Comments (9)
neurolabusc
commented on June 6, 2024
Curious, when I try to replicate your issue on MacOS 10.11.6 I get
./dcm2niix -b y -z i -x n -t n -m n -f fmap -o "~/tst_t1/j" -s n -v n ~/tst_t1
Chris Rorden's dcm2niiX version 1Jan2017 (64-bit MacOS)
Error: Output folder invalid: ~/tst_t1/j
which one would expect due to line 1943 of nii_dicom_batch.cpp. Is it possible that the is_dir function does not work on your operating system (e.g. what does "stat" return when given an invalid path name, should be -1). Should be an easy patch if we can replicate your problem.
While not related to this issue, in general I would suggest -o "/tmp/A00012$A" instead of -o /tmp/A00012$A/. The quote marks ensure that if your variable contains a space the function will still work. Even more pedantically, while my software can handle either a path or a directory, you are specifying an output directory, so the trailing '/' is not required.
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neurolabusc
commented on June 6, 2024
I am also unable to replicate your problem using NeuroDebian 8.0. Anything unusual about your /tmp file system?
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yarikoptic
commented on June 6, 2024
re stat:
(venv)mvdoc@smaug /tmp $ stat nonexisting/; echo $?
stat: cannot stat ‘nonexisting/’: No such file or directory
1
(venv)mvdoc@smaug /tmp $ stat nonexisting; echo $?
stat: cannot stat ‘nonexisting’: No such file or directory
1but I guess you meant syscall? lazy me just did strace on a stat call
(venv)mvdoc@smaug /tmp $ strace stat nonexisting 2>&1 | grep 'stat(.*nonex'
lstat("nonexisting", 0x7fff6a4a4c40) = -1 ENOENT (No such file or directory)re spaces -- you are totally correct, but here I was saving keystrokes and was aware of having no spaces in the variables
re trailing '/' -- I like having those for my own sake -- at times saw -o used as a prefix not necessarily directory specification. Having / guarantees it and in spoiled-by-Python world os.path.join takes care about those ;)
if needed -- could check with minimalistic c program later on...
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neurolabusc
commented on June 6, 2024
Rather than make a minimal program, I would suggest modifying dcm2niix to have it tell you (1) if it recognizes you have used the -o option (e.g. set an output folder) and (2) tell you the folder it will check with stat(). The modifications below should do it:
@@ -1930,11 +1930,14 @@
if (isFile) //if user passes ~/dicom/mr1.dcm we will look at all files in ~/dicom
dropFilenameFromPath(opts->indir);//getParentFolder(opts.indir, opts.indir);
dropTrailingFileSep(opts->indir);
- if (strlen(opts->outdir) < 1)
- strcpy(opts->outdir,opts->indir);
+ if (strlen(opts->outdir) < 1) {
+ printWarning("Output folder not specified using input folder '%s'\n",opts->indir);
+ strcpy(opts->outdir,opts->indir);
+ }
dropTrailingFileSep(opts->outdir);
if (is_fileNotDir(opts->outdir)) //if user passes ~/dicom/mr1.dcm we will look at all files in ~/dicom
dropFilenameFromPath(opts->outdir);//getParentFolder(opts.indir, opts.indir);
+ printWarning("Checking existence of output folder '%s'\n",opts->outdir);
if (!is_dir(opts->outdir,true)) {
#ifdef myUseInDirIfOutDirUnavailable
printWarning("Output folder invalid %s will try %s\n",opts->outdir,opts->indir);
from dcm2niix.
yarikoptic
commented on June 6, 2024
ok -- will do... meanwhile -- seems to be a regression:
new:
(venv)mvdoc@smaug /tmp $ rm -rf nonexisting fmap*; dcm2niix -b y -z i -x n -t n -m n -f fmap -o /tmp/nonexisting -s n -v n /mnt/btrfs/dbic/inbox/DICOM/2016/12/04/A000122/006*fmap*/000001.dcm; echo "exited with $?"; ls -lta | head
Chris Rorden's dcm2niiX version 1Jan2017 (64-bit Linux)
Found 64 DICOM image(s)
Convert 64 DICOM as /tmp/fmap (90x90x64x1)
Conversion required 0.103971 seconds.
exited with 0
total 121284
-rw-r--r-- 1 mvdoc mvdoc 628504 Jan 11 13:02 fmap.nii.gz
drwxrwxrwt 48 root root 12288 Jan 11 13:02 .
-rw-r--r-- 1 mvdoc mvdoc 378 Jan 11 13:02 fmap.json
drwx------ 2 neurodebian neurodebian 4096 Jan 11 11:57 ssh-f6P5rL2ySh
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:09 A000122__
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:09 A000121__
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:03 A000122_
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:03 A000121_
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 10:56 A000122old(er) the one from neurodebian
(venv)mvdoc@smaug /tmp $ rm -rf nonexisting fmap*; dcm2niix -b y -z i -x n -t n -m n -f fmap -o /tmp/nonexisting -s n -v n /mnt/btrfs/dbic/inbox/DICOM/2016/12/04/A000122/006*fmap*/000001.dcm; echo "exited with $?"; ls -lta | head
Chris Rorden's dcm2niiX version 29Sept2016 (64-bit Linux)
Error: output folder invalid: /tmp/nonexisting
exited with 1
total 120664
drwxrwxrwt 48 root root 12288 Jan 11 13:02 .
drwx------ 2 neurodebian neurodebian 4096 Jan 11 11:57 ssh-f6P5rL2ySh
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:09 A000122__
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:09 A000121__
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:03 A000122_
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:03 A000121_
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 10:56 A000122
-rw-r--r-- 1 mvdoc mvdoc 36282 Jan 11 10:56 dcm2niix-v.log
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 10:56 A000121from dcm2niix.
yarikoptic
commented on June 6, 2024
(venv)mvdoc@smaug /tmp $ rm -rf nonexisting fmap*; dcm2niix -b y -z i -x n -t n -m n -f fmap -o /tmp/nonexisting -s n -v n /mnt/btrfs/dbic/inbox/DICOM/2016/12/04/A000122/006*fmap*/000001.dcm; echo "exited with $?"; ls -lta | head
zsh: no matches found: fmap*
Chris Rorden's dcm2niiX version 1Jan2017 (64-bit Linux)
Warning: Checking existence of output folder '/tmp'
Found 64 DICOM image(s)
Convert 64 DICOM as /tmp/fmap (90x90x64x1)
Conversion required 0.098941 seconds.
exited with 0
total 121400
drwxrwxrwt 48 root root 12288 Jan 11 13:27 .
-rw-r--r-- 1 mvdoc mvdoc 628504 Jan 11 13:27 fmap.nii.gz
-rw-r--r-- 1 mvdoc mvdoc 378 Jan 11 13:27 fmap.json
-rw-r--r-- 1 yoh yoh 115612 Jan 11 13:26 dcm2niix_20160921+git59-gbd1b713-1+p1_amd64.deb
drwx------ 2 neurodebian neurodebian 4096 Jan 11 11:57 ssh-f6P5rL2ySh
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:09 A000122__
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:09 A000121__
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:03 A000122_
drwxr-xr-x 2 mvdoc mvdoc 4096 Jan 11 11:03 A000121_patch was (so I didn't screw it up since had to manually paste -- simple diff/patch didn't work out):
$> cat debian/patches/up_verbose_outdir_analysis
--- a/console/nii_dicom_batch.cpp
+++ b/console/nii_dicom_batch.cpp
@@ -1930,11 +1930,14 @@ 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);//getParentFolder(opts.indir, opts.indir);
dropTrailingFileSep(opts->indir);
- if (strlen(opts->outdir) < 1)
+ if (strlen(opts->outdir) < 1) {
+ printWarning("Output folder not specified using input folder '%s'\n",opts->indir);
strcpy(opts->outdir,opts->indir);
+ }
dropTrailingFileSep(opts->outdir);
if (is_fileNotDir(opts->outdir)) //if user passes ~/dicom/mr1.dcm we will look at all files in ~/dicom
dropFilenameFromPath(opts->outdir);//getParentFolder(opts.indir, opts.indir);
+ printWarning("Checking existence of output folder '%s'\n",opts->outdir);
if (!is_dir(opts->outdir,true)) {
#ifdef myUseInDirIfOutDirUnavailable
printWarning("Output folder invalid %s will try %s\n",opts->outdir,opts->indir);
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neurolabusc
commented on June 6, 2024
OK, so it looks like the issue is not with stat() but with how the outdir is set - perhaps due to the expansion of the inputs *fmap*. What does this do:
--- ./console/main_console.cpp 2016-12-14 11:54:19.000000000 -0500
+++ ./main_console.cpp 2017-01-11 13:40:02.000000000 -0500
@@ -186,6 +186,7 @@
i++;
isCustomOutDir = true;
strcpy(opts.outdir,argv[i]);
+ printf("customOutDir set to %s\n", opts.outdir);
}
lastCommandArg = i;
} //if parameter is a command
@@ -204,7 +205,10 @@
clock_t start = clock();
for (i = (lastCommandArg+1); i < argc; i++) {
strcpy(opts.indir,argv[i]); // [argc-1]
+ printf("inDir %s\n", opts.indir);
+ printf("outDir %s\n", opts.outdir);
if (!isCustomOutDir) strcpy(opts.outdir,opts.indir);
+ printf("outDir(again) set to %s\n", opts.outdir);
if (nii_loadDir(&opts) != EXIT_SUCCESS)
return EXIT_FAILURE;
}
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yarikoptic
commented on June 6, 2024
here is more ;) may be tomorrow finally will debug it properly to point the location of the problem
mvdoc@smaug /tmp $ rm -rf nonexisting fmap*; /tmp/dcm2niix -b y -z i -x n -t n -m n -f fmap -o /tmp/nonexisting -s n -v n /mnt/btrfs/dbic/inbox/DICOM/2016/12/04/A000122/006*fmap*/000001.dcm; echo "exited with $?"; ls -lta | head
Chris Rorden's dcm2niiX version 1Jan2017 (64-bit Linux)
customOutDir set to /tmp/nonexisting
inDir /mnt/btrfs/dbic/inbox/DICOM/2016/12/04/A000122/006-fmap_acq-2.4mm/000001.dcm
outDir /tmp/nonexisting
outDir(again) set to /tmp/nonexisting
Warning: Checking existence of output folder '/tmp'
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neurolabusc
commented on June 6, 2024
Fixed in latest release
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