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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>>>>
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