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