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, 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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