Merge pull request #331 from a3sha2/master

new features

designs/fc-36p.dsn

@@ -70,7 +70,6 @@ confound2_sq[2]=2
 confound2_custom[2]=
 confound2_censor[2]=0
 confound2_censor_contig[2]=0
-confound2_framewise[2]=fds:0.167,dv:2
 confound2_rerun[2]=0
 confound2_cleanup[2]=1
 

designs/fc-36p_despike.dsn

@@ -69,7 +69,6 @@ confound2_sq[2]=2
 confound2_custom[2]=
 confound2_censor[2]=0
 confound2_censor_contig[2]=0
-confound2_framewise[2]=fds:0.167,dv:2
 confound2_rerun[2]=1
 confound2_cleanup[2]=1
 

docs/modules/gmd.rst

@@ -42,8 +42,16 @@ temporary files will be retained to facilitate error diagnosis.::
 ``Expected outputs``
 ^^^^^^^^^^^^^^^^^^^^^
 The expected outputs from `gmd` include the following::
+
+ - prefix_gmd.nii.gz # grey matter density
  - prefix_probabilityCSF.nii.gz  # CSF probability map
  - prefix_probabilityGM.nii.gz   # grey matter probability map
  - prefix_probabilityWM.nii.gz  # white matter probability map
  - prefix_raw.nii.gz   # raw image 
- - prefix_segmentation3class.nii.gz  # 3-class tissue segmentation
+ - prefix_segmentation3class.nii.gz  # 3-class tissue segmentation
+
+if the freesurfer is included in the struc module, cifti  files are generated for GM:: 
+
+ - prefix_gmd_rh.cort.gii # right gmd surface
+ - prefix_gmd_lh.cort.gii # left gmd surface
+ - prefix_gmd.dscalar.nii # scalar values of right and left hemispheres 

docs/modules/index.rst

@@ -49,7 +49,7 @@ Anatomical derivatives
 
 Modules that generate derivative maps from anatomical data.
 
- * ``jlf``: Uses the ANTs Joint Label Fusion algorithm to produce a
+ * :ref:`jlf`:: Uses the ANTs Joint Label Fusion algorithm to produce a
    high-resolution anatomical segmentation of the subject’s anatomical data. Generates a
    subject-specific atlas of anatomical landmarks that can be used for regional quantification or
    network mapping.
@@ -122,6 +122,7 @@ Quick Lookup
   seed
   task
   struc
+  jlf
   gmd
   norm
   roiquant

docs/modules/jlf.rst

@@ -0,0 +1,54 @@
+.. _jlf:
+
+``jlf``
+===========
+
+``jlf`` is a module that  uses the ANTs Joint Label Fusion algorithm to produce a
+   high-resolution anatomical segmentation of the subject’s anatomical data. Generates a
+   subject-specific atlas of anatomical landmarks that can be used for regional quantification or
+   network mapping. Presently, the module uses atlases of 103-OASIS labels. 
+
+
+``jlf`` options 
+^^^^^^^^^^^^^^^^^
+
+If to use OASIS atlas labels with skullstrip or not::
+
+  - jlf_extract[cxt]=1 # with skulltrip
+
+If to keep each warped atlas, that is not advisable, it occupy space::
+
+  - jlf_keep_warps[cxt]=0 # dont keep 
+
+Fast joint label fusion is no recommended bcos of poor accuracy::
+
+  - jlf_quick[cxt]=1 # for fast jlf but no recommended
+
+The cohort of OASIS label can be selected based on their ages::
+
+  - jlf_cohort[cxt]=All # Everyone  
+  - jlf_cohort[cxt]=YoungAdult22  # Age range of 18-34
+  - jlf_cohort[cxt]=Older18  # Age range of 23-90
+  - jlf_cohort[cxt]=SexBalanced20  #All male subjects (ages 20-68) plus 10 of the female subjects.
+  - jlf_cohort[cxt]=Subset24 # A subset for general use, slightly more balanced on sex
+  - jlf_cohort[cxt]=Younger24 #Maintains the same 2:1 female:male ratio of the original, but biased towards younger subjects
+
+Tthe number of cpu cores, the default is 2::
+
+  - jlf_ncpu[cxt]=2
+
+Configuring parallelisation,very fast:: 
+
+  - jlf_parallel[3]=1
+
+
+
+Outputs
+^^^^^^^^
+The expected outputs are::
+
+ - prefix_Intensity.nii.gz # atlas intensity 
+ - prefix_Labels.nii.gz # atlas labels
+ - prefix_TargetMaskImageOr.nii.gz # target mask that cover all atlas 
+ - prefix_LabelsGMIntersect.nii.gz # refined atlas with grey matter mask 
+

docs/modules/struc.rst

@@ -227,6 +227,20 @@ fractional intensity threshold should be a positive number greater than 0 and le
   # Fractional intensity threshold of 0.3
   struc_fit[cxt]=0.3
 
+Freesufer run.
+
+Routine: ``FSF``
+
+The freesufer can be run with addition of `FSF` to the procsess as ::
+
+  struc_process[cxt]=FSF-ACT
+
+If the freesufer has be ran before, the directory of freesufer can be copied by including::
+
+  struc_freesurferdir[cxt]=/path/to/freesufer/directory
+this can also be included in the cohort file.
+the cifti files for cortical thickness are generated.  
+
 ``struc_quick``
 ~~~~~~~~~~~~~~~~~~
 
@@ -303,3 +317,4 @@ Permitted codes include:
  * ``FBE``: FSL brain extraction
  * ``SEG``: Atropos image segmentation
  * ``REG``: registration to a template
+ * ``FSF``: Freesufer  or copy freesufer outputs from fmriprep if available

docs/qualitycontrol.rst

@@ -19,7 +19,22 @@ Normalization of T1w/Functional to Template:
          - normCrossCorr - cross correlation 
          - normJaccard - Jaccard index 
          - normDice - Dice index
-         - normCoverage - Coverage index  
+         - normCoverage - Coverage index 
+
+QC for anatomical:
+         - euler_number_rh,euler_number_lh -  Eurler number if freesurfer is included 
+         - meanGMD - mean of Grey matter density
+         - SignalToNoiseRatio - grey matter signal to noise ratio 
+         - BackgroundKurtosis - background intensity Kurtosis
+         - GreyMatterKurtosis - grey matter intensity Kurtosis
+         - EntropyFocusCriterion - entropy focus criterion ( for ghost signals)
+         - CorticalContrasts - coritical contrasts between white matter and grey matter signals
+         - FGBGEnergyRatio - Foreground-to-background energy ratio
+         - ContrastToNoiseRatio - contrast to noise ratio
+         - WhiteMatterSkewness - WhiteMatter Skewness
+         - BackgroundSkewness - background intensity Kurtosis
+
+
 
 Motion/spikes summary.::
          - relMeansRMSMotion - mean value of RMS motion 

modules/struc/struc.mod

@@ -84,7 +84,8 @@ qc reg_cross_corr regCrossCorr      ${prefix}_regCrossCorr.txt
 qc reg_coverage   regCoverage       ${prefix}_regCoverage.txt
 qc reg_jaccard    regJaccard        ${prefix}_regJaccard.txt
 qc reg_dice       regDice           ${prefix}_regDice.txt
-qc euler_number   eulernumber       ${prefix}_eulernumber.txt
+qc euler_rh_number   euler_number_rh       ${prefix}_rh_eulernumber.txt
+qc euler_lh_number   euler_number_lh       ${prefix}_lh_eulernumber.txt
 
 input image mask
 input image segmentation
@@ -494,13 +495,13 @@ while (( ${#rem} > 0 ))
 
    freesurferdir=${outdir}/freesurfer 
 
-    if [[  -d ${struc_fmriprepdir[cxt]}/ ]]
+    if [[  -d ${struc_freesurferdir[cxt]}/ ]]
      then 
-         fmriprepout=${struc_fmriprepdir[cxt]} 
+         fmriprepout=${struc_freesurferdir[cxt]} 
 
-    elif [[ -d ${struc_fmriprepdir[sub]}/ ]] 
+    elif [[ -d ${struc_freesurferdir[sub]}/ ]] 
        then
-         fmriprepout=${struc_fmriprepdir[sub]} 
+         fmriprepout=${struc_freesurferdir[sub]} 
     fi 
 
 
@@ -513,8 +514,10 @@ while (( ${#rem} > 0 ))
        exec_sys cp -r $FREESURFER_HOME/subjects/fsaverage5  $SUBJECTS_DIR/
        ${FREESURFER_HOME}/bin/mris_euler_number -o  /tmp/text_lh.tsv  ${SUBJECTS_DIR}/${subjectid}/surf/lh.orig.nofix
        ${FREESURFER_HOME}/bin/mris_euler_number -o  /tmp/text_rh.tsv  ${SUBJECTS_DIR}/${subjectid}/surf/rh.orig.nofix
-       eulernumber=$(expr $(cat /tmp/text_lh.tsv)  +  $(cat /tmp/text_rh.tsv))
-       exec_sys echo ${eulernumber} > ${euler_number[cxt]}
+       eulerlh=$(cat /tmp/text_lh.tsv)  
+       eulerrh=$(cat /tmp/text_rh.tsv)  
+       exec_sys echo ${eulerrh} > ${euler_rh_number[cxt]}
+       exec_sys echo ${eulerlh} > ${euler_lh_number[cxt]}
        exec_sys rm  -rf /tmp/text_*.tsv
 
     else 
@@ -527,10 +530,12 @@ while (( ${#rem} > 0 ))
       ${FREESURFER_HOME}/bin/recon-all -subjid ${subjectid} \
       -i ${img[sub]} -all -sd ${SUBJECTS_DIR}
       exec_sys cp -r $FREESURFER_HOME/subjects/fsaverage5 $SUBJECTS_DIR/
-       ${FREESURFER_HOME}/bin/mris_euler_number -o  /tmp/text_lh.tsv  ${SUBJECTS_DIR}/${subjectid}/lh.orig.nofix
-       ${FREESURFER_HOME}/bin/mris_euler_number -o  /tmp/text_rh.tsv  ${SUBJECTS_DIR}/${subjectid}/rh.orig.nofix
-       eulernumber=$(expr $(cat /tmp/text_lh.tsv)  +  $(cat /tmp/text_rh.tsv))
-       exec_sys echo ${eulernumber} > ${euler_number[cxt]}
+       ${FREESURFER_HOME}/bin/mris_euler_number -o  /tmp/text_lh.tsv  ${SUBJECTS_DIR}/${subjectid}/surf/lh.orig.nofix
+       ${FREESURFER_HOME}/bin/mris_euler_number -o  /tmp/text_rh.tsv  ${SUBJECTS_DIR}/${subjectid}/surf/rh.orig.nofix
+       eulerlh=$(cat /tmp/text_lh.tsv)  
+       eulerrh=$(cat /tmp/text_rh.tsv)  
+       exec_sys echo ${eulerrh} > ${euler_rh_number[cxt]}
+       exec_sys echo ${eulerlh} > ${euler_lh_number[cxt]}
        exec_sys rm  -rf /tmp/text_*.tsv
 
    fi