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