Hi! I am trying to work around this now using more control points. However, I was wondering whether the fixed version of mri_segment for v4.5 that accepts the -p parameter is still available? Just in case I need to use a different threshold at some point. Thanks, Caspar
2013/5/17 Caspar M. Schwiedrzik cschwiedrz@rockefeller.edu:
Hi Bruce, I only put them in because it was not working without them and that was the solution in the previous discussion. To summarize: Once I put in -p 0.7, mri_segment misinterprets 0.7 as the input file name, no matter whether I use -i or not. Caspar
2013/5/17 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Try leaving out the -i and -seg Those are mandatory parameters and don't need hyphens
On May 17, 2013, at 3:11 PM, "Caspar M. Schwiedrzik" cschwiedrz@mail.rockefeller.edu wrote:
Hi Matt and Bruce, still the same problem. What about the fix that was mentioned in the earlier discussion? Was that not for version 4.5? Caspar
2013/5/17 Matt Glasser matt@ma-tea.com:
Your line continuation isn't working for some reason? Type the command line all on one line and see if that fixes the problem.
Matt.
On 5/17/13 1:37 PM, "Caspar M. Schwiedrzik" cschwiedrz@mail.rockefeller.edu wrote:
set threshold = `echo "7/10" | bc -l` set segment_options = "-v -fillv -fillbg -wlo 104 -ghi 118 -whi 140 -n 4 -p $threshold -keep"
mri_segment ${segment_options} \ -i brain.mgz -seg wm.mgz
filling ventricles filling basal ganglia using white lolim = 104.0 using gray hilim = 118.0 using white hilim = 140.0 running border classification 4 times preserving editing changes in output volume... using 70% threshold mri_read(): couldn't determine type of file mri_segment: could not read source volume from .7000000000000000000 -i: Command not found
2013/5/17 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Caspar
can you include the command line and all the output?
Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
> filling ventricles > filling basal ganglia > using white lolim = 104.0 > using gray hilim = 118.0 > using white hilim = 140.0 > running border classification 4 times > preserving editing changes in output volume... > using 70% threshold > mri_read(): couldn't determine type of file /.../.7000000000000000000 > mri_segment: could not read source volume from .7000000000000000000 > ../mri/brain.mgz: Permission denied > > if I add a -i to the input volume, it says flag not recognized. > to get a floating point number into my tcsh script, I am using `echo > "7/10" | bc -l` > > according to this previous discussion on the mailing list, there > should be a fix available somewhere: > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html > > Thanks, Caspar > > 2013/5/17 Bruce Fischl fischl@nmr.mgh.harvard.edu: >> >> and what happens? Can you send the full screen output? >> >> On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: >> >>> mri_segment \ >>> -v \ >>> -fillv \ >>> -fillbg \ >>> -wlo 104 \ >>> -ghi 118 \ >>> -whi 140 \ >>> -n 4 \ >>> -keep \ >>> brain.mgz wm.mgz >>> >>> The pial surface in the rest of the brain is ok, it is only the >>> orbitofrontal/piriform cortex that is problematic. I now wanted to >>> add >>> -p 0.7. >>> >>> Caspar >>> >>> >>> 2013/5/17 Bruce Fischl fischl@nmr.mgh.harvard.edu: >>>> >>>> >>>> what is your command line? You are probably better off setting >>>> gray_hi, >>>> gray_low, wm_hi, wm_low, etc... >>>> >>>> Bruce >>>> On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: >>>> >>>>> When I try to specify a different threshold using -p, mri_segment >>>>> reads in the threshold as the input volume. >>>>> I tried specifying the input with -i (as explained here: >>>>> >>>>> >>>>> >>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826. >>>>> html), >>>>> but now it does not recognize the -i flag. >>>>> Caspar >>>>> >>>>> >>>>> 2013/5/17 Matt Glasser matt@ma-tea.com: >>>>>> >>>>>> >>>>>> >>>>>> Hard to fix if that is the receive field and you don't have >>>>>> another >>>>>> image >>>>>> like a T2w to remove it with. Perhaps mri_normalize can be tuned >>>>>> to >>>>>> improve this with expert options as the white matter that is being >>>>>> correctly segmented appears to be darker as well. >>>>>> >>>>>> Peace, >>>>>> >>>>>> Matt. >>>>>> >>>>>> On 5/17/13 9:30 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu >>>>>> wrote: >>>>>> >>>>>>> Hi Caspar >>>>>>> >>>>>>> yes, that might help. There are expert opts for this. Sorry, I >>>>>>> have >>>>>>> almost no experience analyzing monkey brains at .5mm, so I'm >>>>>>> really >>>>>>> not >>>>>>> sure what to advise you. Perhaps one of the other people on list >>>>>>> who >>>>>>> have >>>>>>> done a bunch can comment? >>>>>>> Bruce >>>>>>> On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: >>>>>>> >>>>>>>> Hi Bruce, >>>>>>>> I tried adding control points in the white matter in that >>>>>>>> region, >>>>>>>> however, it does not seem to fix the issue. Also, the >>>>>>>> brainmask.mgz >>>>>>>> does not seem to exclude this part of the brain, so that is not >>>>>>>> the >>>>>>>> problem either. >>>>>>>> I am attaching another screenshot (horizontal 119) to illustrate >>>>>>>> the >>>>>>>> problem. >>>>>>>> White matter pixel values range from the high 80ies to >100 in >>>>>>>> this >>>>>>>> area. >>>>>>>> Included grey matter pixel values are in the low 80ies. >>>>>>>> Excluded grey matter pixel values range from the low 60ies to >>>>>>>> low >>>>>>>> 70ies. >>>>>>>> >>>>>>>> Would it make sense to re-run mri_segment with a different >>>>>>>> threshold? >>>>>>>> Thanks, Caspar >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 2013/5/16 Bruce Fischl fischl@nmr.mgh.harvard.edu: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Hi Caspar >>>>>>>>> >>>>>>>>> is the closest white matter captured by the white surface? >>>>>>>>> What is >>>>>>>>> the >>>>>>>>> intensity of voxels there? If < 110 you could try putting >>>>>>>>> control >>>>>>>>> points in >>>>>>>>> them and seeing if that helps (that is, in the closest voxels >>>>>>>>> that >>>>>>>>> are >>>>>>>>> entirely white matter). >>>>>>>>> >>>>>>>>> >>>>>>>>> Bruce >>>>>>>>> >>>>>>>>> On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: >>>>>>>>> >>>>>>>>>> Hi Bruce, >>>>>>>>>> ok. >>>>>>>>>> But in theory, what would you recommend to get around the >>>>>>>>>> darkening >>>>>>>>>> issue? Unfortunately, I do not have a field map available for >>>>>>>>>> this >>>>>>>>>> data set. >>>>>>>>>> Or should I not expect to get a pial surface in this area >>>>>>>>>> since >>>>>>>>>> the >>>>>>>>>> white matter is not discernable? >>>>>>>>>> There are five slices without clear white matter (original >>>>>>>>>> voxel >>>>>>>>>> size >>>>>>>>>> 0.5x0.5x0.5 mm). >>>>>>>>>> Thanks, Caspar >>>>>>>>>> >>>>>>>>>> 2013/5/16 Bruce Fischl fischl@nmr.mgh.harvard.edu: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hi Caspar >>>>>>>>>>> >>>>>>>>>>> if it's primate I don't think I'm going to be able to help - >>>>>>>>>>> you'll >>>>>>>>>>> need >>>>>>>>>>> someone more familiar with primate anatomy >>>>>>>>>>> >>>>>>>>>>> sorry >>>>>>>>>>> Bruce >>>>>>>>>>> On Thu, 16 May 2013, Caspar M. >>>>>>>>>>> Schwiedrzik wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Bruce and Matt, >>>>>>>>>>>> yes, it is primate data. I just dropped an archive on your >>>>>>>>>>>> FTP >>>>>>>>>>>> server >>>>>>>>>>>> in transfer/incoming. >>>>>>>>>>>> Thanks! >>>>>>>>>>>> Caspar >>>>>>>>>>>> >>>>>>>>>>>> 2013/5/16 Matt Glasser matt@ma-tea.com: >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Is the brain extraction removing that part of the brain? >>>>>>>>>>>>> Do >>>>>>>>>>>>> you >>>>>>>>>>>>> know >>>>>>>>>>>>> where the OFC ends and olfactory bulb begins? >>>>>>>>>>>>> >>>>>>>>>>>>> Peace, >>>>>>>>>>>>> >>>>>>>>>>>>> Matt. >>>>>>>>>>>>> >>>>>>>>>>>>> On 5/16/13 11:43 AM, "Caspar M. Schwiedrzik" >>>>>>>>>>>>> cschwiedrz@mail.rockefeller.edu wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi! >>>>>>>>>>>>>> I am failing to get a proper pial surface in orbitofrontal >>>>>>>>>>>>>> cortex. >>>>>>>>>>>>>> See attached screenshot. >>>>>>>>>>>>>> This is NHP data, processed with version 4.5. >>>>>>>>>>>>>> I am not sure how to proceed here, as there is no clear >>>>>>>>>>>>>> with >>>>>>>>>>>>>> matter. >>>>>>>>>>>>>> Any advice would be appreciated. >>>>>>>>>>>>>> Thanks! >>>>>>>>>>>>>> Caspar >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>> >>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe >>>>>>>>>>>>>> r >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> The information in this e-mail is intended only for the >>>>>>>>>>>>>> person >>>>>>>>>>>>>> to >>>>>>>>>>>>>> whom >>>>>>>>>>>>>> it >>>>>>>>>>>>>> is >>>>>>>>>>>>>> addressed. 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