29 Nov
2016
29 Nov
'16
1:58 p.m.
yes, though you should not need to spec the output orientation (redundant) or the in_type (it can figure that out)
On 11/29/2016 01:46 PM, miracle ozzoude wrote:
Thanks bruce and doug. The orientation is wrong hence, why I am using the orientation string. But, the above script is correct?
On Tue, Nov 29, 2016 at 1:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
don't use the orientation strings unless the orientation is wrong On 11/29/2016 01:38 PM, Bruce Fischl wrote: > you may not need the out_orientation, but perhaps someone else knows? > On Tue, 29 Nov 2016, miracle ozzoude wrote: > >> Hello Bruce, >> I wanted to confirm if this is the right script when converting from >> one format to another using mri_convert (if i want to use >> orig.mgz as template volume): >> mri_convert --in_type analyze --in_orientation LAS -rl orig.mgz >> --out_type mgz --out_orientation LAS brainmask.img brainmask.mgz >> Thanks, >> Paul >> >> On Mon, Nov 28, 2016 at 7:15 PM, <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> wrote: >> Awesome. Thank you very much Bruce. >> >> Sent from my BlackBerry 10 smartphone. >> Original Message >> From: Bruce Fischl >> Sent: Monday, November 28, 2016 5:14 PM >> To: Freesurfer support list >> Reply To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all -autorecon2 error. >> >> -rl is for "reslice like" and you include it in the mri_convert >> command >> line with orig.mgz as the template volume. Run mri_convert >> --help and it >> should be clear >> >> Bruce >> >> >> On Mon, 28 >> Nov 2016, miracooloz@gmail.com <mailto:miracooloz@gmail.com> wrote: >> >> > Thanks a lot Bruce. What do you mean by -rl and how do I >> incorporate it to mri_convert? >> > Best, >> > Paul >> > >> > Sent from my BlackBerry 10 smartphone. >> > Original Message >> > From: Bruce Fischl >> > Sent: Monday, November 28, 2016 4:57 PM >> > To: Freesurfer support list >> > Reply To: Freesurfer support list >> > Subject: Re: [Freesurfer] recon-all -autorecon2 error. >> > >> > I think this is your problem - the brainmask is not in the >> same voxel >> > coords as the other volumes. YOu probably need to -rl >> orig.mgz in your >> > conversion, then make sure that the volumes look aligned in >> freeview (and >> > that mri_info gives the same ras2vox and such for them) >> > On Mon, 28 Nov 2016, >> > miracle ozzoude wrote: >> > >> >> Oh. Thanks bruce. For mri_info for my orig.mgz is >> >> Volume information for orig.mgz >> >> type: MGH >> >> dimensions: 256 x 256 x 256 >> >> voxel sizes: 1.000000, 1.000000, 1.000000 >> >> type: UCHAR (0) >> >> fov: 256.000 >> >> dof: 0 >> >> xstart: -128.0, xend: 128.0 >> >> ystart: -128.0, yend: 128.0 >> >> zstart: -128.0, zend: 128.0 >> >> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, >> flip angle: 0.00 degrees >> >> nframes: 1 >> >> PhEncDir: UNKNOWN >> >> FieldStrength: 0.000000 >> >> ras xform present >> >> xform info: x_r = -1.0000, y_r = 0.0000, z_r = >> 0.0000, c_r = -110.0032 >> >> : x_a = 0.0000, y_a = 0.0000, z_a = >> 1.0000, c_a = 110.0032 >> >> : x_s = 0.0000, y_s = -1.0000, z_s = >> 0.0000, c_s = 91.0000 >> >> >> >> talairach xfm >> :/net/synapse/nt/mozzoude/processing/freesurfer/176_001_120223/fsdir1/mri/transforms/tala >> >> irach.xfm >> >> Orientation : LIA >> >> Primary Slice Direction: coronal >> >> >> >> voxel to ras transform: >> >> -1.0000 0.0000 0.0000 17.9968 >> >> 0.0000 0.0000 1.0000 -17.9968 >> >> 0.0000 -1.0000 0.0000 219.0000 >> >> 0.0000 0.0000 0.0000 1.0000 >> >> >> >> voxel-to-ras determinant -1 >> >> >> >> ras to voxel transform: >> >> -1.0000 -0.0000 -0.0000 17.9968 >> >> -0.0000 -0.0000 -1.0000 219.0000 >> >> -0.0000 1.0000 -0.0000 17.9968 >> >> -0.0000 -0.0000 -0.0000 1.0000 >> >> >> >> Here's the mri_info for my new brainmask.mgz: >> >> Volume information for brainmask.mgz >> >> type: MGH >> >> dimensions: 256 x 256 x 182 >> >> voxel sizes: 0.859400, 0.859400, 1.000000 >> >> type: UCHAR (0) >> >> fov: 220.006 >> >> dof: 0 >> >> xstart: -110.0, xend: 110.0 >> >> ystart: -110.0, yend: 110.0 >> >> zstart: -91.0, zend: 91.0 >> >> TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, >> flip angle: 0.00 degrees >> >> nframes: 1 >> >> PhEncDir: UNKNOWN >> >> FieldStrength: 0.000000 >> >> ras xform present >> >> xform info: x_r = -1.0000, y_r = 0.0000, z_r = >> 0.0000, c_r = 0.0000 >> >> : x_a = 0.0000, y_a = 1.0000, z_a = >> 0.0000, c_a = 0.0000 >> >> : x_s = 0.0000, y_s = 0.0000, z_s = >> 1.0000, c_s = 0.0000 >> >> >> >> talairach xfm : >> >> Orientation : LAS >> >> Primary Slice Direction: axial >> >> >> >> voxel to ras transform: >> >> -0.8594 0.0000 0.0000 110.0032 >> >> 0.0000 0.8594 0.0000 -110.0032 >> >> 0.0000 0.0000 1.0000 -91.0000 >> >> 0.0000 0.0000 0.0000 1.0000 >> >> >> >> voxel-to-ras determinant -0.738568 >> >> >> >> ras to voxel transform: >> >> -1.1636 -0.0000 -0.0000 128.0000 >> >> -0.0000 1.1636 -0.0000 128.0000 >> >> -0.0000 -0.0000 1.0000 91.0000 >> >> -0.0000 -0.0000 -0.0000 1.0000 >> >> >> >> >> >> On Mon, Nov 28, 2016 at 4:29 PM, Bruce Fischl >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> Hi Paul >> >> >> >> if you run mri_info on the orig.mgz and your new >> brainmask.mgz they should >> >> give you the same thing in terms of ras2vox and such >> >> cheers >> >> Bruce >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote: >> >> >> >> This was the info from mri_convert when i converted my skull >> >> stripped volume to mgz >> >> before replacing it with the brainmask from FS >> >> mri_convert --in_type analyze --in_orientation LAS >> --out_type mgz >> >> --out_orientation LAS >> >> brainmask.img brainmask.mgz >> >> cp foldername/subjid/brainmask.mgz >> >> foldername/subjd/mri/brainmask.mgz >> >> >> >> INFO: could not find ...mat file for direction cosine >> infoINFO: >> >> use ANALYZE 7.5 hdr -> >> >> hist.orient value: 0, transverse unflipped (default >> >> INFO : if not valid, please provide the information ....... >> .mat >> >> file >> >> analyzeRead() roi_scale 0.00000000 >> >> TR= 1000.00, TE = 0.00, TI = 0.00, flip angle = 0.00 >> >> setting input orientation to LAS >> >> i_ras = (-1, 0, 0) >> >> j_ras = (0,1,0) >> >> k_ras = (0,0,1) >> >> setting output orientation to LAS >> >> writing to brainmask.mgz >> >> >> >> why do i need the orig.mgz? I thought I only had to replace the >> >> brainmask.mgz (from FS) >> >> with mine brainmask,mgz( from lesion explorer after i have >> >> renamed it to brainmask.mgz). >> >> Also, I didn't use the "noskullstrip" flag like you suggested. >> >> Best, >> >> paul >> >> >> >> On Mon, Nov 28, 2016 at 3:50 PM, Bruce Fischl >> >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> I mean after you have converted it >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote: >> >> >> >> Thanks Bruce for the response. mri_info? do you >> mean >> >> when i >> >> converted it from analyze to >> >> mgz or when I ran recon-all autorecon2 after >> >> inserting it to >> >> freesurfer. >> >> >> >> On Mon, Nov 28, 2016 at 3:09 PM, Bruce Fischl >> >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> what is the output of mri_info on your new >> >> brainmask.mgz >> >> and on say the >> >> orig.mgz? You may need to conform you >> brainmask >> >> >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote: >> >> >> >> Hello Freesurfer, I ran recon-all >> >> -autorecon 1 -s >> >> subjID on T1 >> >> (T1_nii) image and after >> >> that, I replaced the skull stripped >> >> volume generated >> >> from FS with >> >> the skull stripped >> >> volume from lesion explorer ( using >> >> mri_convert >> >> in_type analyze >> >> in_orientation LAS >> >> out-type img out_orientation LAS >> mgz; cp >> >> folder/brainmask.mgz >> >> folder/subjID/mri/brainmask.mgz). Then, I >> >> ran >> >> recon-all >> >> -autorecon2 -autorecon2 -s >> >> subjID. My recon-all is stucked at >> >> >> >> CORRECTION DEFECT 0 (vertices=49378, >> >> convex >> >> hull=3422, v0 =0) >> >> XL defect detected.... >> >> >> >> Please how do I resolve this problem? >> >> >> >> I am running freesurfer-6 >> development. I >> >> have >> >> attached the >> >> recon-all/recon-all status to >> >> the email. >> >> >> >> Thank you very much >> >> >> >> >> >> _______________________________________________ >> >> 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. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ 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>
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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/