On Tue, Nov 29, 2016 at 1:39 PM, Douglas N Greve <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> 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 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> 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> 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> 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
>> >>
>> >>
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>> >>
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>> >>
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>> >>
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>> person to whom it is
>> >> addressed. If you believe this e-mail was sent to you in
>> error and the e-mail
>> >> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> >> http://www.partners.org/complianceline . If the e-mail was
>> sent to you in error
>> >> but does not contain patient information, please contact the
>> sender and properly
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>> >>
>> >>
>> >>
>> >>
>> >
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>> >
>>
>>
>>
>>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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