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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