On Tue, Nov 29, 2016 at 3:20 PM, miracle ozzoude <miracooloz@gmail.com> wrote:

Hello Doug and Bruce,

I ran the script and it worked however, volumes did not align on freeview. Here's the mri_info for orig.mgz:
Volume information for orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
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 = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -110.0032
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 110.0032
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 91.0000

talairach xfm : /net/synapse/nt/mozzoude/processing/freesurfer/176_001_120223/fsdir3/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal

voxel to ras transform:
-1.0000 0.0000 0.0000 17.9968
0.0000 0.0000 1.0000 -17.9968
0.0000 -1.0000 0.0000 219.0000
0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform:
-1.0000 -0.0000 -0.0000 17.9968
-0.0000 -0.0000 -1.0000 219.0000
-0.0000 1.0000 -0.0000 17.9968
-0.0000 -0.0000 -0.0000 1.0000
Here's the mri_info for brainmask.mgz after including -rl orig.mgz
Volume information for brainmask.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
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 = -110.0032
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 110.0032
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 91.0000

talairach xfm : /net/synapse/nt/mozzoude/processing/freesurfer/176_001_120223/fsdir3/mri/transforms/talairach.xfm
Orientation : LAS
Primary Slice Direction: axial

voxel to ras transform:
-1.0000 0.0000 0.0000 17.9968
0.0000 1.0000 0.0000 -17.9968
0.0000 0.0000 1.0000 -37.0000
0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform:
-1.0000 -0.0000 -0.0000 17.9968
-0.0000 1.0000 -0.0000 17.9968
-0.0000 -0.0000 1.0000 37.0000
-0.0000 -0.0000 -0.0000 1.0000

I have attached the orig.mgz, brainmask.mgz (my stripped volume from lesion explorer that i converted to mgz) and the HfBd.img/hdr (stripped volume in analyze format which I used to convert to mgz). Please can you inspect to see why both images (orig.mgz and brainmask.mgz) do not align.

THANK YOU VERY MUCH
Paul

On Tue, Nov 29, 2016 at 1:58 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
yes, though you should not need to spec the output orientation
(redundant) or the in_type (it can figure that out)

On 11/29/2016 01:46 PM, miracle ozzoude wrote:
> Thanks bruce and doug. The orientation is wrong hence, why I am using
> the orientation string. But, the above script is correct?
>
> On Tue, Nov 29, 2016 at 1:39 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> don't use the orientation strings unless the orientation is wrong
>
>
> On 11/29/2016 01:38 PM, Bruce Fischl wrote:
> > you may not need the out_orientation, but perhaps someone else
> knows?
> > On Tue, 29 Nov 2016, miracle ozzoude wrote:
> >
> >> Hello Bruce,
> >> I wanted to confirm if this is the right script when converting
> from
> >> one format to another using mri_convert (if i want to use
> >> orig.mgz as template volume):
> >> mri_convert --in_type analyze --in_orientation LAS -rl orig.mgz
> >> --out_type mgz --out_orientation LAS brainmask.img brainmask.mgz
> >> Thanks,
> >> Paul
> >>
> >> On Mon, Nov 28, 2016 at 7:15 PM, <miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>> wrote:
> >> Awesome. Thank you very much Bruce.
> >>
> >> Sent from my BlackBerry 10 smartphone.
> >> Original Message
> >> From: Bruce Fischl
> >> Sent: Monday, November 28, 2016 5:14 PM
> >> To: Freesurfer support list
> >> Reply To: Freesurfer support list
> >> Subject: Re: [Freesurfer] recon-all -autorecon2 error.
> >>
> >> -rl is for "reslice like" and you include it in the
> mri_convert
> >> command
> >> line with orig.mgz as the template volume. Run mri_convert
> >> --help and it
> >> should be clear
> >>
> >> Bruce
> >>
> >>
> >> On Mon, 28
> >> Nov 2016, miracooloz@gmail.com

> <mailto:miracooloz@gmail.com> wrote:
> >>
> >> > Thanks a lot Bruce. What do you mean by -rl and how do I
> >> incorporate it to mri_convert?
> >> > Best,
> >> > Paul
> >> >
> >> > Sent from my BlackBerry 10 smartphone.
> >> > Original Message
> >> > From: Bruce Fischl
> >> > Sent: Monday, November 28, 2016 4:57 PM
> >> > To: Freesurfer support list
> >> > Reply To: Freesurfer support list
> >> > Subject: Re: [Freesurfer] recon-all -autorecon2 error.
> >> >
> >> > I think this is your problem - the brainmask is not in the
> >> same voxel
> >> > coords as the other volumes. YOu probably need to -rl
> >> orig.mgz in your
> >> > conversion, then make sure that the volumes look aligned in
> >> freeview (and
> >> > that mri_info gives the same ras2vox and such for them)
> >> > On Mon, 28 Nov 2016,
> >> > miracle ozzoude wrote:
> >> >
> >> >> Oh. Thanks bruce. For mri_info for my orig.mgz is
> >> >> Volume information for orig.mgz
> >> >> type: MGH
> >> >> dimensions: 256 x 256 x 256
> >> >> voxel sizes: 1.000000, 1.000000, 1.000000
> >> >> type: UCHAR (0)
> >> >> 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 = -1.0000, y_r = 0.0000, z_r =
> >> 0.0000, c_r = -110.0032
> >> >> : x_a = 0.0000, y_a = 0.0000, z_a =
> >> 1.0000, c_a = 110.0032
> >> >> : x_s = 0.0000, y_s = -1.0000, z_s =
> >> 0.0000, c_s = 91.0000
> >> >>
> >> >> talairach xfm
> >>
> :/net/synapse/nt/mozzoude/processing/freesurfer/176_001_120223/fsdir1/mri/transforms/tala
> >> >> irach.xfm
> >> >> Orientation : LIA
> >> >> Primary Slice Direction: coronal
> >> >>
> >> >> voxel to ras transform:
> >> >> -1.0000 0.0000 0.0000 17.9968
> >> >> 0.0000 0.0000 1.0000 -17.9968
> >> >> 0.0000 -1.0000 0.0000 219.0000
> >> >> 0.0000 0.0000 0.0000 1.0000
> >> >>
> >> >> voxel-to-ras determinant -1
> >> >>
> >> >> ras to voxel transform:
> >> >> -1.0000 -0.0000 -0.0000 17.9968
> >> >> -0.0000 -0.0000 -1.0000 219.0000
> >> >> -0.0000 1.0000 -0.0000 17.9968
> >> >> -0.0000 -0.0000 -0.0000 1.0000
> >> >>
> >> >> Here's the mri_info for my new brainmask.mgz:
> >> >> Volume information for brainmask.mgz
> >> >> type: MGH
> >> >> dimensions: 256 x 256 x 182
> >> >> voxel sizes: 0.859400, 0.859400, 1.000000
> >> >> type: UCHAR (0)
> >> >> fov: 220.006
> >> >> dof: 0
> >> >> xstart: -110.0, xend: 110.0
> >> >> ystart: -110.0, yend: 110.0
> >> >> zstart: -91.0, zend: 91.0
> >> >> 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 = 0.0000
> >> >> : x_a = 0.0000, y_a = 1.0000, z_a =
> >> 0.0000, c_a = 0.0000
> >> >> : x_s = 0.0000, y_s = 0.0000, z_s =
> >> 1.0000, c_s = 0.0000
> >> >>
> >> >> talairach xfm :
> >> >> Orientation : LAS
> >> >> Primary Slice Direction: axial
> >> >>
> >> >> voxel to ras transform:
> >> >> -0.8594 0.0000 0.0000 110.0032
> >> >> 0.0000 0.8594 0.0000 -110.0032
> >> >> 0.0000 0.0000 1.0000 -91.0000
> >> >> 0.0000 0.0000 0.0000 1.0000
> >> >>
> >> >> voxel-to-ras determinant -0.738568
> >> >>
> >> >> ras to voxel transform:
> >> >> -1.1636 -0.0000 -0.0000 128.0000
> >> >> -0.0000 1.1636 -0.0000 128.0000
> >> >> -0.0000 -0.0000 1.0000 91.0000
> >> >> -0.0000 -0.0000 -0.0000 1.0000
> >> >>
> >> >>
> >> >> On Mon, Nov 28, 2016 at 4:29 PM, Bruce Fischl
> >> <fischl@nmr.mgh.harvard.edu

> <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
> >> >> Hi Paul
> >> >>
> >> >> if you run mri_info on the orig.mgz and your new
> >> brainmask.mgz they should
> >> >> give you the same thing in terms of ras2vox and such
> >> >> cheers
> >> >> Bruce
> >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote:
> >> >>
> >> >> This was the info from mri_convert when i converted
> my skull
> >> >> stripped volume to mgz
> >> >> before replacing it with the brainmask from FS
> >> >> mri_convert --in_type analyze --in_orientation LAS
> >> --out_type mgz
> >> >> --out_orientation LAS
> >> >> brainmask.img brainmask.mgz
> >> >> cp foldername/subjid/brainmask.mgz
> >> >> foldername/subjd/mri/brainmask.mgz
> >> >>
> >> >> INFO: could not find ...mat file for direction cosine
> >> infoINFO:
> >> >> use ANALYZE 7.5 hdr ->
> >> >> hist.orient value: 0, transverse unflipped (default
> >> >> INFO : if not valid, please provide the information
> .......
> >> .mat
> >> >> file
> >> >> analyzeRead() roi_scale 0.00000000
> >> >> TR= 1000.00, TE = 0.00, TI = 0.00, flip angle = 0.00
> >> >> setting input orientation to LAS
> >> >> i_ras = (-1, 0, 0)
> >> >> j_ras = (0,1,0)
> >> >> k_ras = (0,0,1)
> >> >> setting output orientation to LAS
> >> >> writing to brainmask.mgz
> >> >>
> >> >> why do i need the orig.mgz? I thought I only had to
> replace the
> >> >> brainmask.mgz (from FS)
> >> >> with mine brainmask,mgz( from lesion explorer after i have
> >> >> renamed it to brainmask.mgz).
> >> >> Also, I didn't use the "noskullstrip" flag like you
> suggested.
> >> >> Best,
> >> >> paul
> >> >>
> >> >> On Mon, Nov 28, 2016 at 3:50 PM, Bruce Fischl
> >> >> <fischl@nmr.mgh.harvard.edu

> <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
> >> >> I mean after you have converted it
> >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote:
> >> >>
> >> >> Thanks Bruce for the response. mri_info?
> do you
> >> mean
> >> >> when i
> >> >> converted it from analyze to
> >> >> mgz or when I ran recon-all autorecon2 after
> >> >> inserting it to
> >> >> freesurfer.
> >> >>
> >> >> On Mon, Nov 28, 2016 at 3:09 PM, Bruce Fischl
> >> >> <fischl@nmr.mgh.harvard.edu

> <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
> >> >> what is the output of mri_info on
> your new
> >> >> brainmask.mgz
> >> >> and on say the
> >> >> orig.mgz? You may need to conform you
> >> brainmask
> >> >>
> >> >> On Mon, 28 Nov 2016, miracle ozzoude
> wrote:
> >> >>
> >> >> Hello Freesurfer, I ran recon-all
> >> >> -autorecon 1 -s
> >> >> subjID on T1
> >> >> (T1_nii) image and after
> >> >> that, I replaced the skull
> stripped
> >> >> volume generated
> >> >> from FS with
> >> >> the skull stripped
> >> >> volume from lesion explorer (
> using
> >> >> mri_convert
> >> >> in_type analyze
> >> >> in_orientation LAS
> >> >> out-type img out_orientation LAS
> >> mgz; cp
> >> >> folder/brainmask.mgz
> >> >> folder/subjID/mri/brainmask.mgz). Then, I
> >> >> ran
> >> >> recon-all
> >> >> -autorecon2 -autorecon2 -s
> >> >> subjID. My recon-all is stucked at
> >> >>
> >> >> CORRECTION DEFECT 0 (vertices=49378,
> >> >> convex
> >> >> hull=3422, v0 =0)
> >> >> XL defect detected....
> >> >>
> >> >> Please how do I resolve this
> problem?
> >> >>
> >> >> I am running freesurfer-6
> >> development. I
> >> >> have
> >> >> attached the
> >> >> recon-all/recon-all status to
> >> >> the email.
> >> >>
> >> >> Thank you very much
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> Freesurfer mailing list
> >> >> Freesurfer@nmr.mgh.harvard.edu

> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> >>
> >> >>
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> >> >>
> >> >
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