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 ayendiki@nmr.mgh.harvard.edu 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 ayendiki@nmr.mgh.harvard.edu 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 ayendiki@nmr.mgh.harvard.edu 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 ayendiki@nmr.mgh.harvard.edu 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 >> ayendiki@nmr.mgh.harvard.edu 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 >>>> ayendiki@nmr.mgh.harvard.edu 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 >>>>>> ayendiki@nmr.mgh.harvard.edu 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 >>>>>>>> ayendiki@nmr.mgh.harvard.edu 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 >>>>>>>>>> ayendiki@nmr.mgh.harvard.edu 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 >>>>>>>>>>>> ayendiki@nmr.mgh.harvard.edu 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 >>>>>>>>>>>>>> ayendiki@nmr.mgh.harvard.edu 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 >>>>>>>>>>>>>>>> ayendiki@nmr.mgh.harvard.edu 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 >>>>>>>>>>>>>>>>>> ayendiki@nmr.mgh.harvard.edu 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 >>>>>>>>>>>>>>>>>>>> ayendiki@nmr.mgh.harvard.edu 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 >>>>>>>>>>>>>>>>>>>>>> ayendiki@nmr.mgh.harvard.edu 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. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>> >
