Fixelcfestats error: no DICOM images

1

Hi all,
I’m trying out the new Fixel Based Analysis for single shell DWI. I’ve just followed the latest online tutorial and run into a problem at the fixel stats stage.

After applying the fixelcfestats command:

fixelcfestats fd files.txt design_matrix.txt contrast_matrix.txt input_tracks_2_million_sift.tck stats_fd

I get the following error:

fixelcfestats: number of fixels: 176564
fixelcfestats: [100%] preloading data for "fd/directions.mif"
fixelcfestats: [100%] loading template fixel directions and positions
fixelcfestats: [done] scanning DICOM folder "fd/"
fixelcfestats: [done] validating input files...
fixelcfestats: [ERROR] no DICOM images found in "fd/"
fixelcfestats: [ERROR] error opening image "fd/"

Any ideas?

The ‘fd’ folder contains the subject data as .mif files as well as the ‘directions.mif’ and ‘index.mif’ files.
The ‘files.txt’ folder just contains a list each data file within the fd folder.
ie
001.mif
002.mif
etc…

2

Hi Michael,
Your inputs and command look fine. I’m not sure why it’s trying to scan the ‘fd’ folder as if it were a DICOM.

Can you please report back the output when running fixelcfestats with the -debug option?

Also, maybe check your files.txt doesn’t contain any spaces or empty lines (though it should be robust to this).
Cheers,
Dave

3

Hi Dave,
Thanks for getting back so quickly. Just before I ran the -debug option I checked for empty spaces and you were right, that was the issue.
I had an empty line at the end of the list. Deleted it and now it’s working! Probably should have checked for that myself…
Thanks for your help.
Michael

4

Thanks Michael, I’ll fix this up so users don’t get caught out in the future.

1 Like
5

Hi,

I am also getting this error for fixelcfestats

I have the following files in my files.txt No spaces or extra lines present

HC03.mif
HC04.mif
HC05.mif

I have ran the command with -debug option and get the following description (note only part of an extremely long debug message)

fixelcfestats: [DEBUG] memory-mapping file "fd/index.mif"...
fixelcfestats: [DEBUG] file "fd/index.mif" mapped at 0x7ffab083a000, size 10770252 (read-only)
fixelcfestats: [DEBUG] DICOM magic number not found in file "fd/index.mif" - trying truncated format
fixelcfestats: [DEBUG] file "fd/index.mif" does not have the DICOM magic number or the .dcm extension - assuming not 
DICOM
fixelcfestats: [DEBUG] unmapping file "fd/index.mif"
fixelcfestats: [INFO] error reading file "fd/index.mif" - ignored
fixelcfestats: [.   ] scanning DICOM folder "fd/"... 
fixelcfestats: [DEBUG] memory-mapping file "fd/directions.mif"...
fixelcfestats: [DEBUG] file "fd/directions.mif" mapped at 0x7ffab17be000, size 2607012 (read-only)
fixelcfestats: [DEBUG] DICOM magic number not found in file "fd/directions.mif" - trying truncated format
fixelcfestats: [DEBUG] file "fd/directions.mif" does not have the DICOM magic number or the .dcm extension - 
assuming  not DICOM
fixelcfestats: [DEBUG] unmapping file "fd/directions.mif"
fixelcfestats: [INFO] error reading file "fd/directions.mif" - ignored
fixelcfestats: [DEBUG] memory-mapping file "fd/HC03.mif"...
fixelcfestats: [DEBUG] file "fd/HC03.mif" mapped at 0x7ffab50d1000, size 886916 (read-only)
fixelcfestats: [DEBUG] DICOM magic number not found in file "fd/HC03.mif" - trying truncated format
fixelcfestats: [DEBUG] file "fd/HC03.mif" does not have the DICOM magic number or the .dcm extension - assuming not 
DICOM
fixelcfestats: [DEBUG] unmapping file "fd/HC03.mif"
fixelcfestats: [INFO] error reading file "fd/HC03.mif" - ignored
fixelcfestats: [DEBUG] memory-mapping file "fd/HC04.mif"...
fixelcfestats: [DEBUG] file "fd/HC04.mif" mapped at 0x7ffab50d1000, size 886916 (read-only)
fixelcfestats: [DEBUG] DICOM magic number not found in file "fd/HC04.mif" - trying truncated format
fixelcfestats: [DEBUG] file "fd/HC04.mif" does not have the DICOM magic number or the .dcm extension - assuming not 
DICOM
fixelcfestats: [DEBUG] unmapping file "fd/HC04.mif"
fixelcfestats: [INFO] error reading file "fd/HC04.mif" - ignored
fixelcfestats: [DEBUG] memory-mapping file "fd/HC05.mif"...
fixelcfestats: [DEBUG] file "fd/HC05.mif" mapped at 0x7ffab50d1000, size 886916 (read-only)
fixelcfestats: [DEBUG] DICOM magic number not found in file "fd/HC05.mif" - trying truncated format
fixelcfestats: [DEBUG] file "fd/HC05.mif" does not have the DICOM magic number or the .dcm extension - assuming not 
DICOM
fixelcfestats: [DEBUG] unmapping file "fd/HC05.mif"
fixelcfestats: [INFO] error reading file "fd/HC05.mif" - ignored
fixelcfestats: [done] scanning DICOM folder "fd/"
fixelcfestats: [done] validating input files
fixelcfestats: [DEBUG] deleting scratch buffer for image "scratch fixel mask"...
fixelcfestats: [DEBUG] image "scratch fixel mask" unloaded
fixelcfestats: [DEBUG] unmapping file "fd/index.mif"
fixelcfestats: [DEBUG] image "fd/index.mif" unloaded
fixelcfestats: [ERROR] no DICOM images found in "fd/"
fixelcfestats: [ERROR] error opening image "fd/"

Could you provide any suggestions?