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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