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
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>> 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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