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 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. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>> >> > >