Hi Freesurfer users,
My Name is Francisco Robles, from México City, and I am writing you to ask you a doubt about the selxavg3-sess process with FS-FAST. The error is the following: it seems like the TR from the analysis is 1.75 (specified in mkanalysis gui) and from data (but i dont know in waht file) is 1750 (like it is in milisecs), does anyone knows how can i edit the TR from data to put it similar with the TR from analysis?.
Thak you very much... the incomplete process is the following:
LINGUISTICA:/usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1> selxavg3-sess -s 001 -analysis m1-gamma-fwhm6 -overwrite -------------------------------------------------------------- selxavg3-sess logfile is /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/log/selxavg3-sess-bold-m1-gamma-fwhm6-090109121039.log -------------------------------------------------------------- ------------------------------------------- /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001 vie ene 9 12:10:39 CST 2009 anadir = /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/m1-gamma-fwhm6 analysis m1-gamma-fwhm6 alread exists for 001 ... reanalyzing (deleting old analysis) ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen.
< M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.336 (R2007a) January 29, 2007
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
>> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.2 2007/11/27 18:42:09 greve Exp $
outtop = /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1 Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 in-v-irr.mat 2 in-v-reg.mat 3 ini-v-0.mat 4 inr-v-0.mat 5 inr-v-ini.mat 6 pa-v-pr.mat 7 pai-v-0.mat 8 par-v-0.mat 9 par-v-pai.mat 10 pri-v-0.mat 11 prr-v-0.mat 12 prr-v-pri.mat 13 reg-v-irr.mat Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. nruns = 1 autostimdur = 1
outanadir = /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/m1-gamma-fwhm6 Found 39377/122880 (32.0) voxels in mask Creating Design Matrix Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. ntptot = 239, nX = 15, DOF = 224 XCond = 132.651 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.508299 (t=0.061196) 2 -0.25 -0.274155 (t=0.125188) 3 0 -0.0471794 (t=0.195066) 4 0.25 0.168481 (t=0.239998) 5 0.5 0.361722 (t=0.311806) AR1 Correction M: 0.0685 1.14384 Computing contrast matrices Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 1 in-v-irr J= 1 eff = 3.3 vrf = 3.3163 vrfffx = 3.3163 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 2 in-v-reg J= 1 eff = 3.6 vrf = 3.5874 vrfffx = 3.5874 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 3 ini-v-0 J= 1 eff = 11.1 vrf = 11.0570 vrfffx = 11.0570 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 4 inr-v-0 J= 1 eff = 7.3 vrf = 7.3329 vrfffx = 7.3329 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 5 inr-v-ini J= 1 eff = 5.6 vrf = 5.5884 vrfffx = 5.5884 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 6 pa-v-pr J= 1 eff = 4.3 vrf = 4.2514 vrfffx = 4.2514 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 7 pai-v-0 J= 1 eff = 10.1 vrf = 10.1026 vrfffx = 10.1026 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 8 par-v-0 J= 1 eff = 16.5 vrf = 16.5397 vrfffx = 16.5397 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 9 par-v-pai J= 1 eff = 7.1 vrf = 7.1292 vrfffx = 7.1292 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 10 pri-v-0 J= 1 eff = 16.4 vrf = 16.4187 vrfffx = 16.4187 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 11 prr-v-0 J= 1 eff = 10.4 vrf = 10.3983 vrfffx = 10.3983 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 12 prr-v-pri J= 1 eff = 7.4 vrf = 7.4063 vrfffx = 7.4063 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 13 reg-v-irr J= 1 eff = 3.3 vrf = 3.3480 vrfffx = 3.3480 r = 1.00 OLS Beta Pass run 1 t= 0.1 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. ERROR: TR mismatch between analysis and data analysis TR = 1.75, data TR = 1750
ERROR: fast_selxavg3() failed\n
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That actually means that the TR in the file is 1750000 ms! How was this file created? You can fix it with mri_convert f.nii f.nii --tr 1750
where f.nii is the raw fmri data file
doug
Francisco Robles wrote:
Hi Freesurfer users,
My Name is Francisco Robles, from México City, and I am writing you to ask you a doubt about the selxavg3-sess process with FS-FAST. The error is the following: it seems like the TR from the analysis is 1.75 (specified in mkanalysis gui) and from data (but i dont know in waht file) is 1750 (like it is in milisecs), does anyone knows how can i edit the TR from data to put it similar with the TR from analysis?.
Thak you very much... the incomplete process is the following:
LINGUISTICA:/usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1> selxavg3-sess -s 001 -analysis m1-gamma-fwhm6 -overwrite
selxavg3-sess logfile is /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/log/selxavg3-sess-bold-m1-gamma-fwhm6-090109121039.log
/usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001
vie ene 9 12:10:39 CST 2009 anadir = /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/m1-gamma-fwhm6 analysis m1-gamma-fwhm6 alread exists for 001 ... reanalyzing (deleting old analysis)
------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen.
< M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.336 (R2007a) January 29, 2007To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id:
fast_selxavg3.m,v 1.55.2.2 2007/11/27 18:42:09 greve Exp $ outtop = /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1 Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 in-v-irr.mat 2 in-v-reg.mat 3 ini-v-0.mat 4 inr-v-0.mat 5 inr-v-ini.mat 6 pa-v-pr.mat 7 pai-v-0.mat 8 par-v-0.mat 9 par-v-pai.mat 10 pri-v-0.mat 11 prr-v-0.mat 12 prr-v-pri.mat 13 reg-v-irr.mat Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. nruns = 1 autostimdur = 1
outanadir = /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/m1-gamma-fwhm6 Found 39377/122880 (32.0) voxels in mask Creating Design Matrix Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. ntptot = 239, nX = 15, DOF = 224 XCond = 132.651 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.508299 (t=0.061196) 2 -0.25 -0.274155 (t=0.125188) 3 0 -0.0471794 (t=0.195066) 4 0.25 0.168481 (t=0.239998) 5 0.5 0.361722 (t=0.311806) AR1 Correction M: 0.0685 1.14384 Computing contrast matrices Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 1 in-v-irr J= 1 eff = 3.3 vrf = 3.3163 vrfffx = 3.3163 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 2 in-v-reg J= 1 eff = 3.6 vrf = 3.5874 vrfffx = 3.5874 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 3 ini-v-0 J= 1 eff = 11.1 vrf = 11.0570 vrfffx = 11.0570 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 4 inr-v-0 J= 1 eff = 7.3 vrf = 7.3329 vrfffx = 7.3329 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 5 inr-v-ini J= 1 eff = 5.6 vrf = 5.5884 vrfffx = 5.5884 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 6 pa-v-pr J= 1 eff = 4.3 vrf = 4.2514 vrfffx = 4.2514 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 7 pai-v-0 J= 1 eff = 10.1 vrf = 10.1026 vrfffx = 10.1026 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 8 par-v-0 J= 1 eff = 16.5 vrf = 16.5397 vrfffx = 16.5397 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 9 par-v-pai J= 1 eff = 7.1 vrf = 7.1292 vrfffx = 7.1292 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 10 pri-v-0 J= 1 eff = 16.4 vrf = 16.4187 vrfffx = 16.4187 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 11 prr-v-0 J= 1 eff = 10.4 vrf = 10.3983 vrfffx = 10.3983 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 12 prr-v-pri J= 1 eff = 7.4 vrf = 7.4063 vrfffx = 7.4063 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 13 reg-v-irr J= 1 eff = 3.3 vrf = 3.3480 vrfffx = 3.3480 r = 1.00 OLS Beta Pass run 1 t= 0.1 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. ERROR: TR mismatch between analysis and data analysis TR = 1.75, data TR = 1750
ERROR: fast_selxavg3() failed\n
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Francisco Robles