Hey
I wrote out to .w since I couldn't write to curv. (And I'm old fashioned!)
But actually it's because I am really behind the times and forgot that .mgh was
also used for surface data. And yup, this worked fine.
So in answer to my question 'Bug or stupidity' - the latter!
Thanks Doug,
Fred
On 15 Apr 2013, at 17:58, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote:
> Hi Fred, why do you want to save it as a wfile? We're trying to phase wfiles
> out. Can you use mgh format?
> doug
>
>
> On 4/15/13 12:56 PM, Fred Dick wrote:
>> Hey again
>>
>> sorry, I seem not to be able to accomplish this very simple thing!
>>
>> First wrote out mask as .w file using vol2surf, but mri_cor2label couldn't
>> read ('mri_read(): couldn't determine type of file ./rh.R2MaskBrain.w').
>>
>> Then tried writing out as curv using the following command:
>>
>> mri_vol2surf --mov R2MaskBrain.nii.gz --reg register.dat --hemi $hemi
>> --interp nearest --o ./$hemi.R2MaskBrain --out_type curv --projfrac 0.5
>>
>> and got this error,
>>
>> ################
>> Writing to ./lh.R2MaskBrain
>> Dim: 152308 1 1
>> MRIwriteType(): code inconsistency (file type recognized but not caught)
>> ERROR: saving ./lh.R2MaskBrain
>> #####################
>>
>> Bug, or user stupidity???
>>
>> cheers,
>> Fred
>>
>>
>> On 14 Apr 2013, at 22:56, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Oh, the label should be a surface label. mri_cor2label creates a volume
>>> label (basically it just means that each label point corresponds to a 1mm3
>>> cube instead of a verex -- the vertex numbers should all be -1). Try
>>> running vol2surf on the mask (using nearest interp) to create a surface
>>> mask. Then create a surface label with mri_cor2label using the --surf
>>> option.
>>> doug
>>>
>>>
>>>
>>>
>>> On 4/14/13 5:01 PM, Fred Dick wrote:
>>>> Hi Doug
>>>>
>>>> I've actually tried both inclusive and exclusive and have failed - just
>>>> checked again in tkmedit that the label was coming up correctly and it
>>>> was.
>>>>
>>>> Just to double-check - the label should be in the space of the --mov,
>>>> right?
>>>>
>>>> Thanks!
>>>>
>>>> Fred
>>>>
>>>>
>>>>
>>>> Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try
>>>> inverting you mask.
>>>> doug
>>>> On 4/14/13 4:31 PM, Fred Dick wrote:
>>>> Dear all
>>>>
>>>> I am painting some higher-res anatomical data from a volume to a surface,
>>>> and want to use a mask that excludes the vessels. (The same data but 1x1x1
>>>> conformed were used to create the surface).
>>>> I've created a binary label in the same space
>>>>
>>>> >> mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
>>>>
>>>> made sure that it looks ok when I read in hi-res to tkmedit and display
>>>> label,
>>>> then ran mri_vol2surf
>>>>
>>>> >> mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii
>>>> >> --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp
>>>> >> trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w
>>>> And got the output (pasted below), showing that the output is all zero.
>>>>
>>>> Output is fine without label, or with -cortex.
>>>>
>>>> I've also tried this with a conformed version of the label (also verified
>>>> in tkmedit) and have had the same thing. (I thought maybe it was applying
>>>> it to orig vol, which I admit would be strange).(I noticed someone had a
>>>> similar issue a couple of years ago, but it involved a surface rather than
>>>> volume label, and looked like it had been resolved).
>>>> Am running current stable version on Mountain Lion.
>>>>
>>>> Thanks for any pointers,
>>>>
>>>> best,
>>>> Fred
>>>>
>>>> ##########################################################
>>>> masking output with label R2s.label
>>>> INFO: output format is paint
>>>> srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii
>>>> srcreg = register.dat
>>>> srcregold = 0
>>>> srcwarp unspecified
>>>> surf = white
>>>> hemi = lh
>>>> ProjFrac = 0.5
>>>> thickness = thickness
>>>> reshape = 0
>>>> interp = trilinear
>>>> float2int = round
>>>> GetProjMax = 0
>>>> INFO: float2int code = 0
>>>> Done loading volume
>>>> Loading label R2s.label
>>>> Reading surface
>>>> /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white
>>>> Done reading source surface
>>>> Reading thickness
>>>> /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness
>>>> Done
>>>> Mapping Source Volume onto Source Subject Surface
>>>> 1 0.5 0.5 0.5
>>>> using old
>>>> Done mapping volume to surface
>>>> Number of source voxels hit = 108676
>>>> Surface smoothing by fwhm = 4 (n=10)
>>>> Masking with R2s.label
>>>> Warning: all vertex values are zero
>>>>
>>>>
>>>>
>>>
>>>
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