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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>> contains patient information, please contact the Partners Compliance HelpLine at
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