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/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>>> The information in this e-mail is intended only for the >>>>>>>>> person >>>>>>>>> to >>>>>>>>> whom >>>>>>>>> it >>>>>>>>> is >>>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>>> error >>>>>>>>> and the >>>>>>>>> e-mail >>>>>>>>> contains patient information, please contact the Partners >>>>>>>>> Compliance >>>>>>>>> HelpLine at >>>>>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>>>>> sent >>>>>>>>> to you >>>>>>>>> in >>>>>>>>> error >>>>>>>>> but does not contain patient information, please contact the >>>>>>>>> sender >>>>>>>>> and >>>>>>>>> properly >>>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> > >