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
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
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.
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.
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 onT1 (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.
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.
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 volumegenerated 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 theperson 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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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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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.
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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.
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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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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.
-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
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
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: 0.000000ras 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: 0.000000ras 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 meanwhen 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 newbrainmask.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. Ihave attached the recon-all/recon-all status to the email.
Thank you very much _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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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The information in this e-mail is intended only for the person to whom
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addressed. If you believe this e-mail was sent to you in error and the
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HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
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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 > > >
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_convertcommand 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 Iincorporate 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
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_convertcommand 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 Iincorporate 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 theperson 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 > > >
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-- 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/
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yes, though you should not need to spec the output orientation (redundant) or the in_type (it can figure that out)
On 11/29/2016 01:46 PM, miracle ozzoude wrote:
Thanks bruce and doug. The orientation is wrong hence, why I am using the orientation string. But, the above script is correct?
On Tue, Nov 29, 2016 at 1:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
don't use the orientation strings unless the orientation is wrong On 11/29/2016 01:38 PM, Bruce Fischl wrote: > you may not need the out_orientation, but perhaps someone else knows? > On Tue, 29 Nov 2016, miracle ozzoude wrote: > >> Hello Bruce, >> I wanted to confirm if this is the right script when converting from >> one format to another using mri_convert (if i want to use >> orig.mgz as template volume): >> mri_convert --in_type analyze --in_orientation LAS -rl orig.mgz >> --out_type mgz --out_orientation LAS brainmask.img brainmask.mgz >> Thanks, >> Paul >> >> On Mon, Nov 28, 2016 at 7:15 PM, <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> wrote: >> Awesome. Thank you very much Bruce. >> >> Sent from my BlackBerry 10 smartphone. >> Original Message >> From: Bruce Fischl >> Sent: Monday, November 28, 2016 5:14 PM >> To: Freesurfer support list >> Reply To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all -autorecon2 error. >> >> -rl is for "reslice like" and you include it in the mri_convert >> command >> line with orig.mgz as the template volume. Run mri_convert >> --help and it >> should be clear >> >> Bruce >> >> >> On Mon, 28 >> Nov 2016, miracooloz@gmail.com <mailto:miracooloz@gmail.com> wrote: >> >> > Thanks a lot Bruce. What do you mean by -rl and how do I >> incorporate it to mri_convert? >> > Best, >> > Paul >> > >> > Sent from my BlackBerry 10 smartphone. >> > Original Message >> > From: Bruce Fischl >> > Sent: Monday, November 28, 2016 4:57 PM >> > To: Freesurfer support list >> > Reply To: Freesurfer support list >> > Subject: Re: [Freesurfer] recon-all -autorecon2 error. >> > >> > I think this is your problem - the brainmask is not in the >> same voxel >> > coords as the other volumes. YOu probably need to -rl >> orig.mgz in your >> > conversion, then make sure that the volumes look aligned in >> freeview (and >> > that mri_info gives the same ras2vox and such for them) >> > On Mon, 28 Nov 2016, >> > miracle ozzoude wrote: >> > >> >> Oh. Thanks bruce. For mri_info for my orig.mgz is >> >> Volume information for orig.mgz >> >> type: MGH >> >> dimensions: 256 x 256 x 256 >> >> voxel sizes: 1.000000, 1.000000, 1.000000 >> >> type: UCHAR (0) >> >> fov: 256.000 >> >> dof: 0 >> >> xstart: -128.0, xend: 128.0 >> >> ystart: -128.0, yend: 128.0 >> >> zstart: -128.0, zend: 128.0 >> >> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, >> flip angle: 0.00 degrees >> >> nframes: 1 >> >> PhEncDir: UNKNOWN >> >> FieldStrength: 0.000000 >> >> ras xform present >> >> xform info: x_r = -1.0000, y_r = 0.0000, z_r = >> 0.0000, c_r = -110.0032 >> >> : x_a = 0.0000, y_a = 0.0000, z_a = >> 1.0000, c_a = 110.0032 >> >> : x_s = 0.0000, y_s = -1.0000, z_s = >> 0.0000, c_s = 91.0000 >> >> >> >> talairach xfm >> :/net/synapse/nt/mozzoude/processing/freesurfer/176_001_120223/fsdir1/mri/transforms/tala >> >> irach.xfm >> >> Orientation : LIA >> >> Primary Slice Direction: coronal >> >> >> >> voxel to ras transform: >> >> -1.0000 0.0000 0.0000 17.9968 >> >> 0.0000 0.0000 1.0000 -17.9968 >> >> 0.0000 -1.0000 0.0000 219.0000 >> >> 0.0000 0.0000 0.0000 1.0000 >> >> >> >> voxel-to-ras determinant -1 >> >> >> >> ras to voxel transform: >> >> -1.0000 -0.0000 -0.0000 17.9968 >> >> -0.0000 -0.0000 -1.0000 219.0000 >> >> -0.0000 1.0000 -0.0000 17.9968 >> >> -0.0000 -0.0000 -0.0000 1.0000 >> >> >> >> Here's the mri_info for my new brainmask.mgz: >> >> Volume information for brainmask.mgz >> >> type: MGH >> >> dimensions: 256 x 256 x 182 >> >> voxel sizes: 0.859400, 0.859400, 1.000000 >> >> type: UCHAR (0) >> >> fov: 220.006 >> >> dof: 0 >> >> xstart: -110.0, xend: 110.0 >> >> ystart: -110.0, yend: 110.0 >> >> zstart: -91.0, zend: 91.0 >> >> TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, >> flip angle: 0.00 degrees >> >> nframes: 1 >> >> PhEncDir: UNKNOWN >> >> FieldStrength: 0.000000 >> >> ras xform present >> >> xform info: x_r = -1.0000, y_r = 0.0000, z_r = >> 0.0000, c_r = 0.0000 >> >> : x_a = 0.0000, y_a = 1.0000, z_a = >> 0.0000, c_a = 0.0000 >> >> : x_s = 0.0000, y_s = 0.0000, z_s = >> 1.0000, c_s = 0.0000 >> >> >> >> talairach xfm : >> >> Orientation : LAS >> >> Primary Slice Direction: axial >> >> >> >> voxel to ras transform: >> >> -0.8594 0.0000 0.0000 110.0032 >> >> 0.0000 0.8594 0.0000 -110.0032 >> >> 0.0000 0.0000 1.0000 -91.0000 >> >> 0.0000 0.0000 0.0000 1.0000 >> >> >> >> voxel-to-ras determinant -0.738568 >> >> >> >> ras to voxel transform: >> >> -1.1636 -0.0000 -0.0000 128.0000 >> >> -0.0000 1.1636 -0.0000 128.0000 >> >> -0.0000 -0.0000 1.0000 91.0000 >> >> -0.0000 -0.0000 -0.0000 1.0000 >> >> >> >> >> >> On Mon, Nov 28, 2016 at 4:29 PM, Bruce Fischl >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> Hi Paul >> >> >> >> if you run mri_info on the orig.mgz and your new >> brainmask.mgz they should >> >> give you the same thing in terms of ras2vox and such >> >> cheers >> >> Bruce >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote: >> >> >> >> This was the info from mri_convert when i converted my skull >> >> stripped volume to mgz >> >> before replacing it with the brainmask from FS >> >> mri_convert --in_type analyze --in_orientation LAS >> --out_type mgz >> >> --out_orientation LAS >> >> brainmask.img brainmask.mgz >> >> cp foldername/subjid/brainmask.mgz >> >> foldername/subjd/mri/brainmask.mgz >> >> >> >> INFO: could not find ...mat file for direction cosine >> infoINFO: >> >> use ANALYZE 7.5 hdr -> >> >> hist.orient value: 0, transverse unflipped (default >> >> INFO : if not valid, please provide the information ....... >> .mat >> >> file >> >> analyzeRead() roi_scale 0.00000000 >> >> TR= 1000.00, TE = 0.00, TI = 0.00, flip angle = 0.00 >> >> setting input orientation to LAS >> >> i_ras = (-1, 0, 0) >> >> j_ras = (0,1,0) >> >> k_ras = (0,0,1) >> >> setting output orientation to LAS >> >> writing to brainmask.mgz >> >> >> >> why do i need the orig.mgz? I thought I only had to replace the >> >> brainmask.mgz (from FS) >> >> with mine brainmask,mgz( from lesion explorer after i have >> >> renamed it to brainmask.mgz). >> >> Also, I didn't use the "noskullstrip" flag like you suggested. >> >> Best, >> >> paul >> >> >> >> On Mon, Nov 28, 2016 at 3:50 PM, Bruce Fischl >> >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> I mean after you have converted it >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote: >> >> >> >> Thanks Bruce for the response. mri_info? do you >> mean >> >> when i >> >> converted it from analyze to >> >> mgz or when I ran recon-all autorecon2 after >> >> inserting it to >> >> freesurfer. >> >> >> >> On Mon, Nov 28, 2016 at 3:09 PM, Bruce Fischl >> >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> what is the output of mri_info on your new >> >> brainmask.mgz >> >> and on say the >> >> orig.mgz? You may need to conform you >> brainmask >> >> >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote: >> >> >> >> Hello Freesurfer, I ran recon-all >> >> -autorecon 1 -s >> >> subjID on T1 >> >> (T1_nii) image and after >> >> that, I replaced the skull stripped >> >> volume generated >> >> from FS with >> >> the skull stripped >> >> volume from lesion explorer ( using >> >> mri_convert >> >> in_type analyze >> >> in_orientation LAS >> >> out-type img out_orientation LAS >> mgz; cp >> >> folder/brainmask.mgz >> >> folder/subjID/mri/brainmask.mgz). Then, I >> >> ran >> >> recon-all >> >> -autorecon2 -autorecon2 -s >> >> subjID. My recon-all is stucked at >> >> >> >> CORRECTION DEFECT 0 (vertices=49378, >> >> convex >> >> hull=3422, v0 =0) >> >> XL defect detected.... >> >> >> >> Please how do I resolve this problem? >> >> >> >> I am running freesurfer-6 >> development. I >> >> have >> >> attached the >> >> recon-all/recon-all status to >> >> the email. >> >> >> >> Thank you very much >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. >> >> >> >> >> >> >> >> >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > >> > >> >> >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. 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