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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