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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: March 31, 2020 10:12 AM
To: freesurfer@nmr.mgh.harvard.edu <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.bell@ucalgary.ca
(T) 403-955-2970

www.kidsmigraine.info



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