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