All the MRI lectures until 07/22/11.

Presentation Details:
Title: Fundamentals of MRI, Module 5A: Artifacts, Dr. Dumoulin, 2011
Date: Friday, July 22, 2011
Time: 9:00 AM EDT
Duration: 00:50:29
Link: http://seraph.cchmc.org/mediasiteex/Viewer/?peid=cd1752073f7744ac85ee80202f962962


Fundamentals of MRI, Module 4_Parallel Imaging, Charles Dumoulin 2011 ( http://seraph.cchmc.org/mediasiteex/Viewer/?peid=2c5c0614ed4e45b0900fbfc2e2a7c5a5 )
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 7/8/2011
Air Time: 9:00 AM EDT
Duration: 48 Minutes

Fundamentals of MRI, Module 3_Imaging Principles, Charles Dumoulin 2011 ( http://seraph.cchmc.org/mediasiteex/Viewer/?peid=7d8599fb9333433098f391764a22734d )
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 7/1/2011
Air Time: 9:00 AM EDT
Duration: 1 Hour 3 Minutes 53 Seconds

Fundamentals of MRI, Module 2_Basic Physics, Charles Dumoulin 2011 ( http://seraph.cchmc.org/mediasiteex/Viewer/?peid=8683c292c3834652bc39063a811fb3f1 )
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 6/24/2011
Air Time: 9:00 AM EDT
Duration: 55 Minutes 33 Seconds
Module 1 not recorded, but here is last years lecture.

Fundamentals of MRI, Module 1_Quick Overview, Charles Dumoulin 2010 ( http://seraph.cchmc.org/mediasiteex/Viewer/?peid=33445793c98e46eca9da813194a9bac0 )
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 6/30/2010
Air Time: 9:00 AM EDT
Duration: 1 Hour

September 9 - Perfusion MR Imaging Methods and applications for imaging cerebral perfusion with Gadolinium contrast bolus injection or with RF labeling of inflowing blood (Arterial Spin Labeling) will be discussed.  A new method for combining simulataneous ASL and BOLD fMRI acquisitions will also be explained.   

All previous lectures are available online at:  http://groups/rad/dil/mri.htm

Note: Fundamentals of MRI, Module 1 2011 was not recorded, but you can view last year's presentation.

Fundamentals of MRI, Module 1_Quick Overview, Charles Dumoulin 2010
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 6/30/2010
Air Time: 9:00 AM EDT
Duration: 1 Hour

Fundamentals of MRI
Module 1_Quick Overview
Charles Dumoulin, PhD

Fundamentals of MRI, Module 2_Basic Physics, Charles Dumoulin 2011
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 6/24/2011
Air Time: 9:00 AM EDT
Duration: 55 Minutes 33 Seconds

Fundamentals of MRI Series
Module 2: Basic Physics

Fundamentals of MRI, Module 3_Imaging Principles, Charles Dumoulin 2011
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 7/1/2011
Air Time: 9:00 AM EDT
Duration: 1 Hour 3 Minutes 53 Seconds

Fundamentals of MRI, Module 3
Imaging Principles

Fundamentals of MRI, Module 4_Parallel Imaging, Charles Dumoulin 2011
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 7/8/2011
Air Time: 9:00 AM EDT
Duration: 48 Minutes

Fundamentals of MRI, Module 4
Parallel Imaging
Charles Dumoulin, PhD

Fundamentals of MRI, Module 4_Instrumentation, Chales Dumoulin, 2011
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 7/29/2011
Air Time: 7:45 AM EDT
Duration: 1 Hour 7 Minutes 26 Seconds


Fundamentals of MRI, Module 4: Instrumentation
Charles Dumoulin, PhD

Fundamentals of MRI, Module 5A: Artifacts, Dr. Dumoulin, 2011
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 7/22/2011
Air Time: 9:00 AM EDT
Duration: 50 Minutes 29 Seconds

Fundamentals of MRI, Module 5A: Artifacts
Charles Dumoulin, PhD

Fundamentals of MRI, Module 7_Flow Imaging, Charles Dumoulin
Presenter(s): Charles Dumoulin PhD, Radiology Department, IRC, Scientific Director
Type: On Demand
Air Date: 8/5/2011
Air Time: 9:00 AM EDT
Duration: 56 Minutes 28 Seconds


Fundamentals of MRI
Module 7: Flow Imaging
Charles Dumoulin, PhD

Fundamentals of MRI, Diffusion Tensor Imaging, Weihong Yuan, 2011
Presenter(s): Weihong Yuan PhD, Imaging Research Center, Neuroimaging Research Consortium
Type: On Demand
Air Date: 8/12/2011
Air Time: 9:00 AM EDT
Duration: 58 Minutes 20 Seconds


Fundamentals of MRI, Diffusion Tensor Imaging
Weihong Yuan, PhD

fMRI Physics and Physiology, Scott Holland, 2011
Presenter(s): Scott K Holland PhD, Professor of Radiology, Pediatrics, Otolaryngology, Neuroscience and Physics, Univ. Cincinnati, Imaging Research Center
Type: On Demand
Air Date: 8/19/2011
Air Time: 9:00 AM EDT
Duration: 50 Minutes 18 Seconds


fMRI Physics and Physiology
Scott Holland, PhD

Downloads: HowfMRIworks2011.ppt

fMRI Physics and Physiology Part 2, Scott Holland, 2011
Presenter(s): Scott K Holland PhD, Professor of Radiology, Pediatrics, Otolaryngology, Neuroscience and Physics, Univ. Cincinnati, Imaging Research Center
Type: On Demand
Air Date: 8/26/2011
Air Time: 9:00 AM EDT
Duration: 54 Minutes 18 Seconds


fMRI Physics and Physiology
Scott Holland, PhD

Downloads: HowfMRIworks2011-Part2.ppt

fMRI Physics and Physiology Part 3, Scott Holland, 2011
Presenter(s): Scott K Holland PhD, Professor of Radiology, Pediatrics, Otolaryngology, Neuroscience and Physics, Univ. Cincinnati, Imaging Research Center
Type: On Demand
Air Date: 9/2/2011
Air Time: 9:00 AM EDT
Duration: 25 Minutes 29 Seconds


fMRI Physics and Physiology
Scott Holland, PhD

Perfusion MR Imaging, Part 1, Scott Holland, 2011
Presenter(s): Scott K Holland PhD, Professor of Radiology, Pediatrics, Otolaryngology, Neuroscience and Physics, Univ. Cincinnati, Imaging Research Center
Type: On Demand
Air Date: 9/2/2011
Air Time: 9:00 AM EDT
Duration: 27 Minutes 3 Seconds


Perfusion MR Imaging
Part 1
Scott Holland, PhD

Perfusion MR Imaging, Part 2, Scott Holland, 2011
Presenter(s): Scott K Holland PhD, Professor of Radiology, Pediatrics, Otolaryngology, Neuroscience and Physics, Univ. Cincinnati, Imaging Research Center
Type: On Demand
Air Date: 9/9/2011
Air Time: 9:00 AM EDT
Duration: 49 Minutes 50 Seconds


Perfusion MR Imaging
Part 2
Scott Holland, PhD

Helped Hisako (a former colleague) with MEG data analysis problem

 yw_ft_test('01061792_EPI-SHORT-4KHz_20080317_47_60_03.ds',48,58,30,70,'MLT22');

processing channel { 'MLC11' 'MLC12' 'MLC13' 'MLC14' 'MLC15' 'MLC16' 'MLC17' 'MLC21' 'MLC22' 'MLC23' 'MLC24' 'MLC25' 'MLC31' 'MLC32' 'MLC41' 'MLC42' 'MLC51' 'MLC52' 'MLC53' 'MLC54' 'MLC55' 'MLC61' 'MLC62' 'MLC63' 'MLF11' 'MLF12' 'MLF13' 'MLF14' 'MLF21' 'MLF22' 'MLF23' 'MLF24' 'MLF25' 'MLF31' 'MLF32' 'MLF33' 'MLF34' 'MLF35' 'MLF41' 'MLF42' 'MLF43' 'MLF44' 'MLF45' 'MLF46' 'MLF51' 'MLF52' 'MLF53' 'MLF54' 'MLF55' 'MLF56' 'MLF61' 'MLF62' 'MLF63' 'MLF64' 'MLF65' 'MLF66' 'MLF67' 'MLO11' 'MLO12' 'MLO13' 'MLO14' 'MLO21' 'MLO22' 'MLO23' 'MLO24' 'MLO31' 'MLO32' 'MLO33' 'MLO34' 'MLO41' 'MLO42' 'MLO43' 'MLO44' 'MLO51' 'MLO52' 'MLO53' 'MLP11' 'MLP12' 'MLP21' 'MLP22' 'MLP23' 'MLP31' 'MLP32' 'MLP33' 'MLP34' 'MLP35' 'MLP41' 'MLP42' 'MLP43' 'MLP44' 'MLP45' 'MLP51' 'MLP52' 'MLP53' 'MLP54' 'MLP55' 'MLP56' 'MLP57' 'MLT11' 'MLT12' 'MLT13' 'MLT14' 'MLT15' 'MLT16' 'MLT22' 'MLT23' 'MLT24' 'MLT25' 'MLT26' 'MLT27' 'MLT31' 'MLT32' 'MLT33' 'MLT34' 'MLT35' 'MLT36' 'MLT37' 'MLT41' 'MLT42' 'MLT43' 'MLT44' 'MLT45' 'MLT46' 'MLT47' 'MLT51' 'MLT52' 'MLT53' 'MLT54' 'MLT55' 'MLT56' 'MLT57' 'MRC11' 'MRC12' 'MRC13' 'MRC14' 'MRC15' 'MRC16' 'MRC17' 'MRC21' 'MRC22' 'MRC23' 'MRC24' 'MRC25' 'MRC31' 'MRC32' 'MRC41' 'MRC42' 'MRC52' 'MRC53' 'MRC54' 'MRC55' 'MRC61' 'MRC62' 'MRC63' 'MRF11' 'MRF12' 'MRF13' 'MRF14' 'MRF21' 'MRF22' 'MRF23' 'MRF24' 'MRF25' 'MRF31' 'MRF32' 'MRF33' 'MRF34' 'MRF35' 'MRF41' 'MRF42' 'MRF43' 'MRF44' 'MRF45' 'MRF46' 'MRF51' 'MRF52' 'MRF53' 'MRF54' 'MRF55' 'MRF56' 'MRF61' 'MRF62' 'MRF63' 'MRF64' 'MRF65' 'MRF66' 'MRF67' 'MRO11' 'MRO12' 'MRO13' 'MRO14' 'MRO21' 'MRO22' 'MRO23' 'MRO24' 'MRO31' 'MRO32' 'MRO33' 'MRO34' 'MRO41' 'MRO42' 'MRO43' 'MRO44' 'MRO51' 'MRO52' 'MRO53' 'MRP11' 'MRP12' 'MRP21' 'MRP22' 'MRP23' 'MRP31' 'MRP32' 'MRP33' 'MRP34' 'MRP35' 'MRP41' 'MRP42' 'MRP43' 'MRP44' 'MRP45' 'MRP51' 'MRP52' 'MRP53' 'MRP54' 'MRP55' 'MRP56' 'MRP57' 'MRT11' 'MRT12' 'MRT13' 'MRT14' 'MRT15' 'MRT16' 'MRT21' 'MRT22' 'MRT23' 'MRT24' 'MRT25' 'MRT26' 'MRT27' 'MRT31' 'MRT32' 'MRT33' 'MRT34' 'MRT35' 'MRT36' 'MRT37' 'MRT41' 'MRT42' 'MRT43' 'MRT44' 'MRT45' 'MRT46' 'MRT47' 'MRT52' 'MRT53' 'MRT54' 'MRT55' 'MRT56' 'MRT57' 'MZC01' 'MZC02' 'MZC03' 'MZC04' 'MZF01' 'MZF02' 'MZF03' 'MZO01' 'MZO02' 'MZO03' 'MZP01' }
reading and preprocessing
reading and preprocessing trial 1 from 1
the input is raw data with 272 channels and 1 trials
processing trials
trial 1, frequency 1 (30.00 Hz), 1 tapers
trial 1, frequency 2 (35.00 Hz), 1 tapers
trial 1, frequency 3 (40.00 Hz), 1 tapers
trial 1, frequency 4 (45.00 Hz), 1 tapers
trial 1, frequency 5 (50.00 Hz), 1 tapers
trial 1, frequency 6 (55.00 Hz), 1 tapers
trial 1, frequency 7 (60.00 Hz), 1 tapers
trial 1, frequency 8 (65.00 Hz), 1 tapers
trial 1, frequency 9 (70.00 Hz), 1 tapers
reading layout from file CTF275.lay

function yw_ft_test(ds,begt,endt,lowfq,highfq,chanindx)
% Frequency analysis script sample for Hiskao
%---------------------------------------------------------------
% Copyright (C) 2011 Pediatric Neuroimage Research Center (PNRC)
% Last Modified by Yingying Wang 09-Sep-2011 14:30:00
% Contact information: yingying.wang@cchmc.org
% Phone: 513-636-3495
% Any comments and bug reports are very welcome
% Advisor: Dr. Scott K. Holland
%----------------------------------------------------------------
% How to use it
% For example, your data folder is c:\data\patient01.ds
% put this yw_ft_test.m file in the same folder with patient01.ds
% under c:\data\
% make sure that you change current work path to the c:\data\
% then run yw_ft_test with required variables
% ds: data folder ds name
% begt: start time in second
% endt: end time in second
% lowfq: low frequency limit
% highfq: high frequency limit
% chanindx: single channel you want to plot

% Reference: http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis
% http://fieldtrip.fcdonders.nl/reference/freqanalysis

% check input parameters, none or too many, pop out Error messages
if nargin ~= 6
  fprintf(['Oops, you forgot someting! \n',...
    'function illustration: yw_ft_test(ds,lowfreq,hifreq,startt,endt) \n',...
    'ds: Name of the dataset folder. e.g. patient01.ds \n',...
    'begt: start time in second \n',...
    'endt: end time in second \n',...
    'lowfq: low frequency limit \n',...
    'highfq: high frequency limit \n',...
    'chanindx: single channel you want to plot \n',...
    'This function generate the frequency plot for you. \n\n']);
  return
end

% get MEG data
% find the interesting segments of data
cfg = [];               % empty configuration
cfg.dataset = ds;
cfg.channel = 'MEG';    % defaults: read all MEG channels
% you can change this line to cfg.channel = 'gui'
% then a window will pop up and you can choose your channel
% graphic interface for channel selections
cfg.continuous  = 'yes';
dataFIC = ft_preprocessing(cfg);

% frequency analysis
cfg              = [];
cfg.output       = 'pow';
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = lowfq:5:highfq;
cfg.t_ftimwin    = 7./cfg.foi;  % 7 cycles per time window
cfg.toi          = begt:0.2:endt;
TFRhann7 = ft_freqanalysis(cfg, dataFIC);


% display the whole sensor space
cfg              = [];
cfg.xlim         = [begt endt];
cfg.ylim         = [lowfq highfq];
cfg.layout       = 'CTF275.lay';
figure(1);
ft_multiplotTFR(cfg, TFRhann7);

% display one channel
cfg              = [];
cfg.xlim         = [begt endt];
cfg.ylim         = [lowfq highfq];
cfg.channel      = chanindx;
figure(2);
ft_singleplotTFR(cfg, TFRhann7);

end

DTIquery binary package problem.

dtiquery: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory
go to /usr/lib and /usr/lib32
Then, use the following command.
$ ln -s libexpat.so.1 libexpat.so.0
Bingo!

DTIquery worked. (see pic)

Philips 3T scan

.PAR is like .hdr  (header)
.REC stores real data like .img

PAR to NII

/tmp/foo file:

05F003_B1
05M002_B1
05M003_B1
06F001_B1
06F011_B1
06M001_B1
06M005_B1
06M012_B1
07F002_B1
07F007_B1
07F009_B1
07F010_B1
07F024_B1
07M001_B1
07M005_B1
07M006_B1

$ for ds in `cat /tmp/foo`;do cd ${ds};3dPAR2AFNI.pl -n -s -o ~/tmp *.PAR;cd ../;done


*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 05M002_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.nii -time:zt 64                         33 12172.998ms zero -xFOV 131.308R-124.692L -yFOV 130.114A-125.886P -zFOV 35.832I-92.168S 3D:-1:0:128:128:2112:05M0                        02_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=2112 2D slices
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
++ 3D dataset written to disk
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 05M003_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.nii -time:zt 64                         33 12172.998ms zero -xFOV 132.021R-123.979L -yFOV 125.893A-130.107P -zFOV 52.876I-75.124S 3D:-1:0:128:128:2112:05M0                        03_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=2112 2D slices
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
++ 3D dataset written to disk
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
Use of uninitialized value $fileSize in numeric gt (>) at /home/yyw/abin/3dPAR2AFNI.pl line 319.
Skipping 06F001_B1_Reg_-_WIP_DTI_32dir_mimic_NWU_no_stab_031609_SENSE_10_2.PAR: The corresponding REC file is 0 byte                        s in length

*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 06F001_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.nii -time:zt 64                         33 12172.998ms zero -xFOV 136.396R-119.604L -yFOV 134.063A-121.937P -zFOV 64.466I-63.534S 3D:-1:0:128:128:2112:06F0                        01_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=2112 2D slices
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
++ 3D dataset written to disk
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
Use of uninitialized value $fileSize in numeric gt (>) at /home/yyw/abin/3dPAR2AFNI.pl line 319.
Skipping 06F011_B1_Reg_-_WIP_DTI_32dir_mimic_NWU_no_stab_031609_SENSE_10_2.PAR: The corresponding REC file is 0 byte                        s in length

*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 06F011_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.nii -time:zt 64                         33 12172.998ms zero -xFOV 134.012R-121.988L -yFOV 131.34A-124.66P -zFOV 44.628I-83.372S 3D:-1:0:128:128:2112:06F011                        _B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=2112 2D slices
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
++ 3D dataset written to disk
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (8.25).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 06M001_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.nii -time:zt 64                         8.25 12172.998ms zero -xFOV 133.015R-122.985L -yFOV 135.021A-120.979P -zFOV 47.952I-80.048S 3D:-1:0:128:128:528:06M                        001_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=528 2D slices
** Number of slices on command line   = 528
** Number of slices needed for -time: = 512
** Something is wrong with your command line!
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (6.703125).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 06M005_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.nii -time:zt 64                         6.703125 12172.998ms zero -xFOV 128R-128L -yFOV 146.373A-109.627P -zFOV 27.911I-100.089S 3D:-1:0:128:128:429:06M005                        _B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=429 2D slices
** Number of slices on command line   = 429
** Number of slices needed for -time: = 384
** Something is wrong with your command line!
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (9.796875).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 06M012_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_11_1.nii -time:zt 64                         9.796875 12172.998ms zero -xFOV 128R-128L -yFOV 124.564A-131.436P -zFOV 44.527I-83.473S 3D:-1:0:128:128:627:06M012_                        B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_11_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=627 2D slices
** Number of slices on command line   = 627
** Number of slices needed for -time: = 576
** Something is wrong with your command line!
Unable to open *.PAR for reading: No such file or directory.
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 07F007_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_12_1.nii -time:zt 64                         33 12172.998ms zero -xFOV 132.864R-123.136L -yFOV 129.946A-126.054P -zFOV 26.062I-101.938S 3D:-1:0:128:128:2112:07F                        007_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_12_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=2112 2D slices
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
++ 3D dataset written to disk
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 07F009_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.nii -time:zt 64                         33 12172.998ms zero -xFOV 130.88R-125.12L -yFOV 139.693A-116.307P -zFOV 43.619I-84.381S 3D:-1:0:128:128:2112:07F009                        _B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=2112 2D slices
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
++ 3D dataset written to disk
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 07F010_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_11_1.nii -time:zt 64                         33 12172.998ms zero -xFOV 133.622R-122.378L -yFOV 124.672A-131.328P -zFOV 28.198I-99.802S 3D:-1:0:128:128:2112:07F0                        10_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_11_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=2112 2D slices
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
++ 3D dataset written to disk
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (5.671875).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 07F024_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_11_1.nii -time:zt 64                         5.671875 12172.998ms zero -xFOV 134.289R-121.711L -yFOV 132.193A-123.807P -zFOV 27.662I-100.338S 3D:-1:0:128:128:36                        3:07F024_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_11_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=363 2D slices
** Number of slices on command line   = 363
** Number of slices needed for -time: = 320
** Something is wrong with your command line!
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (26.125).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 07M001_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.nii -time:zt 64                         26.125 12172.998ms zero -xFOV 128.749R-127.251L -yFOV 146.393A-109.607P -zFOV 28.621I-99.379S 3D:-1:0:128:128:1672:                        07M001_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=1672 2D slices
** Number of slices on command line   = 1672
** Number of slices needed for -time: = 1664
** Something is wrong with your command line!
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 07M005_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_12_1.nii -time:zt 64                         33 12172.998ms zero -xFOV 132.021R-123.979L -yFOV 125.128A-130.872P -zFOV 32.983I-95.017S 3D:-1:0:128:128:2112:07M0                        05_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_12_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=2112 2D slices
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
++ 3D dataset written to disk
*** WARNING: The number of volumes from the PAR header does not match the number of slices times the number of image                        s!
*** WARNING: Resetting the number of volumes to be the number of slices times the number of images (33).
to3d -session /home/yyw/tmp/  -skip_outliers -prefix 07M006_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.nii -time:zt 64                         33 12172.998ms zero -xFOV 130.516R-125.484L -yFOV 137.434A-118.566P -zFOV 79.094I-48.906S 3D:-1:0:128:128:2112:07M0                        06_B1_WIP_IRC19B_DTI_32dir_2x2x2_SENSE_10_1.REC
++ to3d: AFNI version=AFNI_2011_05_26_1457 (Aug 31 2011) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=12.172998s
++ Counting images:  total=2112 2D slices
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
++ 3D dataset written to disk

Daily logs

Update my AFNI version. @update.afni.binaries -defaults

Convert .PAR file to .NII  http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dPAR2AFNI.pl.html

DTI wiki (helpful for newbie like me):  http://www.topsupportweb.net/psywiki/index.php?title=NeuroWiki:Processing_DTI_%28FSL%29

On the road!

Something went wrong ... I need to check the gradient table with Weihong tomorrow.