recon-all -autorecon2 error.

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miracle ozzoude

28 Nov 2016 28 Nov '16

1:31 p.m.

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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Bruce Fischl

28 Nov 28 Nov

3:09 p.m.

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

miracle ozzoude

3:23 p.m.

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

Bruce Fischl

3:50 p.m.

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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

miracle ozzoude

4:16 p.m.

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 info INFO: 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

Bruce Fischl

4:29 p.m.

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


        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


        The information in this e-mail is intended only for the 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
        dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

miracle ozzoude

4:41 p.m.

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/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 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


        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


        The information in this e-mail is intended only for the
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 dispose of the e-mail.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

Bruce Fischl

4:56 p.m.

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


                    _______________________________________________
                    Freesurfer mailing list
                    Freesurfer@nmr.mgh.harvard.edu
                   
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


                    The information in this e-mail is intended only for
        the 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
                    dispose of the e-mail.




        _______________________________________________
        Freesurfer mailing list
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        The information in this e-mail is intended only for the 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
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        but does not contain patient information, please contact the
        sender and properly
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

miracooloz＠gmail.com

5:07 p.m.

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.

...

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

Bruce Fischl

5:13 p.m.

-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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the 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 dispose of the e-mail.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

miracooloz＠gmail.com

7:15 p.m.

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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The information in this e-mail is intended only for the 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 dispose of the e-mail.

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miracle ozzoude

29 Nov 29 Nov

12:58 p.m.

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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The information in this e-mail is intended only for the 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

...
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but does not contain patient information, please contact the sender and

properly

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dispose of the e-mail.

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Bruce Fischl

1:38 p.m.

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
  >>
  >>
  >>             _______________________________________________
  >>             Freesurfer mailing list
  >>             Freesurfer@nmr.mgh.harvard.edu
  >>            
  >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >>
  >>
  >>             The information in this e-mail is intended only for
  >> the 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
  >>             dispose of the e-mail.
  >>
  >>
  >>
  >>
  >> _______________________________________________
  >> Freesurfer mailing list
  >> Freesurfer@nmr.mgh.harvard.edu
  >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >>
  >>
  >> The information in this e-mail is intended only for the 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
  >> dispose of the e-mail.
  >>
  >>
  >>
  >>
  >> _______________________________________________
  >> Freesurfer mailing list
  >> Freesurfer@nmr.mgh.harvard.edu
  >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >>
  >>
  >> The information in this e-mail is intended only for the 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
  >> dispose of the e-mail.
  >>
  >>
  >>
  >>
  >
  > _______________________________________________
  > Freesurfer mailing list
  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >

Douglas N Greve

1:39 p.m.

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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for >> the 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 >> dispose of the e-mail. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the 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 >> dispose of the e-mail. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the 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 >> dispose of the e-mail. >> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

miracle ozzoude

1:46 p.m.

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 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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for >> the 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 >> dispose of the e-mail. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the 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
  >> dispose of the e-mail.
  >>
  >>
  >>
  >>
  >> _______________________________________________
  >> Freesurfer mailing list
  >> Freesurfer@nmr.mgh.harvard.edu
  >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >>
  >>
  >> The information in this e-mail is intended only for the
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 >> dispose of the e-mail. >> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Douglas N Greve

1:58 p.m.

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
>>       >>
>>       >>
>>       >> _______________________________________________
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>>       >>
>>       >>
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>>       >>
>>       >>
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only for
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>>       >>
>>       >> _______________________________________________
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>>       >>
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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>       >>
>>       >>
>>       >> The information in this e-mail is intended only for the
>> 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
<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
>>       >> dispose of the e-mail.
>>       >>
>>       >>
>>       >>
>>       >>
>>       >
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
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Bruce Fischl
Douglas N Greve
miracle ozzoude
miracooloz＠gmail.com