From ce72e84a7b01c92049728cce06ab32efccb93dd1 Mon Sep 17 00:00:00 2001 From: mezera Date: Sun, 22 Feb 2015 11:24:12 +0200 Subject: [PATCH 1/5] Update README.md more info about running with nifti --- README.md | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 82 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index ae748c3..141e26f 100644 --- a/README.md +++ b/README.md @@ -44,6 +44,17 @@ For more information please contact - Parallel computing environment (e.g., Sun Grid Engine) - *Not required, but it will make a big difference for running time.* + Optional: + + You can convert your dicom to nifti: + We use code that was developed for the NIMS project. (https://scitran.stanford.edu/nims/) + This code allows an automatic way to make nifti and also save the hdr info. + https://registry.hub.docker.com/u/vistalab/nimsdata/ + You can also find the code they use inside. + +It also an option to you different nifti files. See details below. + + ####Matlab code#### mrQ requires the following openly distributed code repositories: @@ -76,11 +87,17 @@ A modified version of this code is integrated within the mrQ software. GE scanner’s should change the scanner default by editing the a_gzrf0 cv: a_gzrf0=0 3. Use fat suppression. Fat suppression should be spatial-spectral to avoid any slice-selective imperfections. Note: This is the default with GE scanners when slices are less than 4mm thick. -##Scanner dicom types## +##Scanner dicom types and Nifti## The mrQ software was built around GE dicoms. It is possible that different vendors have different conventions in saving dicom information (e.g., header information, data ordering). We are currently working on making the code compatible with different vendor’s dicom conventions. Please let us know if you experience any issues with reading dicoms when using the software. +Nifti: + +If you use the NIMS convertor to make a nifti your file will have all the hdr information and you don’t need the dicoms. + +if you convert the dicom to nifti yourself you will need to add the hdr info (see example below). + ##Data organization## ####Follow these guidelines when organizing your data:#### @@ -117,6 +134,70 @@ mrQ=mrQ_Set(mrQ,'sub','Examp') % run mrQ_run(mrQ.name) ``` +Running with nifti: + +using nifti by NIMS (and Later versions (>V.1) of mrQ) +```matlab +% create mrQ stricture and define the datadir where the nifti are saved and outdir where mrQ output will be saved. +mrQ = mrQ_Create(dataDir,[],outDir); +% One can set many different fit properties by mrQ_set.m +% +% get the image and hdr info form the nifti +mrQ = mrQ_arrangeData_nimsfs(mrQ); +% run it +mrQ_run(mrQ.name) +``` +using diiffrent nifti NOT by NIMS (and Later versions (>V.1) of mrQ) +```matlab +% create mrQ stricture and define the datadir where the nifti are saved and outdir where mrQ output will be saved. +mrQ = mrQ_Create(dataDir,[],outDir); +% Onecan set many different fit properties by mrQ_set.m +% +% Make a structure of images and hdr info of the the nifti +% define the SEIR hdr info: +% +% mrQ.RawDir is the location where the nifti are saved +inputData_spgr.rawDir =mrQ.RawDir; +% +% A list of nifti names (a unique string from the names is enough) +inputData_spgr.name={'0009' '0010' '0011' '0012'}; +% +% the TR of each nifti in the list (msec) +inputData_spgr.TR=[12 12 12 12]; +% +% The TE of each nifti in the list (msec) +inputData_spgr.TE=[2.27 2.27 2.27 2.27]; +% +% The flip angle of each nifti in the list (degree) +inputData_spgr.flipAngle=[4 10 20 30]; +% +% The field strength of each nifti in the list (Tesla) +inputData_spgr.fieldStrength=[3 3 3 3]; +% +% define the SEIR hdr info: +% +% mrQ.RawDir is the location where the nifti are saved +inputData_seir.rawDir=mrQ.RawDir; +% +% A list of nifti names (a unique string from the names is enough) +inputData_seir.name={ '0005' '0006' '0007' '0008'}; + +% the TR of each nifti in the list (msec) +inputData_seir.TR=[3000 3000 3000 3000 ]; + +% The TE of each nifti in the list (msec) +inputData_seir.TE=[49 49 49 49]; + +% The inversion time of each nifti in the list (msec) +inputData_seir.IT=[ 50 400 1200 2400]; + +% add the nifti info to the mrQ stracture +mrQ = mrQ_arrangeData_nimsfs(mrQ,inputData_spgr,inputData_seir); +% +%run it +mrQ_run(mrQ.name) +``` + ##Versions## Version 1 (v.1) is the code to replicate that was used in Nature medicine mezer at. el. 2013 article: https://github.com/mezera/mrQ/tree/v1.0 From 66831dd21a32e0cbdf08d3666da78825bc707e65 Mon Sep 17 00:00:00 2001 From: mezera Date: Sun, 22 Feb 2015 11:27:18 +0200 Subject: [PATCH 2/5] Update README.md --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 141e26f..516189e 100644 --- a/README.md +++ b/README.md @@ -47,9 +47,10 @@ For more information please contact Optional: You can convert your dicom to nifti: - We use code that was developed for the NIMS project. (https://scitran.stanford.edu/nims/) - This code allows an automatic way to make nifti and also save the hdr info. - https://registry.hub.docker.com/u/vistalab/nimsdata/ + We use code that was developed for the NIMS project: (https://scitran.stanford.edu/nims/). + + This code allows an automatic way to make nifti and also save the hdr info: + https://registry.hub.docker.com/u/vistalab/nimsdata/ . You can also find the code they use inside. It also an option to you different nifti files. See details below. From 5b08c01a3bf8992467939b2885ca2f2b99e21b8b Mon Sep 17 00:00:00 2001 From: mezera Date: Sun, 22 Feb 2015 11:32:11 +0200 Subject: [PATCH 3/5] Update README.md --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 516189e..8b012bd 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,10 @@ and the following patent application >Improved methods for detecting abnormalities in soft tissue using magnetic resonance imaging (MRI),USSN 61/437,587 +For application see: + +Yeatman JD,Wandell BA,Mezer A. Lifespan maturation and degeneration of human brain white matter. Nature Communications ,2014. http://www.nature.com/ncomms/2014/140917/ncomms5932/abs/ncomms5932.html + For more information please contact >avivmezer@gmail.com From 8eabdfdf7fc872b358c39c70f4eb522805a88c14 Mon Sep 17 00:00:00 2001 From: mezera Date: Sun, 22 Feb 2015 11:33:03 +0200 Subject: [PATCH 4/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8b012bd..cfc2c2b 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ and the following patent application For application see: -Yeatman JD,Wandell BA,Mezer A. Lifespan maturation and degeneration of human brain white matter. Nature Communications ,2014. http://www.nature.com/ncomms/2014/140917/ncomms5932/abs/ncomms5932.html +>Yeatman JD,Wandell BA,Mezer A. Lifespan maturation and degeneration of human brain white matter. Nature Communications ,2014. http://www.nature.com/ncomms/2014/140917/ncomms5932/abs/ncomms5932.html For more information please contact From acea03fde8c60d9c08664a7b1428c03dfc53d7d1 Mon Sep 17 00:00:00 2001 From: aviv mezer Date: Thu, 28 May 2015 12:58:35 +0300 Subject: [PATCH 5/5] cleaning Dir --- {OLDVer/SPGR => SPGR}/.svn/all-wcprops | 0 {OLDVer/SPGR => SPGR}/.svn/entries | 0 {OLDVer/SPGR => SPGR}/SPGR_HLF/.svn/all-wcprops | 0 {OLDVer/SPGR => SPGR}/SPGR_HLF/.svn/entries | 0 {OLDVer/SPGR => SPGR}/SPGR_HLF/.svn/text-base/mrQ_HLF.m.svn-base | 0 {OLDVer/SPGR => SPGR}/SPGR_HLF/.svn/text-base/mrQ_VIP.m.svn-base | 0 {OLDVer/SPGR => SPGR}/SPGR_HLF/mrQ_HLF.m | 0 {OLDVer/SPGR => SPGR}/SPGR_HLF/mrQ_VIP.m | 0 {OLDVer/SPGR => SPGR}/SPGR_HLF/mrQ_VIP_n.m | 0 {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/all-wcprops | 0 {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/entries | 0 {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/text-base/errT1PD.m.svn-base | 0 .../SPGR => SPGR}/SPGR_T1/.svn/text-base/mrQ_fitT1M0.m.svn-base | 0 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SPGR}/SPGR_pre/.svn/all-wcprops | 0 {OLDVer/SPGR => SPGR}/SPGR_pre/.svn/entries | 0 .../SPGR_pre/.svn/text-base/mrQ_calculateCoilWeights.m.svn-base | 0 .../SPGR => SPGR}/SPGR_pre/.svn/text-base/mrQ_initSPGR.m.svn-base | 0 .../SPGR_pre/.svn/text-base/mrQ_multicoilWeighting.m.svn-base | 0 {OLDVer/SPGR => SPGR}/SPGR_pre/.svn/tmp/mrQ_initSPGR.m.tmp | 0 {OLDVer/SPGR => SPGR}/SPGR_pre/mrQ_calculateCoilWeights.m | 0 {OLDVer/SPGR => SPGR}/SPGR_pre/mrQ_initSPGR.m | 0 {OLDVer/SPGR => SPGR}/SPGR_pre/mrQ_multicoilWeighting.m | 0 177 files changed, 0 insertions(+), 0 deletions(-) rename {OLDVer/SPGR => SPGR}/.svn/all-wcprops (100%) rename {OLDVer/SPGR => SPGR}/.svn/entries (100%) rename {OLDVer/SPGR => SPGR}/SPGR_HLF/.svn/all-wcprops (100%) rename {OLDVer/SPGR => SPGR}/SPGR_HLF/.svn/entries (100%) rename {OLDVer/SPGR => SPGR}/SPGR_HLF/.svn/text-base/mrQ_HLF.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_HLF/.svn/text-base/mrQ_VIP.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_HLF/mrQ_HLF.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_HLF/mrQ_VIP.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_HLF/mrQ_VIP_n.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/all-wcprops (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/entries (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/text-base/errT1PD.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/text-base/mrQ_fitT1M0.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/text-base/mrQ_fitT1PD_LSQ.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/text-base/mrQ_fitT1PD_SGE.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/text-base/mrQfit_T1M0_ver2.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/.svn/tmp/mrQ_fitT1PD_LSQ.m.tmp (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/all-wcprops (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/entries (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/text-base/errB1PD.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_NLANTS_warp_SPGR2EPI_RB.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_RB_ANTS_warp_EPI2SPGR.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_alignSPGR_SEIRepi.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1PD_SGE.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1_LSQ.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitL_GregB1.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_smmothL_B1.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/errB1PD.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/mrQ_NLANTS_warp_SPGR2EPI_RB.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/mrQ_RB_ANTS_warp_EPI2SPGR.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/mrQ_alignSPGR_SEIRepi.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/mrQ_fitB1PD_SGE.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/mrQ_fitB1_LSQ.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/mrQ_fitL_GregB1.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/B1_epi-spgr/mrQ_smmothL_B1.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/LW_fit/mrQ_T1M0_LWFit.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/LW_fit/mrQ_fitT1PDLW_SGE.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/lsq_NL/errT1PD.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/lsq_NL/mrQ_fitT1PD_LSQ.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/lsq_NL/mrQ_fitT1PD_SGE.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/lsq_NL/polyfitweighted.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/mrQ_fitT1M0.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_T1/mrQfit_T1M0_ver2.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.directory (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/all-wcprops (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/entries (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/text-base/.directory.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/text-base/mrQ_AvcoilM0.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/text-base/mrQ_CSF.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/text-base/mrQ_WF.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/text-base/mrQ_WFsmooth.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/text-base/mrQ_WFsmoothPhantom.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/text-base/mrQ_multicoilM0.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/.svn/text-base/mrQ_segmentT1w2tissue.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/CoilFitforPD_v2/BuildPD/mrQ_BoxJoinBox.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/CoilFitforPD_v2/BuildPD/mrQ_BoxsWiseAlignment_step3.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/CoilFitforPD_v2/BuildPD/mrQ_CalBoxPD_step1.m (100%) rename 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{OLDVer/SPGR => SPGR}/SPGR_WF/oldCode/fitPD_andGain/mrQM0fitini_Param_v.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/oldCode/fitPD_andGain/mrQ_FitM0_SGE_v1.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/oldCode/fitPD_andGain/mrQ_fitPD_multicoil.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/oldCode/mrQ_WF.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/oldCode/mrQ_WFsmooth.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/oldCode/mrQ_WFsmoothPhantom.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/oldCode/mrQ_WFsmooth_1.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/segmentation/mrQ_CSF.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_WF/segmentation/mrQ_segmentT1w2tissue.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_phantoms/.svn/all-wcprops (100%) rename {OLDVer/SPGR => SPGR}/SPGR_phantoms/.svn/entries (100%) rename {OLDVer/SPGR => SPGR}/SPGR_phantoms/.svn/text-base/mrQ_initSPGR_pantom.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_phantoms/.svn/text-base/mrQ_initSPGR_pantom.m~.svn-base (100%) 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SPGR}/SPGR_phantoms/mrQfit_T1M0_Phantoms.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_pre/.svn/all-wcprops (100%) rename {OLDVer/SPGR => SPGR}/SPGR_pre/.svn/entries (100%) rename {OLDVer/SPGR => SPGR}/SPGR_pre/.svn/text-base/mrQ_calculateCoilWeights.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_pre/.svn/text-base/mrQ_initSPGR.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_pre/.svn/text-base/mrQ_multicoilWeighting.m.svn-base (100%) rename {OLDVer/SPGR => SPGR}/SPGR_pre/.svn/tmp/mrQ_initSPGR.m.tmp (100%) rename {OLDVer/SPGR => SPGR}/SPGR_pre/mrQ_calculateCoilWeights.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_pre/mrQ_initSPGR.m (100%) rename {OLDVer/SPGR => SPGR}/SPGR_pre/mrQ_multicoilWeighting.m (100%) diff --git a/OLDVer/SPGR/.svn/all-wcprops b/SPGR/.svn/all-wcprops similarity index 100% rename from OLDVer/SPGR/.svn/all-wcprops rename to SPGR/.svn/all-wcprops diff --git a/OLDVer/SPGR/.svn/entries b/SPGR/.svn/entries similarity index 100% rename from OLDVer/SPGR/.svn/entries rename to SPGR/.svn/entries diff --git a/OLDVer/SPGR/SPGR_HLF/.svn/all-wcprops b/SPGR/SPGR_HLF/.svn/all-wcprops similarity index 100% rename from OLDVer/SPGR/SPGR_HLF/.svn/all-wcprops rename to SPGR/SPGR_HLF/.svn/all-wcprops diff --git a/OLDVer/SPGR/SPGR_HLF/.svn/entries b/SPGR/SPGR_HLF/.svn/entries similarity index 100% rename from OLDVer/SPGR/SPGR_HLF/.svn/entries rename to SPGR/SPGR_HLF/.svn/entries diff --git a/OLDVer/SPGR/SPGR_HLF/.svn/text-base/mrQ_HLF.m.svn-base b/SPGR/SPGR_HLF/.svn/text-base/mrQ_HLF.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_HLF/.svn/text-base/mrQ_HLF.m.svn-base rename to SPGR/SPGR_HLF/.svn/text-base/mrQ_HLF.m.svn-base diff --git a/OLDVer/SPGR/SPGR_HLF/.svn/text-base/mrQ_VIP.m.svn-base b/SPGR/SPGR_HLF/.svn/text-base/mrQ_VIP.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_HLF/.svn/text-base/mrQ_VIP.m.svn-base rename to SPGR/SPGR_HLF/.svn/text-base/mrQ_VIP.m.svn-base diff --git a/OLDVer/SPGR/SPGR_HLF/mrQ_HLF.m 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a/OLDVer/SPGR/SPGR_T1/.svn/text-base/mrQfit_T1M0_ver2.m.svn-base b/SPGR/SPGR_T1/.svn/text-base/mrQfit_T1M0_ver2.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_T1/.svn/text-base/mrQfit_T1M0_ver2.m.svn-base rename to SPGR/SPGR_T1/.svn/text-base/mrQfit_T1M0_ver2.m.svn-base diff --git a/OLDVer/SPGR/SPGR_T1/.svn/tmp/mrQ_fitT1PD_LSQ.m.tmp b/SPGR/SPGR_T1/.svn/tmp/mrQ_fitT1PD_LSQ.m.tmp similarity index 100% rename from OLDVer/SPGR/SPGR_T1/.svn/tmp/mrQ_fitT1PD_LSQ.m.tmp rename to SPGR/SPGR_T1/.svn/tmp/mrQ_fitT1PD_LSQ.m.tmp diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/all-wcprops b/SPGR/SPGR_T1/B1_epi-spgr/.svn/all-wcprops similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/all-wcprops rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/all-wcprops diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/entries b/SPGR/SPGR_T1/B1_epi-spgr/.svn/entries similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/entries rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/entries diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/errB1PD.m.svn-base b/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/errB1PD.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/errB1PD.m.svn-base rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/errB1PD.m.svn-base diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_NLANTS_warp_SPGR2EPI_RB.m.svn-base b/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_NLANTS_warp_SPGR2EPI_RB.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_NLANTS_warp_SPGR2EPI_RB.m.svn-base rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_NLANTS_warp_SPGR2EPI_RB.m.svn-base diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_RB_ANTS_warp_EPI2SPGR.m.svn-base b/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_RB_ANTS_warp_EPI2SPGR.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_RB_ANTS_warp_EPI2SPGR.m.svn-base rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_RB_ANTS_warp_EPI2SPGR.m.svn-base diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_alignSPGR_SEIRepi.m.svn-base b/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_alignSPGR_SEIRepi.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_alignSPGR_SEIRepi.m.svn-base rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_alignSPGR_SEIRepi.m.svn-base diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1PD_SGE.m.svn-base b/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1PD_SGE.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1PD_SGE.m.svn-base rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1PD_SGE.m.svn-base diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1_LSQ.m.svn-base b/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1_LSQ.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1_LSQ.m.svn-base rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitB1_LSQ.m.svn-base diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitL_GregB1.m.svn-base b/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitL_GregB1.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitL_GregB1.m.svn-base rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_fitL_GregB1.m.svn-base diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_smmothL_B1.m.svn-base b/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_smmothL_B1.m.svn-base similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_smmothL_B1.m.svn-base rename to SPGR/SPGR_T1/B1_epi-spgr/.svn/text-base/mrQ_smmothL_B1.m.svn-base diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/errB1PD.m b/SPGR/SPGR_T1/B1_epi-spgr/errB1PD.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/errB1PD.m rename to SPGR/SPGR_T1/B1_epi-spgr/errB1PD.m diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_NLANTS_warp_SPGR2EPI_RB.m b/SPGR/SPGR_T1/B1_epi-spgr/mrQ_NLANTS_warp_SPGR2EPI_RB.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_NLANTS_warp_SPGR2EPI_RB.m rename to SPGR/SPGR_T1/B1_epi-spgr/mrQ_NLANTS_warp_SPGR2EPI_RB.m diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_RB_ANTS_warp_EPI2SPGR.m b/SPGR/SPGR_T1/B1_epi-spgr/mrQ_RB_ANTS_warp_EPI2SPGR.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_RB_ANTS_warp_EPI2SPGR.m rename to SPGR/SPGR_T1/B1_epi-spgr/mrQ_RB_ANTS_warp_EPI2SPGR.m diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_alignSPGR_SEIRepi.m b/SPGR/SPGR_T1/B1_epi-spgr/mrQ_alignSPGR_SEIRepi.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_alignSPGR_SEIRepi.m rename to SPGR/SPGR_T1/B1_epi-spgr/mrQ_alignSPGR_SEIRepi.m diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitB1PD_SGE.m b/SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitB1PD_SGE.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitB1PD_SGE.m rename to SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitB1PD_SGE.m diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitB1_LSQ.m b/SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitB1_LSQ.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitB1_LSQ.m rename to SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitB1_LSQ.m diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitL_GregB1.m b/SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitL_GregB1.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitL_GregB1.m rename to SPGR/SPGR_T1/B1_epi-spgr/mrQ_fitL_GregB1.m diff --git a/OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_smmothL_B1.m b/SPGR/SPGR_T1/B1_epi-spgr/mrQ_smmothL_B1.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/B1_epi-spgr/mrQ_smmothL_B1.m rename to SPGR/SPGR_T1/B1_epi-spgr/mrQ_smmothL_B1.m diff --git a/OLDVer/SPGR/SPGR_T1/LW_fit/mrQ_T1M0_LWFit.m b/SPGR/SPGR_T1/LW_fit/mrQ_T1M0_LWFit.m similarity index 100% rename from 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a/OLDVer/SPGR/SPGR_T1/lsq_NL/polyfitweighted.m b/SPGR/SPGR_T1/lsq_NL/polyfitweighted.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/lsq_NL/polyfitweighted.m rename to SPGR/SPGR_T1/lsq_NL/polyfitweighted.m diff --git a/OLDVer/SPGR/SPGR_T1/mrQ_fitT1M0.m b/SPGR/SPGR_T1/mrQ_fitT1M0.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/mrQ_fitT1M0.m rename to SPGR/SPGR_T1/mrQ_fitT1M0.m diff --git a/OLDVer/SPGR/SPGR_T1/mrQfit_T1M0_ver2.m b/SPGR/SPGR_T1/mrQfit_T1M0_ver2.m similarity index 100% rename from OLDVer/SPGR/SPGR_T1/mrQfit_T1M0_ver2.m rename to SPGR/SPGR_T1/mrQfit_T1M0_ver2.m diff --git a/OLDVer/SPGR/SPGR_WF/.directory b/SPGR/SPGR_WF/.directory similarity index 100% rename from OLDVer/SPGR/SPGR_WF/.directory rename to SPGR/SPGR_WF/.directory diff --git a/OLDVer/SPGR/SPGR_WF/.svn/all-wcprops b/SPGR/SPGR_WF/.svn/all-wcprops similarity index 100% rename from OLDVer/SPGR/SPGR_WF/.svn/all-wcprops rename to SPGR/SPGR_WF/.svn/all-wcprops diff --git 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