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. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>> >>
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. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>> >
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. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>> >> > >
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. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>> >>> >> >> >
Glad things are moving in the right direction. Now it looks like maybe one of the control points of the path is not moving around, which is why you get that very bright thin spot in the distribution. I can't tell by looking at that one slice of the mask only, but could it be that there voxels missing from the mask around there? If so you could fill them in and try again. You can also overlay the path.pd on the FA map and check if that part is off the white matter or on its edge.
On Wed, 19 Oct 2011, Ping-Hong Yeh wrote:
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. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>> >>>> >>> >>> >> > >
Hi Anastasia,
I am still struggling and not convinced that brain mask is the sole reason causing the problems. Attached are another data before and after fixing brain masks (brainmasks.png) ,which has holes in the fronto-parietal regions in the first recon-all attempt (red-yellow) and after inhomogeneity correction (gray-scale). However, both of them have poor results of forceps major (blue ones are first and the reds are the second attempt), where the brain masks look fine.
Thanks. Ping
On Wed, Oct 19, 2011 at 4:58 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Glad things are moving in the right direction. Now it looks like maybe one of the control points of the path is not moving around, which is why you get that very bright thin spot in the distribution. I can't tell by looking at that one slice of the mask only, but could it be that there voxels missing from the mask around there? If so you could fill them in and try again. You can also overlay the path.pd on the FA map and check if that part is off the white matter or on its edge.
On Wed, 19 Oct 2011, Ping-Hong Yeh wrote:
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. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>> >>>>> >>>> >>>> >>> >> >> >
Hi Ping - Thanks for the images. It looks like the initial path for forceps major (which is chosen from the atlas) is not well-aligned with your subject's forceps major (it's almost going into CSF). This could mean that the registration between your subject and the atlas (MNI) is less than perfect. If the registration is ok, then you can try the reinit trick that I've mentioned in an earlier email to pick another initial path.
Hope this helps, a.y
On Fri, 21 Oct 2011, Ping-Hong Yeh wrote:
Hi Anastasia,
I am still struggling and not convinced that brain mask is the sole reason causing the problems. Attached are another data before and after fixing brain masks (brainmasks.png) ,which has holes in the fronto-parietal regions in the first recon-all attempt (red-yellow) and after inhomogeneity correction (gray-scale). However, both of them have poor results of forceps major (blue ones are first and the reds are the second attempt), where the brain masks look fine.
Thanks. Ping
On Wed, Oct 19, 2011 at 4:58 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Glad things are moving in the right direction. Now it looks like maybe one of the control points of the path is not moving around, which is why you get that very bright thin spot in the distribution. I can't tell by looking at that one slice of the mask only, but could it be that there voxels missing from the mask around there? If so you could fill them in and try again. You can also overlay the path.pd on the FA map and check if that part is off the white matter or on its edge.
On Wed, 19 Oct 2011, Ping-Hong Yeh wrote:
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. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >> > >
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Ping-Hong Yeh