Andy: Update from Wiki

2006-12-18T13:35:17Z

Update from Wiki

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* DTMRI vs. DTMRI_Matlab:
** [[DBP:Harvard:Software:Testing:DTI:Slicer:DTMRIvsDTMRIMatlab|Table]]
** Updated table (12/13/05): [[Media:DTMRI_comparison.xls|Media:DTMRI_comparison.xls]]
* DTMRI vs LSDI (ADC/Trace):
** [[DBP:Harvard:Software:Testing:DTI:Slicer:DTMRIvsLSDI_ADC|Table]]
** Updated table (12/13/05): [[Media:ADC.xls|Media:ADC.xls]]
* DTMRI vs. LSDI (FAI):
** [[DBP:Harvard:Software:Testing:DTI:Slicer:DTMRIvsLSDI_FAI|Table]]
** Updated table (12/13/05): [[Media:FAI.xls|Media:FAI.xls]]

 

 '''11/15/05''' More comparison of LSDIrecon vs. DTMRI

* Table with new testing data [http://pnl.bwh.harvard.edu/namic/chart.html here]
* Notes:
** Using Matlab scripts to compute this data appears to be safe, except for:
**# LSDIrecon DICOM files
**# Marc: calculating Mode with Matlab?
** ADC vs. Trace: Why the 251X difference?
*** NRRD headers give same results as DTMRI
** Can we use Matlab scripts on DTMRI scalar measures for our studies?
*** Would this mean not using LSDIrecon?

 

'''9/28/05''' Comparison of LSDIrecon vs. DTMRI

* Trace values are very small compared to ADC (may be a Scale Factor issue)
** We have tried testing this using NRRD header data (as suggested), but we need Gordon to confirm that we are doing it correctly. Next week...
* The "Include Zeros" button in slicer_lmi DOES work correctly.
** FAI and trace values are NOT different when including zeros.
*** Does this mean there are no actual "zero" values?
** Now that the button is there, do we want to keep including zeros?
*** Currently the default is set to include zeros in slicer_lmi, but the function does not exist in slicer24, etc.

 

 '''9/21/05''' Comparison of LSDIrecon vs. DTMRI, using FA & ADC/trace as test variables. Also a comparison of the "include zeros" functionality that Steve included.

# Differences in FA are always <0.25% (usually much smaller)
# Raul removed the Scale Factor, which seems to make Trace values very small compared to ADC
#* BUT DTMRI trace values are still consistent (in relative terms) with LSDIrecon ADC, i.e., always 250X smaller
# Including zeros (Steve's added button) did not make a difference. Does this mean 1) there is no difference, or 2) the "include zeros" button does not work?

[[Image:Scalar_measures_test_9-21-05.jpg|[[Image:1300px-Scalar_measures_test_9-21-05.jpg]]]]

 

 '''6/14/05:''' Comparison of LSDIrecon output (FA and Diffusivity) to DTMRI scalar volumes

# Differences in FA are small (typically less than 0.25%), but why are there differences?
# Differences in ADC/Trace exist, probably due to the Scale Factor. Mark has emailed Raul about this.
# Can other measures be compared between LSDIrecon and DTMRI?
#* LSDIrecon outputs: AAI, ADC, DWI, FAI, FIL, L1x, L1y, L1z, RAI, T2W, VAI
#* See a [[DBP:Harvard:Software:Testing:DTI:Slicer:LSDIrecon|description]] of Stephan's LSDIrecon program (from /projects/schiz/software/bin/LSDIrecon.HOWTO, 6/15/05, but is this an older version of the file, 2003?)
# ''Note''<nowiki>: Diffusion images were sagittally acquired, and the labelmap used was Mark's manual corpus callosum drawings </nowiki>

[[Image:6-14-05.jpg|[[Image:1000px-6-14-05.jpg]]]]

 

'''6/1/05:''' Sylvain and Mark met with Stephan a couple weeks ago to discuss the slice corruption problem with the lsdi2dwi script and DICOM cases (see notes from 5/13/05). Stephan discovered the source of the problem: the swab function behaves slightly differently under Linux and SUN.

# Stephan fixed the problem
# Sylvain implemented the code in the lsdi2dwi script
# Mark confirmed that the new script is reliable.
#* '''It is now safe to use the lsdi2dwi-all.pl script on DICOM cases.'''

 '''5/20/05:''' Below is the table confirming that Gordon's matlab scripts accurately differentiate Fermi-filtered from non-filtered cases.

* '''NOTE:''' T2W or DWI must be available to use this method.

 ''Notes for this table:''

# "Fermi filter" column was determined from Gordon's images, and confirmed using the test data below.
# Note that for highlighted cases, data in the "original .pic file" column was NOT filtered, and results are different from data using the Fermi-filtered lsdi2dwi script.

[[Image:LSDItest_5-20-05.jpg|[[Image:600px-LSDItest_5-20-05.jpg]]]]

 

 '''5/18/05:''' Gordon's [http://lmi.bwh.harvard.edu/~gk/fermi-test/ results]

 '''5/17/05:''' Erin and Mark found out that a majority of cases were potentially reconstructed before Stephan's LSDIrecon v1.3 was implemented, so they are working with Gordon on a method to retroactively determine whether cases were reconstructed with a Fermi filter.

* Question for Stephan: What were the exact dates that changes in LSDIrecon were created?

 '''5/13/05:''' Sylvain modified the lsdi2dwi-all.pl script, and Erin & Mark compared the output of this script with the original versions of the LSDIrecon scripts. The output table is below.

 ''Important notes/summary:''

# The lsdi2dwi-all.pl script is (as of now) reliable for '''GENESIS CASES ONLY'''
# Two problems were discovered regarding the use of lsdi2dwi-all.pl script with DICOM cases:
#* Output is in Little Endian format
#* Several slices in each case become corrupt, leading to slight changes in FA/ADC values (see highlighted cases below)
# We will once again recruit help from Stephan to fix the problem of using this new script with DICOM cases.
# '''For now, it is ok to use the lsdi2dwi-all.pl script WITH GENESIS CASES ONLY. DO NOT ANALYZE DICOM CASES UNTIL FURTHER NOTICE!'''

 ''In the table below:''

* CB = Cingulum Bundle
* caseD00760 (highlighted) is DICOM

[[Image:LSDItest_5-13-05.jpg|[[Image:700px-LSDItest_5-13-05.jpg]]]]

 

 '''5/11/05:''' Mark and Marek met with Stephan Meier and identified one source of the differences found in the LSDIrecon scripts.

* Data in /projects/schiz/diff/chronic/males was obtained using either LSDIrecon version 1.2 or 1.3, which differ in the use of a Fermi filter in the latter version
* It is unclear which cases were run with and without the Fermi filter, and it will be difficult to determine this in most cases
* It has been proposed that anyone using data in /projects/schiz/diff/chronic/males in the past 2 years should re-analyze their data

 '''5/11/05:''' Stephan also brought up the issue of a threshold used in his LSDIrecon scripts, which could also change numbers slightly.

 The following is a copy of the parameters in the LSDIrecon_par file:

* 1.3 # DO NOT CHANGE (LSDIrecon version)
* 1 # parameter file: 0=long, 1=short for LSDI, 2=short for other
* '''1 # Fermi filter in read direction: 0=off, 1=on'''
* 1 # correct missing lines: 0=no, 1=normal, 2=strong
* 2 # correct eddy current distortion: 0=no, 1=yes, 2=yes incl. NEX
* '''-10 # clipping threshold (<0 noise multiple, =0 none, >0 absolute)'''
* 1000 # b-value for reconstructed DWI, 0=maximum b-value
* 1 0.2 2.2 0.4 -0.3 0.5 0.2 # fit order (order: >0 constant amplitudes, <0 tensor amplitudes), min ADC1, max ADC1, step ADC1, min ADC2, max ADC2, step ADC2
* 1 # data type: 0=Signa 5.4; 1=5.6, 5.7, LX
* 1 # output: 0=nothing (for testing), 1=basic, 2=basic with header, 3=everything, 4=everything with header
* ./ # Path for output files, use ./ for local directory
* test # Prefix for output file names
* ./ # Path for input files, use ./ for local directory
* 0 # nr of images to offset during autoloading (usually 0)

 

 

'''4/25/05:''' The DTMRI module in slicer_lmi now produces more reliable results (see below).

* A DICOM case is now included (caseD00760)
* DTMRI now gives results similar to the lsdi2dwi-all.pl script (but not exactly the same in all cases?)
* We must now determine how to use the "Scale Factor" to report correct ADC/Trace values
* The problem still exists of why the new lsdi2dwi-all.pl gives slightly different results from Stephan's old lsdirecon script (located in /projects/schiz/software/bin)

 [[Image:TestBed_4-25-05.jpg|[[Image:1100px-TestBed_4-25-05.jpg]]]]

 

 

'''4/20/05:''' DTI data was obtained using 3 different "background" data sets:

* 1) Stephan's "old" LSDIrecon scripts
* 2) the new lsdi2dwi-all.pl script created by Sylvain and Stephan
* 3) tensor data, by converting DWI data and creating Scalar volumes, then casting float --> short to mask using labelmaps

[[Image:TestBed_4-19-05_150.jpg|[[Image:850px-TestBed_4-19-05_150.jpg]]]]

Notes:

* labelmaps were of the cingulum bundle used in Marek's study
* both cases shown were obtained in Genesis format
** caseD2 acquired 1/9/00
** caseD0667 acquired 7/19/03

DBP:Harvard:Software:Testing:DTI:Slicer - Revision history

Andy: Update from Wiki