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Which is the best volume to use to get intensity statistics?
by Guido Orlando Pascariello 23 Nov '15

23 Nov '15

Hi FS Expert I have just looked for this subject a long the list but I haven't found anything about. I have been working with FreeSurfer and I could get some segmentation from my T1 data. I used 'mri_segstats' to quantify volume of some subcortical region. Also I want to get intensity statistics from these regions, so I used --in parameter. In the 'recon-all' pipeline, you use 'norm.mgz' but.. . I wonder is not better to use nu.mgz in order to get intensity values more related to original data? If is not. Can you explain me what '-canorm' step does? Because I don't get it I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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Re: [Freesurfer] How to create a 3g4v matrix
by nellie 23 Nov '15

23 Nov '15

Hi Lee, Thank you for your reply. I had read the example tables, but I'm still not sure how to alter them into my study.May be you could help to check the matrix I designed and tell me my mistake? 3 classes ( A / B / C group) and 4 variables (gender, age, education, and Moca test score). group.diff.mtx 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 group-x-gender.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 group-x-age.mtx 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 group-x-education.mtx 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 group-x-moca.mtx 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 group-x-gender-x-age-x-education.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 group-x-gender-x-age-x-education-x-moca.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 group.diff.mtx also can write as: 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 group-x-age.mtx aslo can write as: 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 Thank you in advence. Wishes, Li > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. Re: How to create a 3g4v matrix (Lee Tirrell) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 23 Nov 2015 10:27:42 -0500 (EST) >From: Lee Tirrell <ltirrell(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] How to create a 3g4v matrix >To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: > <alpine.LRH.2.20.1511231020130.5623(a)vermis.nmr.mgh.harvard.edu> >Content-Type: text/plain; charset="iso-8859-7" > >Hi Li, > >You can find some example FSGD tables here, which you can alter to fit your >analyses. > >https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > >Best, >Lee > >On Sun, 22 Nov 2015, nellie wrote: > >> >> Hi Freesurfer Experts, >> >> I?m a new user of Freesurfer, and I learn how to use this software mainly through Wiki. When I came to the step of using GLM to compare group differences, I was confused on the design of 3g4v matrix. In my study, there were 3 classes ( >> A / B / C group) and 4 concomitant?variables (gender, age, education, and Moca test score). It?s supposed to be 15 regressors in this design, but I don?t know how to use the numbers (like 1, -1, 0, 0.5, -0.5, etc.) to create a correct >> matrix. I wonder if you could provide a 3g4v matrix in detail for me. I?ll be grateful if you can help. I hope I?m not bothering you too much, and I?m looking for your reply. >> >> Best wishes, >> >> Li? >> >> >> >> ? >> >> >> > >------------------------------ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >End of Freesurfer Digest, Vol 141, Issue 40 >******************************************* > > >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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Get white and pial surfaces without using aseg.mgz
by Guido Orlando Pascariello 23 Nov '15

23 Nov '15

Hi FS Experts I'm using FreeSurfer to process my T1 data in order to get white and pial surfaces from it. I have a questions about usages of this file 'aseg.mgz'. In the 'recon-all' pipeline, there are some steps in which I can use it or don't use it depend on if I want or don't. I wonder What are the differences in the result in each option? My goal is skip the '-careg' step to save time because I'm not interested in volumetry. I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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Re: [Freesurfer] fsl_rigid_register fails with wrong orientation
by Caspar M. Schwiedrzik 23 Nov '15

23 Nov '15

Red Hat Enterprise Linux Server release 5.9 (Tikanga) freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Caspar 2015-11-23 14:37 GMT-05:00 <zkaufman(a)nmr.mgh.harvard.edu>: > What system are you running on? Also, what are the contents of your > build-stamp.txt file (in your FREESURFER_HOME directory)? > > -Zeke > > > > Hi Zeke, > > I tried the is new version. Now I am getting: > > > > mri_coreg: /lib64/libuuid.so.1: no version information available > (required > > by mri_coreg) > > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_coreg) > > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_coreg) > > mri_coreg: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_coreg) > > > > Caspar > > > > > > 2015-11-23 14:20 GMT-05:00 <zkaufman(a)nmr.mgh.harvard.edu>: > > > >> There were some recent changes in the build that eliminated the > >> necessity > >> for that library. Casper, can you try using this most recent version and > >> let me know if it works? > >> > >> > >> > ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_… > >> > >> Thanks, > >> > >> -Zeke > >> > >> > >> > Zeke, is this a new library that we need for v6? > >> > doug > >> > > >> > On 11/20/2015 09:42 AM, Caspar M. Schwiedrzik wrote: > >> >> Hi Doug, > >> >> when I try to execute mri_coreg, I get the following error message: > >> >> > >> >> error while loading shared libraries: libnetcdf.so.6: cannot open > >> >> shared object file: no such file or directory > >> >> > >> >> Caspar > >> >> > >> >> > >> >> 2015-11-19 18:49 GMT-05:00 Douglas Greve <greve(a)nmr.mgh.harvard.edu > >> >> <mailto:greve@nmr.mgh.harvard.edu>>: > >> >> > >> >> > >> >> Can you try mri_coreg instead of fsl? > >> >> > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg > >> >> > >> >> > >> >> > >> >> > >> >> On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote: > >> >>> Hi! > >> >>> I am trying to align a mean EPI volume and a Bruker magnitude > >> map > >> >>> from a fieldmap measurement using tkregister2, > >> fsl_rigid_register > >> >>> and mri_vol2vol. Unfortunately, it seems that somewhere, most > >> >>> likely during fsl_rigid_register, the image orientation get > >> >>> scrambled, and the output has the wrong orientation. > >> >>> > >> >>> Here is what I get from*tkregister2:* > >> >>> > >> >>> target volume epi.nii > >> >>> movable volume fieldmap0001.nii > >> >>> reg file mag_2_mocovol.register.dat > >> >>> LoadVol 0 > >> >>> ZeroCRAS 0 > >> >>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > >> >>> Diagnostic Level -1 > >> >>> INFO: loading target epi.nii > >> >>> Setting targ orientation to RIA > >> >>> INFO: target does not conform to COR format, so I'm going to > >> >>> reslice to COR. This will not affect the final registration. > >> >>> Ttarg: -------------------- > >> >>> -1.000 0.000 0.000 128.000; > >> >>> 0.000 0.000 1.000 -128.000; > >> >>> 0.000 -1.000 0.000 128.000; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> INFO: loading movable fieldmap0001.nii > >> >>> Setting mov orientation to RIA > >> >>> Tmov: -------------------- > >> >>> -0.547 0.000 0.000 17.500; > >> >>> 0.000 0.000 0.547 -17.500; > >> >>> 0.000 -0.547 0.000 17.500; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> mkheaderreg = 1, float2int = 0 > >> >>> Computing reg from header (and possibly input matrix) > >> >>> ---- Input registration matrix (computed) -------- > >> >>> -1.000 0.000 0.000 -0.587; > >> >>> 0.000 1.000 0.000 -2.150; > >> >>> 0.000 0.000 1.000 -2.188; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> --------------------------------------- > >> >>> ---- Input registration matrix -------- > >> >>> -1.000 0.000 0.000 -0.587; > >> >>> 0.000 1.000 0.000 -2.150; > >> >>> 0.000 0.000 1.000 -2.188; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> Determinant -1 > >> >>> subject = rat > >> >>> RegMat --------------------------- > >> >>> 1.000 0.000 0.000 -0.587; > >> >>> 0.000 1.000 0.000 -2.150; > >> >>> 0.000 0.000 1.000 -2.188; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> FSLOUTPUTTYPE NIFTI_GZ > >> >>> tkreg2FSL: mov det = 0.163555, ref det = 0.154688 > >> >>> INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det, > >> >>> applying LR flip to registration matrix. > >> >>> INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, > >> >>> applying LR flip to registration matrix. > >> >>> > >> >>> here is what I get from fsl_rigid_register: > >> >>> $Id: fsl_rigid_register,v 1.31 2011/03/02 20:16:39 nicks Exp $ > >> >>> Thu Nov 19 17:13:48 EST 2015 > >> >>> fieldmap0001_reg.nii > >> >>> Reference is nifti, not converting > >> >>> Input is nifti, not converting > >> >>> Output is nifti, not converting > >> >>> -------------------------------------- > >> >>> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap > >> >>> calling eval flirt.fsl -in ./fieldmap0001.hdr -out > >> >>> ./fieldmap0001_reg.hdr -bins 256 -cost corratio -searchrx -10 10 > >> >>> -searchry -10 10 -searchrz -10 10 -interp trilinear -dof 6 -ref > >> >>> ./epi.hdr -init initxfm.fslmat -omat ./fieldmap0001_reg.fslmat > >> >>> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap > >> >>> mri_copy_params --pulse fieldmap0001_reg.nii fieldmap0001.nii > >> >>> fieldmap0001_reg.nii > >> >>> only copying pulse parameters > >> >>> WARNING: volume sizes are different > >> >>> in_vol : 80, 80, 22 > >> >>> temp_vol : 64, 64, 64 > >> >>> WARNING: voxel sizes are different > >> >>> in_vol : 0.375, 0.375, 1.1 > >> >>> temp_vol : 0.546875, 0.546875, 0.546875 > >> >>> -------------------------------------- > >> >>> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap > >> >>> tkregister2_cmdl --targ epi.nii --mov fieldmap0001.nii --reg > >> >>> ./fsl_rigid_register.28592/reg.dat --fslreg > >> >>> fieldmap0001_reg.nii.fslmat --noedit > >> >>> tkregister_tcl > >> >>> > >> > /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full/tktools/tkregister2.tcl > >> >>> ---- FSL registration matrix -------- > >> >>> 0.987 -0.164 0.002 0.247; > >> >>> 0.157 0.943 -0.295 -5.691; > >> >>> 0.046 0.291 0.956 7.475; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> --------------------------------------- > >> >>> target volume epi.nii > >> >>> movable volume fieldmap0001.nii > >> >>> reg file ./fsl_rigid_register.28592/reg.dat > >> >>> LoadVol 0 > >> >>> ZeroCRAS 0 > >> >>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > >> >>> Diagnostic Level -1 > >> >>> INFO: loading target epi.nii > >> >>> INFO: target does not conform to COR format, so I'm going to > >> >>> reslice to COR. This will not affect the final registration. > >> >>> Ttarg: -------------------- > >> >>> -1.000 0.000 0.000 128.000; > >> >>> 0.000 0.000 1.000 -128.000; > >> >>> 0.000 -1.000 0.000 128.000; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> INFO: loading movable fieldmap0001.nii > >> >>> Tmov: -------------------- > >> >>> -0.547 0.000 0.000 17.500; > >> >>> 0.000 0.000 0.547 -17.500; > >> >>> 0.000 -0.547 0.000 17.500; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> mkheaderreg = 0, float2int = 0 > >> >>> FSLOUTPUTTYPE NIFTI > >> >>> fsl2TkReg: mov det = 0.163555, ref det = 0.154688 > >> >>> INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det, > >> >>> applying LR flip to registration matrix. > >> >>> INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, > >> >>> applying LR flip to registration matrix. > >> >>> ---- Input registration matrix (computed) -------- > >> >>> -0.987 0.046 -0.157 0.692; > >> >>> -0.002 0.956 0.295 -19.148; > >> >>> -0.164 -0.291 0.943 -0.998; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> --------------------------------------- > >> >>> ---- Input registration matrix -------- > >> >>> -0.987 0.046 -0.157 0.692; > >> >>> -0.002 0.956 0.295 -19.148; > >> >>> -0.164 -0.291 0.943 -0.998; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> Determinant -1 > >> >>> subject = subject-unknown > >> >>> RegMat --------------------------- > >> >>> 0.987 0.046 -0.157 0.692; > >> >>> 0.002 0.956 0.295 -19.148; > >> >>> 0.164 -0.291 0.943 -0.998; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> Cleaning up > >> >>> > >> >>> Started at Thu Nov 19 17:13:48 EST 2015 > >> >>> Ended at Thu Nov 19 17:13:50 EST 2015 > >> >>> > >> >>> fsl_rigid_register Done > >> >>> > >> >>> if I check the results here using tkmedit -f epi.nii -aux > >> >>> fieldmap0001_reg.nii > >> >>> the orientation of fieldmap0001_reg.nii is already wrong. > >> >>> > >> >>> here is what I get from mri_vol2vol: > >> >>> movvol fieldmap_rads.nii.gz > >> >>> targvol epi.nii > >> >>> outvol fieldmap_rads_reg.nii.gz > >> >>> regfile mag_2_mocovol.register.dat > >> >>> invert 0 > >> >>> tal 0 > >> >>> talres 2 > >> >>> regheader 0 > >> >>> noresample 0 > >> >>> interp trilinear (1) > >> >>> precision float (3) > >> >>> Gdiag_no -1 > >> >>> Synth 0 > >> >>> SynthSeed 1448209916 > >> >>> > >> >>> Final tkRAS-to-tkRAS Matrix is: > >> >>> 0.987 0.046 -0.157 0.692; > >> >>> 0.002 0.956 0.295 -19.148; > >> >>> 0.164 -0.291 0.943 -0.998; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> > >> >>> > >> >>> Vox2Vox Matrix is: > >> >>> 0.676 -0.108 -0.093 8.999; > >> >>> 0.112 0.646 0.586 -2.959; > >> >>> -0.002 -0.202 1.922 -16.003; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> > >> >>> Resampling > >> >>> Output registration matrix is identity > >> >>> INFO: wAriting registration matrix to > >> fieldmap_rads_reg.nii.gz.reg > >> >>> > >> >>> checking the result with > >> >>> tkregister2 --mov fieldmap_rads_reg.nii.gz --targ epi.nii --reg > >> >>> fieldmap_rads_reg.nii.gz.reg > >> >>> also yields the wrong orientation, obviously. > >> >>> > >> >>> In this case, I am changing the fieldmap to RIA orientation, > >> >>> although it is actually IPL; doing the same steps with the > >> >>> original IPL orientation gives the same faulty results. > >> >>> > >> >>> this is the code: > >> >>> > >> >>> tkregister2 --s rat \ > >> >>> --targ $epi \ > >> >>> --mov fieldmap0001.nii \ > >> >>> --reg mag_2_mocovol.register.dat \ > >> >>> --fslregout initxfm.fslmat \ > >> >>> --noedit \ > >> >>> --regheader \ > >> >>> --mov-orientation $fieldmap_orient \ > >> >>> --targ-orientation $epi_orient > >> >>> > >> >>> flirt_opts="-maxangle 10 -dof 6 -interp trilinear -bins 256 > >> -cost > >> >>> corratio" > >> >>> fsl_rigid_register -r $epi \ > >> >>> -i fieldmap0001.nii \ > >> >>> -o fieldmap0001_reg.nii \ > >> >>> -regmat mag_2_mocovol.register.dat \ > >> >>> -initxfm initxfm.fslmat \ > >> >>> ${flirt_opts} > >> >>> > >> >>> # apply registration to phase > >> >>> mri_vol2vol --mov fieldmap_rads.nii.gz --targ $epi --o > >> >>> fieldmap_rads_reg.nii.gz --reg mag_2_mocovol.register.dat > >> --trilin > >> >>> > >> >>> Any advice would be appreciated. > >> >>> Thanks! Caspar > >> >>> > >> >>> > >> >>> > >> >>> _______________________________________________ > >> >>> Freesurfer mailing list > >> >>> Freesurfer(a)nmr.mgh.harvard.edu > >> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> >>> 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 > >> >> > >> >> > >> >> 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(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/ > >> > > >> > > >> > > >> > >> > > > >

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fsl_rigid_register fails with wrong orientation
by Caspar M. Schwiedrzik 23 Nov '15

23 Nov '15

Hi! I am trying to align a mean EPI volume and a Bruker magnitude map from a fieldmap measurement using tkregister2, fsl_rigid_register and mri_vol2vol. Unfortunately, it seems that somewhere, most likely during fsl_rigid_register, the image orientation get scrambled, and the output has the wrong orientation. Here is what I get from* tkregister2:* target volume epi.nii movable volume fieldmap0001.nii reg file mag_2_mocovol.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target epi.nii Setting targ orientation to RIA INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fieldmap0001.nii Setting mov orientation to RIA Tmov: -------------------- -0.547 0.000 0.000 17.500; 0.000 0.000 0.547 -17.500; 0.000 -0.547 0.000 17.500; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -1.000 0.000 0.000 -0.587; 0.000 1.000 0.000 -2.150; 0.000 0.000 1.000 -2.188; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -1.000 0.000 0.000 -0.587; 0.000 1.000 0.000 -2.150; 0.000 0.000 1.000 -2.188; 0.000 0.000 0.000 1.000; Determinant -1 subject = rat RegMat --------------------------- 1.000 0.000 0.000 -0.587; 0.000 1.000 0.000 -2.150; 0.000 0.000 1.000 -2.188; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = 0.163555, ref det = 0.154688 INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det, applying LR flip to registration matrix. INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, applying LR flip to registration matrix. here is what I get from fsl_rigid_register: $Id: fsl_rigid_register,v 1.31 2011/03/02 20:16:39 nicks Exp $ Thu Nov 19 17:13:48 EST 2015 fieldmap0001_reg.nii Reference is nifti, not converting Input is nifti, not converting Output is nifti, not converting -------------------------------------- /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap calling eval flirt.fsl -in ./fieldmap0001.hdr -out ./fieldmap0001_reg.hdr -bins 256 -cost corratio -searchrx -10 10 -searchry -10 10 -searchrz -10 10 -interp trilinear -dof 6 -ref ./epi.hdr -init initxfm.fslmat -omat ./fieldmap0001_reg.fslmat /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap mri_copy_params --pulse fieldmap0001_reg.nii fieldmap0001.nii fieldmap0001_reg.nii only copying pulse parameters WARNING: volume sizes are different in_vol : 80, 80, 22 temp_vol : 64, 64, 64 WARNING: voxel sizes are different in_vol : 0.375, 0.375, 1.1 temp_vol : 0.546875, 0.546875, 0.546875 -------------------------------------- /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap tkregister2_cmdl --targ epi.nii --mov fieldmap0001.nii --reg ./fsl_rigid_register.28592/reg.dat --fslreg fieldmap0001_reg.nii.fslmat --noedit tkregister_tcl /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.987 -0.164 0.002 0.247; 0.157 0.943 -0.295 -5.691; 0.046 0.291 0.956 7.475; 0.000 0.000 0.000 1.000; --------------------------------------- target volume epi.nii movable volume fieldmap0001.nii reg file ./fsl_rigid_register.28592/reg.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target epi.nii INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fieldmap0001.nii Tmov: -------------------- -0.547 0.000 0.000 17.500; 0.000 0.000 0.547 -17.500; 0.000 -0.547 0.000 17.500; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = 0.163555, ref det = 0.154688 INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det, applying LR flip to registration matrix. INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, applying LR flip to registration matrix. ---- Input registration matrix (computed) -------- -0.987 0.046 -0.157 0.692; -0.002 0.956 0.295 -19.148; -0.164 -0.291 0.943 -0.998; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.987 0.046 -0.157 0.692; -0.002 0.956 0.295 -19.148; -0.164 -0.291 0.943 -0.998; 0.000 0.000 0.000 1.000; Determinant -1 subject = subject-unknown RegMat --------------------------- 0.987 0.046 -0.157 0.692; 0.002 0.956 0.295 -19.148; 0.164 -0.291 0.943 -0.998; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Nov 19 17:13:48 EST 2015 Ended at Thu Nov 19 17:13:50 EST 2015 fsl_rigid_register Done if I check the results here using tkmedit -f epi.nii -aux fieldmap0001_reg.nii the orientation of fieldmap0001_reg.nii is already wrong. here is what I get from mri_vol2vol: movvol fieldmap_rads.nii.gz targvol epi.nii outvol fieldmap_rads_reg.nii.gz regfile mag_2_mocovol.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1448209916 Final tkRAS-to-tkRAS Matrix is: 0.987 0.046 -0.157 0.692; 0.002 0.956 0.295 -19.148; 0.164 -0.291 0.943 -0.998; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: 0.676 -0.108 -0.093 8.999; 0.112 0.646 0.586 -2.959; -0.002 -0.202 1.922 -16.003; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity INFO: wAriting registration matrix to fieldmap_rads_reg.nii.gz.reg checking the result with tkregister2 --mov fieldmap_rads_reg.nii.gz --targ epi.nii --reg fieldmap_rads_reg.nii.gz.reg also yields the wrong orientation, obviously. In this case, I am changing the fieldmap to RIA orientation, although it is actually IPL; doing the same steps with the original IPL orientation gives the same faulty results. this is the code: tkregister2 --s rat \ --targ $epi \ --mov fieldmap0001.nii \ --reg mag_2_mocovol.register.dat \ --fslregout initxfm.fslmat \ --noedit \ --regheader \ --mov-orientation $fieldmap_orient \ --targ-orientation $epi_orient flirt_opts="-maxangle 10 -dof 6 -interp trilinear -bins 256 -cost corratio" fsl_rigid_register -r $epi \ -i fieldmap0001.nii \ -o fieldmap0001_reg.nii \ -regmat mag_2_mocovol.register.dat \ -initxfm initxfm.fslmat \ ${flirt_opts} # apply registration to phase mri_vol2vol --mov fieldmap_rads.nii.gz --targ $epi --o fieldmap_rads_reg.nii.gz --reg mag_2_mocovol.register.dat --trilin Any advice would be appreciated. Thanks! Caspar

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fMRI maps without clusters on ventricle
by stdp82＠virgilio.it 23 Nov '15

23 Nov '15

Hi list,I'm performing fcMRI-seed based by FS-FAST.After group comparison and Monte Carlo correction I obtained cortical and subcortical clusters in pos and neg maps.On subcortiacal maps, significant clusters at grf.th1.3.pos.sig.cluster.nii.gz showed some voxels on ventricle or white matter. At 3.pos.sig.cluster.nii.gz the maps are clearly defined.Thus, I'd like to delete voxel on white matter or ventricle to shows activation only on grey matter from grf.th1.3.pos.sig.cluster.nii.gz.Is it possible to do it?Thanks Stefano

2 1

sheered CT in tkregister2
by Borzello, Mia 23 Nov '15

23 Nov '15

Hi Freesurfers, I am trying to coregister with a high-res CT, but for some reason am getting a very sheered image when I am in tkregister. Should I use another CT? Thank you! 1) MG93 2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3) no error message, just a sheered image FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 'build-stamp.txt file does not exist! This appears to be a very old version of FreeSurfer! RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.3.1.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri

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creating ROIs for cortical thickness measurements
by Elissa Ash 23 Nov '15

23 Nov '15

Dear Freesurfers, I am new to freesurfer and I am trying to understand how to best perform a cortical thickness analysis for an ROI that is not pre-defined in freesurfer, such as the IFJ or V5. Should I create a surface ROI label using tksurfer (or freeview) or should I create an ROI in volume space? What is the difference? Which way is methodologically correct? Can I obtain the average cortical thickness for my ROI if it is created as a label? Also, is there a tutorial explaining how to draw an anatomical ROI that is not designated in either atlas, either as a label or as a volume? I would like to compare cortical thickness of my ROI to a behavioral measure in a group of subjects that were treated with TMS to this ROI. I have looked through the listserve and tutorials but I have not found my answer. Thank you, Elissa -- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center 6 Weizmann St. Tel Aviv 64239, Israel 972-3-6973698 fax: 972-3-695-0365

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How to create a 3g4v matrix
by nellie 23 Nov '15

23 Nov '15

Hi Freesurfer Experts, I’m a new user of Freesurfer, and I learn how to use this software mainly through Wiki. When I came to the step of using GLM to compare group differences, I was confused on the design of 3g4v matrix. In my study, there were 3 classes (A / B / C group) and 4 concomitant variables (gender, age, education, and Moca test score). It’s supposed to be 15 regressors in this design, but I don’t know how to use the numbers (like 1, -1, 0, 0.5, -0.5, etc.) to create a correct matrix. I wonder if you could provide a 3g4v matrix in detail for me. I’ll be grateful if you can help. I hope I’m not bothering you too much, and I’m looking for your reply. Best wishes, Li

2 1

Re: [Freesurfer] Issue with Talaraich in recon-all
by Amlung, Michael 23 Nov '15

23 Nov '15

We are getting an error with recon-all at the stage of Talairach slignment. The error is the one described on the known issues: Can't locate shellwords.pl in @INC. We are running perl5.18, so I downloaded and installed perl5.12 and changed the first line of mritotal as indicated on the ReleaseNotes. We are now getting a different error (pasted below). It appears I need to do manual Talairach alignment, but not entirely sure how to proceed with that (is there documentation available)? Any other suggestions? #@# Talairach Failure Detection Mon Nov 16 12:48:42 EST 2015 /Users/PBCAR/neuro/TNE/freesurfer_data/309/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach recon-all -s 309 exited with ERRORS at Mon Nov 16 12:48:42 EST 2015 ******************************************** Michael Amlung, Ph.D. Assistant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter Boris Centre for Addictions Research 100 West 5th Street Hamilton, Ontario L8N 3K7 Canada Telephone: (+1) 905-522-1155, ext. 39014 Email: amlungm(a)mcmaster.ca Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab) -----Original Message----- From: Amlung, Michael Sent: Monday, November 23, 2015 9:03 AM To: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Issue with Talaraich in recon-all I was hoping someone could help with this issue... ******************************************** Michael Amlung, Ph.D. Assistant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter Boris Centre for Addictions Research 100 West 5th Street Hamilton, Ontario L8N 3K7 Canada Telephone: (+1) 905-522-1155, ext. 39014 Email: amlungm(a)mcmaster.ca Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab)

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