Hi Bruce,
I only put them in because it was not working without them and that
was the solution in the previous discussion.
To summarize: Once I put in -p 0.7, mri_segment misinterprets 0.7 as
the input file name, no matter whether I use -i or not.
Caspar
2013/5/17 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
> 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
>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>> Freesurfer mailing list
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>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe
>>>>>>>>>>>>>>>>>>> r
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
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