>>>>>>>>>>>>>>>>>>>>> images) >>>>>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>>>>> distortion correction? Do the fieldmap images >>>>>>>>>>>>>>>>>>>>>>>>>>>> need >>>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>>> be >>>>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>> same >>>>>>>>>>>>>>>>>>>>>>>>>>>> matrix size and resolution as DWI? ) >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 3. I wonder why these suboptimal segmented >>>>>>>>>>>>>>>>>>>>>>>>>>>> tracts >>>>>>>>>>>>>>>>>>>>>>>>>>>> are >>>>>>>>>>>>>>>>>>>>>>>>>>>> not >>>>>>>>>>>>>>>>>>>>>>>>>>>> terribly >>>>>>>>>>>>>>>>>>>>>>>>>>>> off the white matter paths but just fewer >>>>>>>>>>>>>>>>>>>>>>>>>>>> voxels? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Would >>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>> probabilistic tractography implemented in FSL be >>>>>>>>>>>>>>>>>>>>>>>>>>>> good >>>>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>>>> working >>>>>>>>>>>>>>>>>>>>>>>>>>>> around this problem by lowering the threshold >>>>>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>>>>> tract >>>>>>>>>>>>>>>>>>>>>>>>>>>> segmentation? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Ping >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 22, 2011 at 1:18 PM, Anastasia >>>>>>>>>>>>>>>>>>>>>>>>>>>> Yendiki >>>>>>>>>>>>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Ping - There are 2 possibilities: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1. You can try to fiddle with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> initialization >>>>>>>>>>>>>>>>>>>>>>>>>>>>> points >>>>>>>>>>>>>>>>>>>>>>>>>>>>> yourself >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> make >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sure they're well in the CST. The point >>>>>>>>>>>>>>>>>>>>>>>>>>>>> coordinates >>>>>>>>>>>>>>>>>>>>>>>>>>>>> are >>>>>>>>>>>>>>>>>>>>>>>>>>>>> saved >>>>>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> text >>>>>>>>>>>>>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>>>>>>>>>>>>> - look at the --init argument of the dmri_paths >>>>>>>>>>>>>>>>>>>>>>>>>>>>> command >>>>>>>>>>>>>>>>>>>>>>>>>>>>> line, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> which >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>>>> find in trac-all.log. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2. You can let trac-all select a different >>>>>>>>>>>>>>>>>>>>>>>>>>>>> initialization >>>>>>>>>>>>>>>>>>>>>>>>>>>>> by >>>>>>>>>>>>>>>>>>>>>>>>>>>>> adding >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "set >>>>>>>>>>>>>>>>>>>>>>>>>>>>> reinit = 1" to your dmrirc file, then running >>>>>>>>>>>>>>>>>>>>>>>>>>>>> trac-all >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -prior >>>>>>>>>>>>>>>>>>>>>>>>>>>>> again. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Once you change the initialization by doing >>>>>>>>>>>>>>>>>>>>>>>>>>>>> either >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> or >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>>>>>>>>>>>>>> need >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to run trac-all -path to reconstruct this path >>>>>>>>>>>>>>>>>>>>>>>>>>>>> again. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> You can change the pathlist in dmrirc to do >>>>>>>>>>>>>>>>>>>>>>>>>>>>> only >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> path >>>>>>>>>>>>>>>>>>>>>>>>>>>>> that >>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> We jump through various hoops to make sure this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sort >>>>>>>>>>>>>>>>>>>>>>>>>>>>> of >>>>>>>>>>>>>>>>>>>>>>>>>>>>> thing >>>>>>>>>>>>>>>>>>>>>>>>>>>>> doesn't >>>>>>>>>>>>>>>>>>>>>>>>>>>>> happen >>>>>>>>>>>>>>>>>>>>>>>>>>>>> but in a few cases it can't be prevented, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> unfortunately. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know if this has helped or if you have >>>>>>>>>>>>>>>>>>>>>>>>>>>>> any >>>>>>>>>>>>>>>>>>>>>>>>>>>>> other >>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions! >>>>>>>>>>>>>>>>>>>>>>>>>>>>> a.y >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, 22 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Anastasia, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The both ends were not terribly off of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> white >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> matter, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> though >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lower end was a bit off at the level of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> decussation. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suggestion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fixing this? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ping >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Sep 22, 2011 at 12:51 PM, Anastasia >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Yendiki >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Ping - It looks like the path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> initialization >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> may >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> algorithm needs an initial guess for the path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> iterates >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial guess is chosen based on the tracts >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> atlas >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> subject >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is not perfectly aligned with the atlas this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> guess >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> going off the white matter for example. Does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blue >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> snapshot >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> look like it may not coincide well with you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> subject's >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CST, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> going >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> off >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> white matter close to the end, etc? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a.y >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, 22 Sep 2011, Ping-Hong Yeh wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hello, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The segmented left CST tracts of one of our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3T >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> satisfactory, which has only few voxels with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> gray >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> values >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (see >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> attached snapshot pictures for "trac-all" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "cst_prob"). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> manually tracking using deterministic >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tractography >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> seems >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> OK >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (see >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cst_stremline). Any suggestions on which >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> step >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> may >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrong >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> trac-all? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ping >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>> >
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_______________________________________________ Freesurfer mailing list [email protected] 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.
