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 >>>> >>>> >>>> >>>> >>>> >>>> >>> >>