Explicit exit code for missing input/output folder (https://discourse…

….slicer.org/t/import-error-in-dicom-module/8511/7)

Philips/README.md

@@ -94,7 +94,7 @@ MyCustomDirections
 
 Philips DICOMs do not contain all the information desired by many neuroscientists. Due to this, the [BIDS](http://bids.neuroimaging.io/) files created by dcm2niix are impoverished relative to data from other vendors. This reflects a limitation in the Philips DICOMs, not dcm2niix.
 
-[Slice timing correction](https://www.mccauslandcenter.sc.edu/crnl/tools/stc) can account for some variability in fMRI datasets. Unfortunately, Philips DICOM data [does not encode slice timing information](https://neurostars.org/t/heudiconv-no-extraction-of-slice-timing-data-based-on-philips-dicoms/2201/4). Therefore, dcm2niix is unable to populate the "SliceTiming" BIDS field. However, one can typically infer slice timing by recording the [mode and number of packages](https://en.wikibooks.org/w/index.php?title=SPM/Slice_Timing&stable=0#Philips_scanners) reported for the sequence on the scanner console.
+[Slice timing correction](https://www.mccauslandcenter.sc.edu/crnl/tools/stc) can account for some variability in fMRI datasets. Unfortunately, Philips DICOM data [does not encode slice timing information](https://neurostars.org/t/heudiconv-no-extraction-of-slice-timing-data-based-on-philips-dicoms/2201/4). Therefore, dcm2niix is unable to populate the "SliceTiming" BIDS field. However, one can typically infer slice timing by recording the [mode and number of packages](https://en.wikibooks.org/w/index.php?title=SPM/Slice_Timing&stable=0#Philips_scanners) reported for the sequence on the scanner console or the [sequence PDF](http://adni.loni.usc.edu/wp-content/uploads/2017/09/ADNI-3-Basic-Philips-R5.pdf). For precise timing, it is also worth knowing if equidistant "temporal slice spacing" is set and whether "prospect. motion corr." is on or off (if on, a short delay occurs between volumes).
 
 Likewise, the BIDS tag "PhaseEncodingDirection" allows tools like [eddy](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy) and [TOPUP](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup) to undistort images. While the Philips DICOM header distinguishes the phase encoding axis (e.g. anterior-posterior vs left-right) it does not encode the polarity (A->P vs P->A).
 

console/nii_dicom.cpp

@@ -4048,6 +4048,8 @@ struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, stru
 #define  kDirectoryRecordSequence 0x0004+(0x1220 << 16 )
 //#define  kSpecificCharacterSet 0x0008+(0x0005 << 16 ) //someday we should handle foreign characters...
 #define  kImageTypeTag 0x0008+(0x0008 << 16 )
+//#define  kSOPInstanceUID 0x0008+(0x0018 << 16 ) //Philips inserts time as last item, e.g. ?.?.?.YYYYMMDDHHmmSS.SSSS
+// not reliable  https://neurostars.org/t/heudiconv-no-extraction-of-slice-timing-data-based-on-philips-dicoms/2201/21
 #define  kStudyDate 0x0008+(0x0020 << 16 )
 #define  kAcquisitionDate 0x0008+(0x0022 << 16 )
 #define  kAcquisitionDateTime 0x0008+(0x002A << 16 )

console/nii_dicom.h

@@ -86,6 +86,10 @@ static const int kMaxSlice2D = 64000; //maximum number of 2D slices in 4D (Phili
 #define kEXIT_NO_VALID_FILES_FOUND  2
 #define kEXIT_REPORT_VERSION  3
 #define kEXIT_CORRUPT_FILE_FOUND  4
+#define kEXIT_INPUT_FOLDER_INVALID  5
+#define kEXIT_OUTPUT_FOLDER_INVALID  6
+#define kEXIT_OUTPUT_FOLDER_READ_ONLY  7
+
 static const int kSliceOrientUnknown = 0;
 static const int kSliceOrientTra = 1;
 static const int kSliceOrientSag = 2;

console/nii_dicom_batch.cpp

@@ -2159,6 +2159,8 @@ int nii_createFilename(struct TDICOMdata dcm, char * niiFilename, struct TDCMopt
         strcpy(pth, opts.outdir);
         int w =access(pth,W_OK);
         if (w != 0) {
+        	//should never happen except with "-b i": see kEXIT_OUTPUT_FOLDER_READ_ONLY for early termination
+        	// with "-b i" the code below generates a warning but no files are created
 			if (getcwd(pth, sizeof(pth)) != NULL) {
 				#ifdef USE_CWD_IF_OUTDIR_NO_WRITE //optional: fall back to current working directory
 				w =access(pth,W_OK);
@@ -4462,6 +4464,7 @@ void sliceTimingGE(struct TDCMsort *dcmSort,struct TDICOMdata *dcmList, struct n
 
 int sliceTimingCore(struct TDCMsort *dcmSort,struct TDICOMdata *dcmList, struct nifti_1_header * hdr, int verbose, const char * filename, int nConvert) {
 	int sliceDir = 0;
+	if (hdr->dim[3] < 2) return sliceDir;
 	//uint64_t indx0 = dcmSort[0].indx;
 	//uint64_t indx1 = dcmSort[1].indx;
 	struct TDICOMdata * d0 = &dcmList[dcmSort[0].indx];
@@ -6072,6 +6075,11 @@ int nii_loadDir(struct TDCMopts* opts) {
     if (isFile) //if user passes ~/dicom/mr1.dcm we will look at all files in ~/dicom
         dropFilenameFromPath(opts->indir);
     dropTrailingFileSep(opts->indir);
+    if (!is_dir(opts->indir,true)) {
+		printError("Input folder invalid: %s\n",opts->indir);
+		return kEXIT_INPUT_FOLDER_INVALID;    		
+    }
+
 #ifdef USING_R
     // Full file paths are only used by R/divest when reorganising DICOM files
     if (opts->isRenameNotConvert) {
@@ -6086,9 +6094,29 @@ int nii_loadDir(struct TDCMopts* opts) {
 		strcpy(opts->outdir,opts->indir);
 		#else
 		printError("Output folder invalid: %s\n",opts->outdir);
-		return EXIT_FAILURE;
+		return kEXIT_OUTPUT_FOLDER_INVALID;
 		#endif
     }
+    //check file permissions
+    if ((opts->isCreateBIDS != false) || (opts->isOnlyBIDS != true)) { //output files expected: either BIDS or images
+    	int w =access(opts->outdir,W_OK);
+    	if (w != 0) {
+    		#ifdef USE_CWD_IF_OUTDIR_NO_WRITE
+    		char outdir[512];
+    		strcpy(outdir,opts->outdir);
+			strcpy(opts->outdir,opts->indir);
+			w =access(opts->outdir,W_OK);
+			if (w != 0) {
+				printError("Unable to write to output folder: %s\n",outdir);
+				return kEXIT_OUTPUT_FOLDER_READ_ONLY;				
+			} else
+				printWarning("Writing to working directory, unable to write to output folder: %s\n",outdir);
+			#else
+    		printError("Unable to write to output folder: %s\n",opts->outdir);
+			return kEXIT_OUTPUT_FOLDER_READ_ONLY;
+    		#endif
+		}
+	}	
 #ifdef USING_R
     }
 #endif