Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.
by Knut J Bjuland 30 Nov '16

30 Nov '16

Hi, I would like to to obtain FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a DWI file, either produced by dt_recon (or perhaps better - from Tracula) and an anatomy file in atlas space and then use WMParcStatsLUT.txt or FreeSurferColorLUT.txt (not sure which) to obtain the wm ROIs containing FA data. And then register the aparc+aseg.mgz to the FA image and use mri_segstats to retrieve FA data from the white matter ROIs. I have done this: # Register DTI file to individual anatomy space 1) dt_recon --i 1/dti/1.dcm --s 001 --b 1/dti/bval 1/dti/bvec --o 1/dtrecon # Register fa.nii to wmparc.mgz and aparc+aseg.mgz 2) mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 001v4/mri/wmparc.mgz --inv --interp nearest --o 1/mri/aseg2DTI.mgz --no-save-reg mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 001v4/mri/aparc+aseg.mgz --inv --interp nearest --o 1/mri/aparc-aseg2DTI.mgz --no-save-reg 3) It works for wmparc, in that I get data that range from 0.0 to 0.4 with mean = 0.04 (which is a little low for FA values): mri_segstats --seg 1/mri/wmparc2DTI.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i 1/dtrecon/fa.nii --sum fa.stats_wm-lh-medialorbitofrontal But for aparc+aseg, it doesn't produce any data: mri_segstats --seg 1/mri/aparc-aseg2DTI.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i 1/dtrecon/fa.nii --sum fa.stats_wm-lh-medialorbitofrontal output: Found 1 segmentations Computing statistics for each segmentation 0 3014 wm-lh-medialorbitofrontal 0 0.000 Reporting on 0 segmentations mri_segstats done Questions: 1) Am I right to use FreeSurferColorLUT.txt and not WMParcStatsLUT.txt? 2) In order to get FA data from the wm regions corresponding to cortical ROIs, should I use the FA registrated to wmparc.mgz or aparc+aseg.mgz? 3) If I want to use Tracula DTI files instead, which file do I choose: Is it FA_ditifit.nii? sincerely yours, Knut Jørgen Bjuland PhD

2 1

Re: [Freesurfer] recon-all -autorecon2 error.
by miracle ozzoude 29 Nov '16

29 Nov '16

Hello Doug and Bruce, I ran the script and it worked however, volumes did not align on freeview.* Here's the mri_info for orig.mgz: * 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/fsdir3/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 brainmask.mgz after including -rl orig.mgz* Volume information for brainmask.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: 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 = -110.0032 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 110.0032 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 91.0000 talairach xfm : /net/synapse/nt/mozzoude/processing/freesurfer/176_001_ 120223/fsdir3/mri/transforms/talairach.xfm Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -1.0000 0.0000 0.0000 17.9968 0.0000 1.0000 0.0000 -17.9968 0.0000 0.0000 1.0000 -37.0000 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 1.0000 -0.0000 17.9968 -0.0000 -0.0000 1.0000 37.0000 -0.0000 -0.0000 -0.0000 1.0000 I sent the orig.mgz, brainmask.mgz (my stripped volume from lesion explorer that i converted to mgz) and the HfBd.img/hdr (stripped volume in analyze format which I used to convert to mgz) to the freesurfer file drop (subject = recon-all -autorecon2 error Paul) https://gate.nmr.mgh.harvard.edu/filedrop2/index.php Please can you inspect to see why both images (orig.mgz and brainmask.mgz) do not align and cannot finish recon-all -autorecon2? THANK YOU VERY MUCH Paul On Tue, Nov 29, 2016 at 3:20 PM, miracle ozzoude <miracooloz(a)gmail.com> wrote: > Hello Doug and Bruce, > > I ran the script and it worked however, volumes did not align on freeview.* > Here's the mri_info for orig.mgz: * > 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/fsdir3/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 brainmask.mgz after including -rl orig.mgz* > Volume information for brainmask.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: 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 = > -110.0032 > : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = > 110.0032 > : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = > 91.0000 > > talairach xfm : /net/synapse/nt/mozzoude/processing/freesurfer/176_001_ > 120223/fsdir3/mri/transforms/talairach.xfm > Orientation : LAS > Primary Slice Direction: axial > > voxel to ras transform: > -1.0000 0.0000 0.0000 17.9968 > 0.0000 1.0000 0.0000 -17.9968 > 0.0000 0.0000 1.0000 -37.0000 > 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 1.0000 -0.0000 17.9968 > -0.0000 -0.0000 1.0000 37.0000 > -0.0000 -0.0000 -0.0000 1.0000 > > I have attached the orig.mgz, brainmask.mgz (my stripped volume from > lesion explorer that i converted to mgz) and the HfBd.img/hdr (stripped > volume in analyze format which I used to convert to mgz). Please can you > inspect to see why both images (orig.mgz and brainmask.mgz) do not align. > > THANK YOU VERY MUCH > Paul > > On Tue, Nov 29, 2016 at 1:58 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> 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(a)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(a)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(a)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_120 >> 223/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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har >> vard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >

1 0

TRACULA Error in virtualbox
by Alexander Zent 29 Nov '16

29 Nov '16

I am trying to run TRACULA and keep getting the error FSLDIR: Undefined Variable. I have looked at the answers to this question that have been previously posted but cannot seem to remedy this problem. I'm running freesurfer 5.3 via virtualbox on windows. I have applied for a license and added that to the license.txt file but to no avail. Thank you and I look forward to hearing from you. Thanks, Alex

3 2

Using mri_glmfit to generate R (correlation) maps
by Morenikeji Adebayo 29 Nov '16

29 Nov '16

Hello Freesurfers, I'm interested in creating a group map where each vertex represents the correlation (as a correlation coefficient) between a task-related BOLD contrast value (ces.nii.gz) and a single covariate. This is analogous to a cortical thickness GLM with one group and one covariate, but I'd want an r-map instead of a sig-map. How might I accomplish this? It appears that mri_glmfit generates sig-maps, gamma-maps, etc, but not r-maps. Thanks in advance, Keji

2 8

recon-all -autorecon2 error.
by miracle ozzoude 29 Nov '16

29 Nov '16

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

4 15

Request for patch for mri_convert, nifti1Read(): unsupported slice timing pattern 5 error
by Jennifer Barredo 29 Nov '16

29 Nov '16

Hello Freesurfer experts, I'm trying to run the TRACULA preprocessing pipeline using data in NIFTI-1 format, but am receiving the following error: "nifti1Read(): unsupported slice timing pattern 5" Several other users have run into this problem. In the archives, there are a few links to dead file transfer protocols for a patch for mri_convert that might solve my problem. May I please have a patch for mri_convert? I'm using freesurfer-Darwin-lion-stable-pub-v5.3.0 and OSX Yosemite. Thank you, Jennifer -- Jennifer Barredo, PhD Staff Scientist Providence VA Medical Center Research Affiliate Brown Institute for Brain Sciences jlbarredo(a)gmail.com Jennifer.Barredo(a)va.gov

1 0

running freesurfer 5.3 on Ubuntu 16.04
by Parzer, Peter 28 Nov '16

28 Nov '16

Hi, there is an old thread about an recon-all error on Ubuntu 16.04, that is caused by an incompatibility between the MNI tools and the perl version 5.22 distributed with Ubuntu 16.04. This has been fixed in the development version. Has someone a more detailed description how this was fixed so that I could try to back-port this fix to freesurfer 5.3? Downgrading perl in Ubuntu 16.04 is not possible, there are to many packages depending on it and there is no other version of perl in the repositories. We have already about 100 subjects analyzed with version 5.3 and I hesitate to re-analyze all of them with the development version. Since we had to update Ubuntu to 16.04 for other reasons, we use freesurfer 5.3 now inside a virtual machine with Ubuntu 14.04 installed, which is not very efficient. Peter

2 1

recon-all error with nii file
by Htet, Aung Thu 28 Nov '16

28 Nov '16

Hi Everybody, I am trying to use an nii file in recon-all, where subject_dir does not exist yet. recon-all -subject <subject-name> -i <file.nii> -all But I am having this error: niiRead(): unsupported datatype 128 (with scl_slope != 0) in /home/fsuser/aung/18991230_000000s001a000A.nii Any help in understanding the error would be appreciated. Thanks in advance. Aung

2 1

Download latest version of mris_pmake
by Garikoitz Lerma-Usabiaga 28 Nov '16

28 Nov '16

Hi, I am using the 2011 of mris_pmake and I've seen in the list that there are newer versions. I am using both linux and mac. It's giving several errors when computing distances in fsaverage (just in some of the pairs), so I hope that the new version will be able to solve them. Thank you very much. Gari

2 3

Trouble with Two Stage Longitudinal Analysis
by Timothy Hendrickson 28 Nov '16

28 Nov '16

I was able to figure out my design matrix issue. I had not originally appreciated that there were no data sets from a particular class. Thanks! -Tim FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I belive I have cross-checked my qdec, fsgd, design matrix, and contrast files and they all match so I do not think the problem is a mismatch. I am wondering if I made some sort of mistake in my script design or design matrix creation... Anyway here is the command line input: mri_glmfit --glmdir lh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat --y lh.testretest.thickness-pc1.stack.fwhm10.mgh --C age_AcctGroup_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AgeSlope_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AcctSite_AcctDiagnosis_AcctAge_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AgeSlope_AcctSite_AcctDiagnosis_twoStage.DOSSDS.mtx --label lh.testretest.fsaverage.cortex.label --surf fsaverage lh The error message is attached within file AllSite_twoStageLongitudinal_DsgnMtxErr.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) Design matrix ------------------ 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.600 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.800 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.500 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.200 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.295 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.800 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.495 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.095 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.895 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.665 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.745 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 12.500 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.995; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.740; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.265 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.240 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.415 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.835 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.240 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.835 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.825 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.835 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 15.820; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.675 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 15.420; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.245 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.695; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.400 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.310 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.450; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.400; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 10.955 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.410 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.905 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.210 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.500; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.200 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.305; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.435 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.895 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.795 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.500 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.900 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.985 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.390 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.180; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.380 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.200; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.090 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.790 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.090; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.090; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.685 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.085 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.810 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.885 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.900 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.995 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.595 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.200 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.950 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.490 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.495 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.295 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.595 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.415 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.605 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.605 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.600; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.600; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.005 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.705 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.585 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.795 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.690 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.190 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.400 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.605 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.210 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.090 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.495 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.195 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.595; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.400 0.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: *[image: Attachment:] <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/AllSite…> AllSite_longAnalysis_11_16_16_noYears.table.dat <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/AllSite…>* *Description:* Binary data *[image: Attachment:] <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/cross.A…> cross.AllSite_longAnalysis_11_16_16_noYears.table.dat <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/cross.A…>* *Description:* Binary data *[image: Attachment:] <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/DOSSDS.…> DOSSDS.twoStage_AllSite_Gender_Group_Age.dat <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/DOSSDS.…>* *Description:* Binary data *[image: Attachment:] <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/twoStag…> twoStageLongitudinal_AllSite_Gender_Group_Age.fsgd <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/twoStag…>* *Description:* Binary data #!/bin/bash #Author Timothy Hendrickson #Modified last -July 12, 2016 #This is a script which will run the two-stage model from Freesurfer. #debugging set -x # set nice priority to 19 for given job renice -n 19 -p $$ # set command argument to determine hemisphere hemi=$1 #will accept '$hemi' or 'lh' #set qdec file for first stage qdec=AllSite_longAnalysis_11_16_16_noYears.table.dat #set qdec file for second stage tempAvgQdec=cross.AllSite_longAnalysis_11_16_16_noYears.table.dat #set fsgd file for second stage, created in part by performing the following command to average covariates #fsgdfile=twoStageLongitudinal_AllSite_Gender_Group_StanAges.fsgd fsgdfile=twoStageLongitudinal_AllSite_Gender_Group_Age.fsgd #set data dir and SUBJECTS_DIR for freesurfer datadir=`pwd -P` SUBJECTS_DIR=$datadir #set base up to be used later when determining .mgh and .glmdir base=$hemi.AllSite.gender.group.Age.thickness.fwhm10.twoStage smooth=10 # First stage: Prepare the Data long_mris_slopes --qdec $qdec --meas thickness --hemi $hemi --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time age --qcache fsaverage --sd $SUBJECTS_DIR #Second stage: Perform tests on data. #long_mris_slopes: Computes slope maps (e.g. of thickness) in a longitudinal study. #The slope is computed within subject from the longitudinally processed #results (taken from the <tpNid>.long.<template> directories) and the #output is written into the subjects <template>/surf directory for further #processing long_mris_slopes --qdec $tempAvgQdec \ --meas thickness \ --hemi $hemi \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm $smooth \ --qcache fsaverage \ --stack-pc1 $hemi.testretest.thickness-pc1.stack.mgh \ --isec-labels $hemi.testretest.fsaverage.cortex.label mri_glmfit \ --glmdir $base.glmdir \ --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat \ --y $hemi.testretest.thickness-pc1.stack.fwhm${smooth}.mgh \ --C age_AcctGroup_AcctSite_AcctGender_twoStage.DOSSDS.mtx \ --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_twoStage.DOSSDS.mtx \ --C DiffDiagnosis_ControlMore_AgeSlope_AcctSite_AcctGender_twoStage.DOSSDS.mtx \ --C DiffGender_MaleMore_AcctSite_AcctDiagnosis_AcctAge_twoStage.DOSSDS.mtx \ --C DiffGender_MaleMore_AgeSlope_AcctSite_AcctDiagnosis_twoStage.DOSSDS.mtx \ --label $hemi.testretest.fsaverage.cortex.label \ --surf fsaverage $hemi for i in abs pos neg do mri_glmfit-sim \ --glmdir ${base}.glmdir \ --cache 1.3 $i \ --cwp 0.05 \ --2spaces & done _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

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Freesurfer November 2016