Merge pull request #19 from khanlab/cs-gre

added compressed sensing GRE and ASPIRE to cfmm_base
khanlab · Aug 17, 2021 · 53e3956 · 53e3956
2 parents 0646e9a + 6a4012a
commit 53e3956
Showing 1 changed file with 50 additions and 0 deletions.
diff --git a/heuristics/cfmm_base.py b/heuristics/cfmm_base.py
@@ -186,6 +186,17 @@ def infotodict(seqinfo):
     DIS2D_T2_star = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_rec-DIS2D_T2star')
     DIS3D_T2_star = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_rec-DIS3D_T2star')
 
+    #me-gre with compressed sensing
+    mag_echo_CS_GRE = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-CS_run-{item:02d}_part-mag_echo_GRE')
+    phase_echo_CS_GRE = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-CS_run-{item:02d}_part-phase_echo_GRE')    
+
+    #aspire:
+    DIS2D_aspire_mag_echo_GRE = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-ASPIRE_part-mag_rec-DIS2D_echo_GRE')
+    DIS2D_aspire_phase_echo_GRE = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-ASPIRE_part-phase_rec-DIS2D_echo_GRE')
+    DIS2D_aspire_T2_star_GRE = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-ASPIRE_rec-DIS2D_T2star')
+    DIS2D_aspire_R2_star_GRE = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-ASPIRE_rec-DIS2D_R2star')
+
+
     # MEMP2RAGE #
     me_t1     = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_echo_acq-MP2RAGE_run-{item:02d}_T1w')
     me_t1map  = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_echo_acq-MP2RAGE_run-{item:02d}_T1map')
@@ -223,6 +234,16 @@ def infotodict(seqinfo):
          TOF_angio:[], DIS2D_TOF_SAG:[], DIS2D_TOF_COR:[], DIS2D_TOF_TRA:[], DIS2D_TOF_angio:[], DIS3D_TOF_angio:[],
          mag_echo_GRE:[],
          phase_echo_GRE:[],
+
+         mag_echo_CS_GRE:[],
+         phase_echo_CS_GRE:[],
+
+         DIS2D_aspire_mag_echo_GRE:[],
+         DIS2D_aspire_phase_echo_GRE:[],
+         DIS2D_aspire_T2_star_GRE:[],
+         DIS2D_aspire_R2_star_GRE:[],
+
+
          DIS2D_mag_echo_GRE:[],
          DIS2D_phase_echo_GRE:[],
          DIS3D_mag_echo_GRE:[],
@@ -503,6 +524,35 @@ def infotodict(seqinfo):
                  if ('DIS3D' in (s.image_type[3].strip())):
                     info[DIS3D_phase_echo_GRE] =  [s.series_id]
 
+        #susceptibility ND multiecho
+        if ('ASPIRE' in s.series_description ):
+            if 'R2star' in s.series_description:
+                 if ('DIS2D' in (s.image_type[3].strip())):
+                    info[DIS2D_aspire_R2_star_GRE] =  [s.series_id]
+            elif 'T2star' in s.series_description:
+                  if ('DIS2D' in (s.image_type[3].strip())):
+                    info[DIS2D_aspire_T2_star_GRE] =  [s.series_id]
+            elif len(s.image_type) > 3 :
+                if (('M' in (s.image_type[2].strip()) ) and ('ASPIRE' not in s.image_type )):
+                     if ('DIS2D' in (s.image_type[3].strip())):
+                        info[DIS2D_aspire_mag_echo_GRE] =  [s.series_id]
+                if ('P' in (s.image_type[2].strip()) and len(s.image_type) >4):
+                     if ('DIS2D' in (s.image_type[4].strip())):
+                        info[DIS2D_aspire_phase_echo_GRE] =  [s.series_id]
+
+
+        #multi-echo GRE with compressed sensing
+        if ('gre_CS_C41' in s.series_description):
+            if ('M' in (s.image_type[2].strip())):
+                 if ('ND' in (s.image_type[3].strip())):
+                    info[mag_echo_CS_GRE] =  [s.series_id]
+
+
+            if ('P' in (s.image_type[2].strip())):
+                 if ('ND' in (s.image_type[3].strip())):
+                    info[phase_echo_CS_GRE] =  [s.series_id]
+
+
         # MTon GRE (excludes phase image since not needed)
         if ('gre_ptx_MT_On' in s.series_description ):
             if ('M' in (s.image_type[2].strip())):