Merge pull request #49 from MELDProject/report_text

updated text for report

scripts/manage_results/plot_prediction_report.py

@@ -533,7 +533,7 @@ def generate_prediction_report(
                 location = get_cluster_location(predictions[hemi] == cluster)
                 info_cl['location'] = location
                 # get confidence
-                confidence = round(confidences[f'confidence_{cluster}'],2)
+                confidence = round(confidences[f'confidence_{cluster}'],2) * 100
                 info_cl['confidence'] = confidence
                 info_cl['high_low_threshold']=threshold_text
                 # plot info in text box in upper left in axes coords
@@ -545,7 +545,7 @@ def generate_prediction_report(
                         " ",
                         f" Cortical region =  {location}",
                         " ",
-                        f" Confidence score =  {confidence}",
+                        f" Confidence score =  {confidence}%",
                         " ",
                         f"-{threshold_text}",
 
@@ -584,7 +584,7 @@ def generate_prediction_report(
                         alpha=0.7,
                         linestyles="solid",
                     )
-                # display cluster salient vertices
+                # display cluster salient vertices 
                 map_img = new_img_like(imgs["pred"], as_ndarray(data==cluster*100).astype(float), imgs["pred"].affine)
                 display3.add_contours(
                         map_img,
@@ -636,11 +636,11 @@ def generate_prediction_report(
 
         logo = os.path.join(SCRIPTS_DIR, "MELD_logo.png")
 
-        text_info_1 = "Information: \n The MRI data of this patient has been processed through the MELD surface-based FCD detection algorithm. \n Page 1 of this report will show all detected clusters on an inflated view of the brain. \n Subsequent pages characterise individual predicted clusters. \n The last page summarises the software version used to create this report."
-
-        text_info_2 = "The following pages characterise each cluster according to: \n   -The hemisphere the cluster is on \n   -The cortical surface area of the cluster \n   -The cortical region in which the cluster is located \n   -The average of cortical morphological features within the cluster. \n   -The saliency of each feature to the network - if a feature is brighter pink, that feature was more important to the network. \n \n For more information, please read the Guide to using the MELD surface-based FCD detection."
+        text_info_1 = "Information: \n The MRI data of this patient has been processed through the MELD Graph surface-based FCD detection algorithm. \n Page 1 of this report will show all detected clusters on an inflated view of the brain. \n Subsequent pages characterise individual predicted clusters. \n The last page summarises the software version used to create this report."
+        
+        text_info_2 = "The following pages characterise each cluster according to: \n   -The hemisphere the cluster is on \n   -The cortical surface area of the cluster \n   -The cortical region in which the cluster-centre is located \n  -MELD Graph's confidence in the cluster prediction \n  -The average abnormality score - Z-score - of cortical morphological features within the cluster. \n   -The saliency of each feature to the network - if a feature is brighter pink, that feature was more important to the network. \n \n For more information, please read the Guide to using the MELD Graph surface-based FCD detection."
 
-        disclaimer = "Disclaimer: The MELD surface-based FCD detection algorithm is intended for research purposes only and has not been reviewed or approved by the Medicines and Healthcare products Regulatory Agency (MHRA),European Medicine Agency (EMA) or by any other agency. Any clinical application of the software is at the sole risk of the party engaged in such application. \nThere is no warranty of any kind that the software will produce useful results in any way. Use of the software is at the recipient's own risk."
+        disclaimer = "Disclaimer: The MELD Graph surface-based FCD detection algorithm is intended for research purposes only and has not been reviewed or approved by the Medicines and Healthcare products Regulatory Agency (MHRA),European Medicine Agency (EMA) or by any other agency. Any clinical application of the software is at the sole risk of the party engaged in such application. \nThere is no warranty of any kind that the software will produce useful results in any way. Use of the software is at the recipient's own risk."
 
         footer_txt = "This report was automatically generated by software by Mathilde Ripart, Hannah Spitzer, Sophie Adler and Konrad Wagstyl on behalf of the MELD Project"