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 <m...@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"
> <cschwie...@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 <fis...@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 <fis...@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 <fis...@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 <m...@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" <fis...@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 <fis...@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 <fis...@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 <m...@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"
>>>>>>>>>>>>>>>> <cschwie...@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
>>>>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>>>>r
>>>>>>>>>>>>>>>>>
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