Merge pull request #84 from aces/dev

Preparation for release.

cbrain_task/civet/bourreau/civet.rb

@@ -91,30 +91,31 @@ def setup #:nodoc:
 
     self.results_data_provider_id ||= collection ? collection.data_provider_id : t1.data_provider_id
 
+    input_symlink_base = prefix.present? ? "#{mincfiles_dir}/#{prefix}_#{dsid}" : "#{mincfiles_dir}/#{dsid}"
     # MODE A (collection) symlinks
     if collection
 
       t1ext = t1_name.match(/.gz$/i) ? ".gz" : ""
-      t1sym = "#{mincfiles_dir}/#{prefix}_#{dsid}_t1.mnc#{t1ext}"
+      t1sym = "#{input_symlink_base}_t1.mnc#{t1ext}"
       make_available(collection, t1sym, t1_name)
       return false unless validate_minc_file(t1sym)
 
       if mybool(file0[:multispectral]) || mybool(file0[:spectral_mask])
         if t2_name.present?
           t2ext = t2_name.match(/.gz$/i) ? ".gz" : ""
-          t2sym = "#{mincfiles_dir}/#{prefix}_#{dsid}_t2.mnc#{t2ext}"
+          t2sym = "#{input_symlink_base}_t2.mnc#{t2ext}"
           make_available(collection, t2sym, t2_name)
           return false unless validate_minc_file(t2sym)
         end
         if pd_name.present?
           pdext = pd_name.match(/.gz$/i) ? ".gz" : ""
-          pdsym = "#{mincfiles_dir}/#{prefix}_#{dsid}_pd.mnc#{pdext}"
+          pdsym = "#{input_symlink_base}_pd.mnc#{pdext}"
           make_available(collection, pdsym, pd_name)
           return false unless validate_minc_file(pdsym)
         end
         if mk_name.present?
           mkext = mk_name.match(/.gz$/i) ? ".gz" : ""
-          mksym = "#{mincfiles_dir}/#{prefix}_#{dsid}_mask.mnc#{mkext}"
+          mksym = "#{input_symlink_base}_mask.mnc#{mkext}"
           make_available(collection, mksym, mk_name)
           return false unless validate_minc_file(mksym)
         end
@@ -124,7 +125,7 @@ def setup #:nodoc:
 
       t1_name = t1.name
       t1ext   = t1_name.match(/.gz$/i) ? ".gz" : ""
-      t1sym   = "#{mincfiles_dir}/#{prefix}_#{dsid}_t1.mnc#{t1ext}"
+      t1sym   = "#{input_symlink_base}_t1.mnc#{t1ext}"
       make_available(t1,t1sym)
       return false unless validate_minc_file(t1sym)
 
@@ -133,7 +134,7 @@ def setup #:nodoc:
           t2      = Userfile.find(t2_id)
           t2_name = t2.name
           t2ext   = t2_name.match(/.gz$/i) ? ".gz" : ""
-          t2sym   = "#{mincfiles_dir}/#{prefix}_#{dsid}_t2.mnc#{t2ext}"
+          t2sym   = "#{input_symlink_base}_t2.mnc#{t2ext}"
           make_available(t2,t2sym)
           return false unless validate_minc_file(t2sym)
         end
@@ -142,7 +143,7 @@ def setup #:nodoc:
           pd      = Userfile.find(pd_id)
           pd_name = pd.name
           pdext   = pd_name.match(/.gz$/i) ? ".gz" : ""
-          pdsym   = "#{mincfiles_dir}/#{prefix}_#{dsid}_pd.mnc#{pdext}"
+          pdsym   = "#{input_symlink_base}_pd.mnc#{pdext}"
           make_available(pd,pdsym)
           return false unless validate_minc_file(pdsym)
         end
@@ -151,7 +152,7 @@ def setup #:nodoc:
           mk      = Userfile.find(mk_id)
           mk_name = mk.name
           mkext   = mk_name.match(/.gz$/i) ? ".gz" : ""
-          mksym   = "#{mincfiles_dir}/#{prefix}_#{dsid}_mask.mnc#{mkext}"
+          mksym   = "#{input_symlink_base}_mask.mnc#{mkext}"
           make_available(mk,mksym)
           return false unless validate_minc_file(mksym)
         end
@@ -209,6 +210,10 @@ def cluster_commands_single(options_to_ignore={}) #:nodoc:
     prefix = file0[:prefix] || "unkpref"
     dsid   = file0[:dsid]   || "unkdsid"
 
+    is_version_1_1_12         = self.tool_config.is_version("1.1.12")
+    is_at_least_version_2_0_0 = self.tool_config.is_at_least_version("2.0.0")
+    is_at_least_version_2_1_0 = self.tool_config.is_at_least_version("2.1.0")
+
     # -----------------------------------------------------------
     # More validations of params that are substituted in commands
     # -----------------------------------------------------------
@@ -221,10 +226,10 @@ def cluster_commands_single(options_to_ignore={}) #:nodoc:
     # Model
     if params[:model].present?
       cb_error "Bad model name."         unless params[:model]        =~ /^\s*[\w\.]+\s*$/
-      cb_error "Model is not valid for this CIVET version" if params[:model] == "ADNInl" && !self.tool_config.is_version("1.1.12")
-      cb_error "Model is not valid for this CIVET version" if params[:model] == "icbm152nl_09a" && !self.tool_config.is_at_least_version("2.0.0")
-      cb_error "Model is not valid for this CIVET version" if params[:model] == "icbm152nl_09s" && !self.tool_config.is_at_least_version("2.0.0")
-      cb_error "Model is not valid for this CIVET version" if params[:model] == "ADNIhires" && !self.tool_config.is_at_least_version("2.0.0")
+      cb_error "Model is not valid for this CIVET version" if params[:model] == "ADNInl"        && !is_version_1_1_12
+      cb_error "Model is not valid for this CIVET version" if params[:model] == "icbm152nl_09a" && !is_at_least_version_2_0_0
+      cb_error "Model is not valid for this CIVET version" if params[:model] == "icbm152nl_09s" && !is_at_least_version_2_0_0
+      cb_error "Model is not valid for this CIVET version" if params[:model] == "ADNIhires"     && !is_at_least_version_2_0_0
     end
 
     # Interp
@@ -244,7 +249,11 @@ def cluster_commands_single(options_to_ignore={}) #:nodoc:
 
     # LSQ
     if params[:lsq].present?
-      cb_error "Bad LSQ value."         unless params[:lsq]           =~ /^\s*(?:6|9|12)\s*$/
+      if is_at_least_version_2_1_0
+        cb_error "Bad LSQ value."         unless params[:lsq]           =~ /^\s*(?:0|6|9|12)\s*$/
+      else
+        cb_error "Bad LSQ value."         unless params[:lsq]           =~ /^\s*(?:6|9|12)\s*$/
+      end
     end
 
     # Resamp surf kern area
@@ -274,7 +283,11 @@ def cluster_commands_single(options_to_ignore={}) #:nodoc:
     args += "-N3-distance #{params[:N3_distance].bash_escape} "     if params[:N3_distance].present?
     args += "-headheight #{params[:headheight].bash_escape} "       if params[:headheight].present?        && !options_to_ignore[:headheight]
     args += "-mask-blood-vessels "                                  if mybool(params[:mask_blood_vessels]) && !options_to_ignore[:mask_blood_vessels]
-    args += "-lsq#{params[:lsq]} "                                  if params[:lsq] && params[:lsq].to_i != 9 # there is NO -lsq9 option!
+    if params[:lsq] != 0
+      args += "-lsq#{params[:lsq]} "                                if params[:lsq] && params[:lsq].to_i != 9 # there is NO -lsq9 option!
+    else
+      args += "-input_is_stx "
+    end
     args += "-no-surfaces "                                         if mybool(params[:no_surfaces])
     args += "-correct-pve "                                         if mybool(params[:correct_pve])
     args += "-hi-res-surfaces "                                     if mybool(params[:high_res_surfaces])  && !options_to_ignore[:high_res_surfaces]
@@ -283,12 +296,30 @@ def cluster_commands_single(options_to_ignore={}) #:nodoc:
     args += "-multispectral "                                       if mybool(file0[:multispectral])
     args += "-spectral_mask "                                       if mybool(file0[:spectral_mask])
 
+    # PVE
+    if is_at_least_version_2_1_0
+      if    params[:pve] == "classic"
+        args += "-no-correct-pve -no-subcortical -no-mask-cerebellum "
+      elsif params[:pve] == "advanced"
+        args += "-correct-pve -subcortical -mask-cerebellum "
+      end
+    end
+
     # Thickness methods and kernel
     if ( params[:thickness_method].present? &&
          params[:thickness_kernel].present? &&
          is_valid_integer_list(params[:thickness_kernel], allow_blanks: false)
        )
-      args += "-thickness #{params[:thickness_method].bash_escape} #{params[:thickness_kernel].bash_escape} "
+      if is_at_least_version_2_1_0
+        thickness_methods = Array(params[:thickness_method])
+        thickness_methods = thickness_methods & ["tlaplace", "tlink","tfs"]
+        thickness_methods = thickness_methods.unshift(params[:thickness_method_for_qc]) if params[:thickness_method_for_qc].present?
+        thickness_string  = thickness_methods.uniq.join(":")
+      else
+        # Safegard should already be a String
+        thickness_string  = Array(params[:thickness_method])[0].to_s
+      end
+      args += "-thickness #{thickness_string.bash_escape} #{params[:thickness_kernel].bash_escape} "
     end
 
     # Surface resampling
@@ -302,7 +333,7 @@ def cluster_commands_single(options_to_ignore={}) #:nodoc:
       # Atlas
       if params[:atlas].present? && ! options_to_ignore[:atlas]
         atlas_name = params[:atlas].strip
-        if self.tool_config.is_at_least_version("2.0.0")
+        if is_at_least_version_2_0_0
           args += "-surface-atlas #{atlas_name.bash_escape} "
         else
           args += "-surface-atlas $MNI_CIVET_ROOT/models/AAL_atlas_left.txt $MNI_CIVET_ROOT/models/AAL_atlas_right.txt " if atlas_name == "AAL"
@@ -331,8 +362,10 @@ def cluster_commands_single(options_to_ignore={}) #:nodoc:
       args += "-reset-from #{reset_from.bash_escape} "
     end
 
-    mincfiles_dir = "mincfiles_input"
-    civet_command = "CIVET_Processing_Pipeline -prefix #{prefix.bash_escape} -source #{mincfiles_dir} -target civet_out -spawn #{args} -run #{dsid.bash_escape}"
+    mincfiles_dir  = "mincfiles_input"
+    civet_command  = "CIVET_Processing_Pipeline -source #{mincfiles_dir} -target civet_out -spawn #{args} "
+    civet_command += "-prefix #{prefix.bash_escape} " if prefix.present?
+    civet_command += "-run #{dsid.bash_escape}"       if dsid.present?
 
     self.addlog("Full CIVET command:\n  #{civet_command.gsub(/ -/, "\n  -")}") if self.user.has_role? :admin_user
 

cbrain_task/civet/common/civet.rb

@@ -31,9 +31,9 @@ def job_walltime_estimate #:nodoc:
     else
       # Added 2 extra hours, just in case user specify ANIMAL.
       if mybool(params[:high_res_surfaces])
-        params[:template] == "1.00" ? 16.hours : 22.hours
+        params[:template] == "1.00" ? 24.hours : 36.hours
       else
-        params[:template] == "1.00" ? 10.hours : 12.hours
+        params[:template] == "1.00" ? 22.hours : 30.hours
       end
     end
   end
@@ -110,6 +110,9 @@ def identify_options_to_ignore(ignored_options={}) #:nodoc:
       ignored_options[:animal]                           = true
       ignored_options[:lobe_atlas]                       = true
     end
+    if !self.tool_config.is_at_least_version("2.1.0")
+      ignored_options[:pve]                              = true
+    end
 
     ignored_options
   end

cbrain_task/civet/portal/civet.rb

@@ -133,7 +133,11 @@ def self.default_launch_args #:nodoc:
   def before_form #:nodoc:
     params    = self.params
 
-    params[:model] = "icbm152nl_09s" if self.tool_config && self.tool_config.is_version("2.0.0")
+    params[:model] = "icbm152nl_09s" if self.tool_config && self.tool_config.is_at_least_version("2.0.0")
+    if self.tool_config && self.tool_config.is_at_least_version("2.1.0")
+      params[:thickness_method]        = ["tlaplace"]
+      params[:thickness_method_for_qc] = "tlaplace"
+    end
 
     file_ids  = params[:interface_userfile_ids]
 
@@ -238,6 +242,8 @@ def after_form #:nodoc:
       dsid = (fa[:dsid] || "").strip
       fa[:dsid] = dsid
 
+      is_at_least_version_2_1_0 = self.tool_config && self.tool_config.is_at_least_version("2.1.0")
+
       # Verify the subject ID
       message = nil
       if dsid.blank?
@@ -258,7 +264,9 @@ def after_form #:nodoc:
 
       # Verify the prefix
       message = nil
-      if prefix.blank?
+      if prefix.blank?  && is_at_least_version_2_1_0
+        message = nil
+      elsif prefix.blank?
         message = " is blank?"
       elsif prefix !~ /^\w[\w\-]*$/
         message = " is not a simple identifier."
@@ -439,8 +447,8 @@ def old_get_default_args_for_collection(collection) #:nodoc:
         prefix = Regexp.last_match[1]
         dsid   = Regexp.last_match[2]
       else
-        prefix = "prefix"
-        dsid   = "subject"   # maybe "auto_#{idx}"
+        prefix = self.tool_config && !self.tool_config.is_version("2.1.0") ? "prefix"  : ""
+        dsid   = "subject"  # maybe "auto_#{idx}"
       end
 
       file_args_array << {
@@ -496,8 +504,8 @@ def old_get_default_args_for_t1list(minc_userfiles) #:nodoc:
         prefix = Regexp.last_match[1]
         dsid   = Regexp.last_match[2]
       else
-        prefix = "prefix"
-        dsid   = "subject"   # maybe "auto_#{idx}"
+        prefix = self.tool_config && !self.tool_config.is_version("2.1.0") ? "prefix"  : ""
+        dsid   = "subject"  # maybe "auto_#{idx}"
       end
 
       file_args_array << {
@@ -569,7 +577,6 @@ def create_combiner(study_name,tids) #:nodoc:
     combiner.description      = study_name
     combiner.status           = 'New'
     combiner.group_id         = self.group_id
-    combiner.launch_time      = self.launch_time
     combiner.batch_id         = self.batch_id
     combiner.params = {
       :civet_study_name     => study_name,
@@ -595,7 +602,6 @@ def create_qc(cid) #:nodoc:
     qc.description = params[:study_name]
     qc.status      = 'New'
     qc.group_id    = self.group_id
-    qc.launch_time = self.launch_time
     qc.batch_id    = self.batch_id
     qc.params      = { :study_from_task_id => cid }
     qc.add_prerequisites_for_setup(cid)

cbrain_task/civet/views/_civet_file_from_col.html.erb

@@ -34,7 +34,7 @@
   <%= form.params_hidden_field "file_args[#{idx}][mk_name]" %>
 </td>
 
-<td><%= form.params_text_field "file_args[#{idx}][prefix]" %></td>
+<td><%= form.params_text_field "file_args[#{idx}][prefix]"  %></td>
 <td><%= form.params_text_field "file_args[#{idx}][dsid]"   %></td>
 
 <% if file[:t2_name].blank? %>

cbrain_task/civet/views/_task_params.html.erb

@@ -33,6 +33,7 @@
   not_at_least_1_1_11 = !@tool_config || !@tool_config.is_at_least_version("1.1.11")
   not_at_least_1_1_12 = !@tool_config || !@tool_config.is_at_least_version("1.1.12")
   not_at_least_2_0_0  = !@tool_config || !@tool_config.is_at_least_version("2.0.0")
+  not_at_least_2_1_0  = !@tool_config || !@tool_config.is_at_least_version("2.1.0")
 
   # Models
   default_models  = [ "icbm152nl", "icbm152lin" ]
@@ -51,6 +52,7 @@
 
 
   default_template = not_at_least_2_0_0 ? ["1.00"] : ["0.50","0.75","1.00"]
+  default_lsq      = not_at_least_2_1_0 ? [ "6", "9", "12" ] : [ "0", "6", "9", "12" ]
 %>
 
 
@@ -83,8 +85,9 @@
 
   <br>
 
-  <%= form.params_label  :lsq, "Degrees of freedom for linear registration:", :title => "Degrees of freedom for linear registration to stereotaxic space" %>
-  <%= form.params_select :lsq, [ "6", "9", "12" ] %>
+  <%= form.params_label  :lsq, "Degrees of freedom for linear registration:", :title => "Degrees of freedom for linear registration to stereotaxic space.\n0 means that the input volume is already in stereotaxic space and linear registration will be skipped.
+" %>
+  <%= form.params_select :lsq, default_lsq %>
 
   <br>
 
@@ -107,6 +110,13 @@
 
   <%= form.params_label      :N3_distance, "N3 distance:", :title => "N3 spline distance in mm (suggested values: 200 for 1.5T scan; 125 or 100 for 3T scan; 0 for MP2RAGE scan in later version than 1.1.12)" %>
   <%= form.params_text_field :N3_distance, :size => 4 %>
+
+  <% if !not_at_least_2_1_0 %>
+    <br>
+
+    <%= form.params_label  :pve, "PVE:", :title => "PVE: advanced = -correct-pve -subcortical -mask-cerebellum\nclassic = -no-correct-pve -no-subcortical -no-mask-cerebellum (old behaviour)" %>
+    <%= form.params_select :pve, [ "advanced", "classic" ] %>
+  <% end %>
 </fieldset>
 
 <P>
@@ -144,7 +154,6 @@
 
     <br>
 
-    <%= form.params_label      :thickness_method,  "Thickness method:", :title => "Thickness method" %>
     <%
        tmethods =  [ "tlink", "tlaplace"]
        if !@task.new_record? && ! @task.params[:thickness_method].blank?
@@ -153,16 +162,23 @@
            tmethods << old_val
          end
        end
-       # tnear only for version < 2.0.0
-       tnear_disabled = not_at_least_2_0_0 ? {} : { :disabled => '1' }
-       params[:thickness_method] = nil if tnear_disabled.present? && params[:thickness_method] == 'tnear'
-       tmethods << [ "tnear", "tnear", tnear_disabled ]
        # Add tfs for version >= 2.0.0
        tfs_disabled = not_at_least_2_0_0 ? { :disabled => '1' } : {}
        params[:thickness_method] = nil if tfs_disabled.present? && params[:thickness_method] == 'tfs'
        tmethods << [ "tfs", "tfs", tfs_disabled ]
     %>
-    <%= form.params_select     :thickness_method, tmethods %>
+
+    <% if not_at_least_2_1_0 %>
+      <%= form.params_label  :thickness_method,  "Thickness method:", :title => "Thickness method" %>
+      <%= form.params_select :thickness_method, tmethods %>
+    <% else %>
+      <%= form.params_label  "thickness_method[]",  "Thickness methods:", :title => "Thickness methods" %>
+      <%= form.params_select "thickness_method[]", tmethods, {}, :multiple => true, :size => 3 %>
+      <p>
+      <%= form.params_label  :thickness_method_for_qc,  "Thickness method for QC:", :title => "Thickness method for QC" %>
+      <%= form.params_select :thickness_method_for_qc, tmethods %>
+    <% end %>
+
     <%= form.params_label      :thickness_kernel, "and kernel size:",
                                :title => "FWHM for surface blurring,\n default: 20 for version 1.1.11 and lower,\n default: 30 for version 1.1.12 and later\nList of integers separated by a ':' is accepted for version 2.0.0 and later" %>
     <%= form.params_text_field :thickness_kernel, :size => not_at_least_2_0_0 ? 4 : 12 %>

cbrain_task/civet/views/public/edit_params_help.html

@@ -42,6 +42,7 @@ <h1>Civet Options</h1>
     <li><b>Head height:</b> Head height in mm for neck cropping. Suggested value: 170. Only available for version 1.1.12 and later.</li>
     <li><b>Mask blood vessels:</b> Mask blood vessels prior to white surface extraction. Only available for version 1.1.12 and later.</li>
     <li><b>N3 distance:</b> N3 spline distance in mm (suggested values: 200 for 1.5T scan; 50-125 for 3T scan. For older 3T scans, low values nearer 50 may work best; for newer 3T scans, high values nearer 125 may work best).</li>
+    <li><b>PVE:</b> advanced = -correct-pve -subcortical -mask-cerebellum or classic = -no-correct-pve -no-subcortical -no-mask-cerebellum (default for version lower than 2.1.0).</li>
 </ul>
 
 
@@ -50,7 +51,8 @@ <h1>Civet Options</h1>
     <li><b>Do NOT build surfaces:</b> Don't build surfaces, if checked.</li>
     <li><b>High resolution surface:</b> Build high resolution surfaces. Only available for version 2.0.0 and later.</li>
     <li><b>Combine left/right surfaces:</b> Combine left and right cortical surfaces, if checked.</li>
-    <li><b>Thickness method:</b> Choose cortical thickness metric [default: tlink; also available:  tlaplace, tnear (only for version 2.0.0 and lower), tfs (Freesurfer's metric, only for version 2.0.0 and later)].</li>
+    <li><b>Thickness method:</b> Choose cortical thickness metric [default: tlink; also available: tlaplace, tfs (Freesurfer's metric, only for version 2.0.0 and later)], starting to version 2.1.0 you can select more than one method.</li>
+    <li><b>Thickness method for QC: Choose the cortical thickness that will be used for the QC, is accepted for version 2.1.0 and later.</b> </li>
     <li><b>Kernel size:</b> Default: 20mm for version 1.1.11 and lower and 30mm for version 1.1.12 and later.
     List of integers separated by a ':' is accepted for version 2.0.0 and later, e.g. 10:20:30.</li>
     <li><b>Resample surfaces:</b> Resample cortical surfaces, if checked.</li>