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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