External Email - Use Caution Hi Douglas
Just checking in to see if you had any insight into my issue? Thanks! Tiffany On Apr 2, 2020, at 5:57 PM, Tiffany Bell <tiffany.b...@ucalgary.ca<mailto:tiffany.b...@ucalgary.ca>> wrote: External Email - Use Caution When I try with fsl 6.0 I get: gh907107@neurodebian-1022:/storage/gold/cinn/2013/neuroade/LTFI_Analysis$ flirt -ref LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.fsl.mat -init LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch -o LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/outvol.fslregister.nii error: inv(): matrix appears to be singular inv(): matrix appears to be singular When I try with fsl 5.0.9 I get: gh907107@neurodebian-1022:/storage/gold/cinn/2013/neuroade/LTFI_Analysis$ flirt -ref LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.fsl.mat -init LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch -o LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/outvol.fslregister.nii terminate called after throwing an instance of 'NEWMAT::SingularException' Aborted Thanks! ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> Sent: April 2, 2020 3:01 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Issue with tkregister command Hmm, not sure. It could be the version of flirt that we are distributing. Can you try the command below using flirt instead of flirt.fsl ? /storage/gold/cinn/2013/neuroade/LTFI_Analysis flirt.fsl -ref LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.fsl.mat -init LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch -o LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/outvol.fslregister.nii On 4/2/2020 1:18 PM, Tiffany Bell wrote: External Email - Use Caution Thank you for your quick response. I've updated the command but now I get a new error (see below for full output) terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt Any thoughts? I have tried with fsl5.0.9 and fsl6.0 Thanks! gh907107@neurodebian-1022:/storage/gold/cinn/2013/neuroade/LTFI_Analysis$ reg-feat2anat --feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02 FeatDir is LTFI_FEAT_PE_FB_R1/LTFI_02.feat template volume is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz log file is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/reg-feat2anat.log Thu 2 Apr 18:13:05 BST 2020 /storage/gold/cinn/2013/neuroade/LTFI_Analysis /usr/local/freesurfer/bin/reg-feat2anat --feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02 Linux neurodebian-1022 4.4.0-165-generic #193-Ubuntu SMP Tue Sep 17 17:42:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux example_func ras_good_flag 1 ------------------------------------------------------- Initializing exf2anat with header tkregister2_cmdl --targ /storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz --mov LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz --reg LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit target volume /storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz movable volume LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz reg file LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/anat2exf.register.dat.init LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $ Diagnostic Level -1 INFO: loading target /storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz Tmov: -------------------- -1.79688 0.00000 0.00000 115.00000; 0.00000 0.00000 1.79985 -53.99551; 0.00000 -1.79688 0.00000 115.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.00000 0.00000 0.00000 2.10062; 0.00000 -0.55915 0.82907 -27.95589; 0.00000 -0.82907 -0.55915 7.65067; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.00000 0.00000 0.00000 2.10062; 0.00000 -0.55915 0.82907 -27.95589; 0.00000 -0.82907 -0.55915 7.65067; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.00000 0.00000 0.00000 2.10062; 0.00000 -0.55915 0.82907 -27.95589; 0.00000 -0.82907 -0.55915 7.65067; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -5.81129, ref det = -1 fslregister --s LTFI_02 --reg LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/anat2exf.register.dat --mov LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask.mgz --maxangle 90 --initfslmat LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp --out LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz Log file is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/anat2exf.register.dat.fslregister.log Thu 2 Apr 18:13:05 BST 2020 --s LTFI_02 --reg LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/anat2exf.register.dat --mov LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask.mgz --maxangle 90 --initfslmat LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp --out LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz $Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $ neurodebian-1022 Linux neurodebian-1022 4.4.0-165-generic #193-Ubuntu SMP Tue Sep 17 17:42:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /storage/gold/cinn/2013/neuroade/LTFI_Analysis mri_convert /storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert /storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/refvol.fslregister.nii $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/refvol.fslregister.nii... -------------------------------------- /storage/gold/cinn/2013/neuroade/LTFI_Analysis mri_convert LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0 mri_convert LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz... TR=812.50, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.829069, 0.559146) k_ras = (0, -0.559146, 0.829069) keeping frame 0 writing to LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/movvol.fslregister.nii... Mov determinant is -5.81129 Thu 2 Apr 18:13:07 BST 2020 /storage/gold/cinn/2013/neuroade/LTFI_Analysis flirt.fsl -ref LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.init.fsl.mat Thu 2 Apr 18:13:15 BST 2020 /storage/gold/cinn/2013/neuroade/LTFI_Analysis flirt.fsl -ref LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.fsl.mat -init LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch -o LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/tmp/outvol.fslregister.nii terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: March 31, 2020 10:12 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Issue with tkregister command I think this is a bug. Can you try this version? https://gate.nmr.mgh.harvard.edu/safelinks/greve/reg-feat2anat copy it to $FREESURFER_HOME/bin and run chmod a+x $FREESURFER_HOME/bin/reg-feat2anat On 3/31/2020 11:46 AM, Tiffany Bell wrote: External Email - Use Caution Hello I am trying to transform a free surfer segmentation to functional space using reg-feat2anat but I get the error tkregister2_cmdl_cmdl: Command not found. I am running freesufer on linux through a virtual machine. See below for the full command and output. Any help would be greatly appreciated. reg-feat2anat --feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02 FeatDir is LTFI_FEAT_PE_FB_R1/LTFI_02.feat template volume is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz log file is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/reg-feat2anat.log Thu 26 Mar 17:17:56 GMT 2020 /storage/gold/cinn/2013/neuroade/LTFI_Analysis /usr/local/freesurfer7/freesurfer/bin/reg-feat2anat --feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02 Linux neurodebian-1022 4.4.0-165-generic #193-Ubuntu SMP Tue Sep 17 17:42:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux example_func ras_good_flag 1 ------------------------------------------------------- Initializing exf2anat with header tkregister2_cmdl_cmdl --targ /storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz --mov LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz --reg LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit tkregister2_cmdl_cmdl: Command not found. Many Thanks Tiffany ------------------------------------------------------ Tiffany Bell, PhD Postdoctoral Associate Cumming School of Medicine University of Calgary Alberta Children’s Hospital 2888 Shaganappi Trail, NW Calgary, AB T3B 6A8 (E) tiffany.b...@ucalgary.ca<mailto:tiffany.b...@ucalgary.ca> (T) 403-955-2970 www.kidsmigraine.info<http://www.kidsmigraine.info/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
