I looked at their orientation differences using mri_info and used this command;
mri_convert --in_orientation LIA --out_orientation AIL native.template.mgh
native.corrected.nii
But still there is an alignment problem. Looks like the xform info differs so
can I use the mri_mask command with specifying the xform option?
This info is for the mask volume I want to use;
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = 3.2153
: x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = -10.8083
: x_s = -0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -8.7367
talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 -0.0000 131.2153
0.0000 -0.0000 1.0000 -138.8083
-0.0000 -1.0000 0.0000 119.2633
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 -0.0000 0.0000 131.2153
0.0000 0.0000 -1.0000 119.2633
0.0000 1.0000 -0.0000 138.8084
-0.0000 -0.0000 -0.0000 1.0000
This information is of the volume file I want to overlay the mask on;
Volume information for MW_IIHC_aTAL.nii
type: nii
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -0.0553, y_r = 0.0101, z_r = -0.9984, c_r = -3.7597
: x_a = 0.9863, y_a = 0.1563, z_a = -0.0530, c_a = 11.9244
: x_s = 0.1555, y_s = -0.9877, z_s = -0.0186, c_s = -9.5782
Orientation : AIL
Primary Slice Direction: sagittal
voxel to ras transform:
-0.0553 0.0101 -0.9984 129.8205
0.9863 0.1563 -0.0530 -127.5422
0.1555 -0.9877 -0.0186 99.3136
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform:
-0.0553 0.9863 0.1555 117.5212
0.0101 0.1563 -0.9877 116.7140
-0.9984 -0.0530 -0.0186 124.7003
0.0000 0.0000 0.0000 1.0000
Best,
Idil
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19
[yozdemi...@amherst.edu]
Sent: Thursday, August 17, 2017 7:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mask alignment problem/mri_mask
Yes; sorry. The mask is created by an applied docker image which produced
volume and surface files of the template in both the brain's native and
freesurfer origin orientation. MW_IIHC_aTAL.nii is the brain file of the same
subject I exported from another software-I am hoping to export the template
eventually to use in there-. native.template.mgh is the template file produced
by the docker; it is the red/orange areas in the picture I sent.
native.orientation.mgh is just a random name I gave to the output file.
Best,
Idil
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 17, 2017 7:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mask alignment problem/mri_mask
Hi Idil
you need to give us much more information to be able to help you. How did
you create the mask? Why volume to you expect it to be in register with?
What are the volumes MW_IIHC_aTAL.nii native.template.mgh and
native.orientation.mgh ?
Bruce
On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
> It seems to be in the right orientation now but there is still an alignment
> problem; the mask is too far off from the brain. Sorry to be constantly
> asking questions; but do you have any suggestions onto how to fix this?
>
> Best,
> Idil
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, August 17, 2017 6:55 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>
> if you want to reslice the mask to be like a template volume, use "-rl"
> instead of "-at"
>
> cheers
> Bruce
> On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
>
>> I do not have a transform file I can use so I was wondering if I can simply
>> use the volume file I am trying to adapt the mask to as the transform file
>> in the -at option. But looks like I cannot;
>>
>> mri_convert -at MW_IIHC_aTAL.nii native.template.mgh native.orientation.mgh
>> mri_convert.bin -at MW_IIHC_aTAL.nii native.template_.mgh
>> native.orientation.mgh
>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>> reading from native.template.mgh...
>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, -9.31323e-10)
>> j_ras = (0, -1.49012e-08, -1)
>> k_ras = (-1.62981e-09, 1, 1.49012e-08)
>> INFO: Reading transformation from file MW_IIHC_aTAL.nii...
>> Reading transform with LTAreadEx()
>> INFO: This REGISTER_DAT transform is valid only for volumes between COR
>> types with c_(r,a,s) = 0.
>> regio_read_register(): No such file or directory
>> Error reading inplaneres from MW_IIHC_aTAL.nii
>> ltaReadRegisterDat: could not read MW_IIHC_aTAL.nii
>> No such file or directory
>> ERROR: Reading transform from file MW_IIHC_aTAL.nii
>>
>> ________________________________________
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, August 17, 2017 6:50 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>>
>> sorry, I don't understand
>> Bruce
>> On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
>>
>>> Thank you!
>>>
>>> Then I guess I would use the volume as the transform file to convert my
>>> mask.
>>>
>>> Best,
>>> Idil
>>> ________________________________________
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, August 17, 2017 6:41 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>>>
>>> ok, but your mri_mask command line has the string "%s" in it, which is
>>> not correct. You need to specify an actual file name. I also think you
>>> are better off using mri_convert -at <transform file name> .... to map
>>> the mask into the right coordinate system so that you can then view it in
>>> freeview to make sure it is correct
>>>
>>> cheers
>>> Bruce
>>> On Thu, 17 Aug 2017, Yagmur Ozdemir 19
>>> wrote:
>>>
>>>> The mask in volume format was created using a docker image and it works
>>>> well both with my freesurfer origin and native volume files; the one that
>>>> it doesn't align with is the volume file I am trying to adapt to/from a
>>>> different software. The command line I used for transforming is this;
>>>>
>>>> mri_vol2vol --mov native.template_areas.mgh --targ MW_IIHC_aTAL.nii
>>>> --regheader --o template.mgz --no-save-reg
>>>>
>>>> Best,
>>>> Idil
>>>>
>>>> ________________________________________
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>>> [fis...@nmr.mgh.harvard.edu]
>>>> Sent: Thursday, August 17, 2017 6:14 PM
>>>> To: Freesurfer support list
>>>> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>>>>
>>>> Hi Idil
>>>>
>>>> how did you create the mask and the transform? Also, you can't specify "%s"
>>>> on the command line - you need an actual name of a transform file.
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, 17 Aug 2017, Yagmur Ozdemir
>>>> 19 wrote:
>>>>
>>>>> Hello freesurfer experts,
>>>>>
>>>>> A volume file I want to save as a mask(the orange/red shaded areas in the
>>>>> picture) on top of my volume file does not align as seen in the picture. I
>>>>> have used mri_vol2vol to align the mask to my native volume but apparently
>>>>> it did not work out. I am trying to correct this by using mri_mask now; I
>>>>> tried to use the option -xform %s which apparently applies the LTA
>>>>> transform
>>>>> to align mask to input volume, but now I get this error;
>>>>>
>>>>>>> lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects/sub-01_MW/mri$
>>>>> mri_mask -xform %s MW_IIHC_aTAL.nii native.areas_MW_aTAL.nii
>>>>> MW_aTAl_masked.nii
>>>>> transform file name is %s
>>>>> WARNING: hdr.dim[4] = 0 (nframes), setting to 1
>>>>> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
>>>>> DoAbs = 0
>>>>> Apply the given LTA xfrom to the mask volume
>>>>> Reading transform ...
>>>>> ltaReadFile(%s): can't open file
>>>>> No such file or directory
>>>>> mri_mask.bin: could not read transform file %s
>>>>> No such file or directory
>>>>>
>>>>>
>>>>> I would deeply appreciate if someone could help me sort out this mess.
>>>>>
>>>>> Thank you all!
>>>>> Best,
>>>>> Idil
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
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