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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