Faster conversion when opts.numSeries != 0

README.md

@@ -71,6 +71,7 @@ If you have any problems with the cmake build script described above or want to
   - [divest](https://github.com/jonclayden/divest) R interface to dcm2niix.
   - [sci-tran dcm2niix](https://github.com/scitran-apps/dcm2niix) docker.
   - [neuro_docker](https://github.com/Neurita/neuro_docker) includes dcm2niix as part of a single, static Dockerfile.
+  - [https://github.com/lalet/boutiques-dcm2niix boutiques-dcm2niix] is a dockerfile for installing and validating dcm2niix.
   - [neurodocker](https://github.com/kaczmarj/neurodocker) generates [custom](https://github.com/rordenlab/dcm2niix/issues/138) Dockerfiles given specific versions of neuroimaging software.
   - [dcm2niix_afni](https://afni.nimh.nih.gov/pub/dist/doc/program_help/dcm2niix_afni.html) is a version of dcm2niix included with the [AFNI](https://afni.nimh.nih.gov/) distribution.
   - [MRIcroGL](https://github.com/neurolabusc/MRIcroGL) is available for MacOS, Linux and Windows and provides a graphical interface for dcm2niix. You can get compiled copies from the [MRIcroGL NITRC web site](https://www.nitrc.org/projects/mricrogl/).

console/main_console.cpp

@@ -297,7 +297,7 @@ int main(int argc, const char * argv[])
                     opts.isCreateText = true;
     		#if !defined(_WIN64) && !defined(_WIN32) //shell script for Unix only
             } else if (argv[i][1] == 'u') {
-				checkUpToDate();
+				return checkUpToDate();
 			#endif
             } else if ((argv[i][1] == 'v') && ((i+1) < argc)) {
                 i++;
@@ -340,7 +340,6 @@ int main(int argc, const char * argv[])
               if (seriesNumber < 0)
               	opts.numSeries = -1; //report series: convert none
               else if ((opts.numSeries >= 0) && (opts.numSeries < MAX_NUM_SERIES)) {
-
                   opts.seriesNumber[opts.numSeries] = seriesNumber;
                   opts.numSeries += 1;
                 }

console/nii_dicom_batch.cpp

@@ -2477,8 +2477,12 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis
         free(imgM);
         return EXIT_FAILURE;
     }
-    if (opts.numSeries < 0) { //report series but do not convert
+    // Prevent these DICOM files from being reused.
+    for(int i = 0; i < nConvert; ++i)
+      dcmList[dcmSort[i].indx].converted2NII = 1;
+    if (opts.numSeries < 0) { //report series number but do not convert
     	printMessage("\t%d\t%s\n", dcmList[dcmSort[0].indx].seriesNum, pathoutname);
+    	printMessage(" %s\n",nameList->str[dcmSort[0].indx]);
     	return EXIT_SUCCESS;
     }
     checkSliceTiming(&dcmList[indx0], &dcmList[indx1]);
@@ -2515,7 +2519,6 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis
         free(imgM);
         return EXIT_SUCCESS;
     }
-
 	nii_SaveText(pathoutname, dcmList[dcmSort[0].indx], opts, &hdr0, nameList->str[indx]);
 	int numADC = 0;
     int * volOrderIndex = nii_SaveDTI(pathoutname,nConvert, dcmSort, dcmList, opts, sliceDir, dti4D, &numADC);
@@ -2586,20 +2589,13 @@ int saveDcm2Nii(int nConvert, struct TDCMsort dcmSort[],struct TDICOMdata dcmLis
     }
     if ((opts.isCrop) && (dcmList[indx0].is3DAcq)   && (hdr0.dim[3] > 1) && (hdr0.dim[0] < 4))//for T1 scan: && (dcmList[indx0].TE < 25)
         returnCode = nii_saveCrop(pathoutname, hdr0, imgM,opts); //n.b. must be run AFTER nii_setOrtho()!
-
 #ifdef HAVE_R
     // Note that for R, only one image should be created per series
     // Hence the logical OR here
     if (returnCode == EXIT_SUCCESS || nii_saveNII(pathoutname,hdr0,imgM,opts) == EXIT_SUCCESS)
         nii_saveAttributes(dcmList[dcmSort[0].indx], hdr0, opts);
 #endif
-
     free(imgM);
-
-    // Prevent these DICOM files from being reused.
-    for(int i = 0; i < nConvert; ++i)
-      dcmList[dcmSort[i].indx].converted2NII = 1;
-
     return returnCode;//EXIT_SUCCESS;
 }// saveDcm2Nii()