Try leaving out the -i and -seg
Those are mandatory parameters and don't need hyphens
On May 17, 2013, at 3:11 PM, "Caspar M. Schwiedrzik"
<cschwie...@mail.rockefeller.edu> wrote:
> 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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