Hello!
We just moved to a new location with a new scanner and we are having trouble with our processing pipeline. Our Seimens scanner outputs all the scans from a scanning session (localizer, MPR, etc.) into one folder. A few examples are listed in the attached png. When I unpack the files using freesurfer (unpacksdcmdir), it tells me the info below.
1 Localizer ok 256 256 3 1 MR.1.3.12.2.1107.5.2.19.45407.2017120111250035990000191
2 T1w_MPR ok 320 300 224 1 MR.1.3.12.2.1107.5.2.19.45407.2017120111331335771600696
3 T1w_MPR ok 320 300 224 1 MR.1.3.12.2.1107.5.2.19.45407.2017120111331335072100695
4 ep2d_bold_1_speech ok 448 448 1 3 MR.1.3.12.2.1107.5.2.19.45407.2017120111364684688802025
5 ep2d_bold_1_speech ok 448 448 1 25 MR.1.3.12.2.1107.5.2.19.45407.2017120111453666582902396
6 ep2d_bold_2_speech ok 448 448 1 20 MR.1.3.12.2.1107.5.2.19.45407.2017120111573891098805295
7 ep2d_bold_3_speech ok 448 448 1 42 MR.1.3.12.2.1107.5.2.19.45407.2017120112125922493307559
8 ep2d_bold_rest ok 560 560 1 150 MR.1.3.12.2.1107.5.2.19.45407.2017120112213624227612316
Our previous data was packaged into folders for each run and we would apply the below sequence
Dimon -infile_prefix (dicom data e.g. 123) -dicom_org -use_last_elem -GERT_Reco -save_file_list dimon.list -quit
to3d -prefix (s999_MPRAGE_1) -@ <dimon.list
However, now when I input Dimon -infile_prefix MR -dicom_org -use_last_elem -GERT_Reco -save_file_list dimon.list -quit, I get the output below.
Dimon -infile_prefix MR -dicom_org -use_last_elem -GERT_Reco -save_file_list dimon.list -quit
Dimon running, use <ctrl-c> to quit...
-- scanning for first volume
-- reading 691 image files *+ WARNING: Image Positions do not lie in same direction as cross product vector: 0.707107
..........
-- first volume found (2 slices)
-- scanning for additional volumes...
-- run 1: 1 - zoffset outside volume range of 0.000000 to 30.000000
- banishing image MR.1.3.12.2.1107.5.2.19.45407.2017120111331335771600696 to FAILED state
--> will try to continue...
** bad image state: ind 4, errs 0, state -2 (FSTATE_FAILED), file MR.1.3.12.2.1107.5.2.19.45407.2017120111331335771600696
. . .
final run statistics:
volume info :
slices : 2
z_first : 0
z_last : 30
z_delta : 30
oblique : no
mos_nslices : 0
run # 1 : volumes = 1, first file (#0) = MR.1.3.12.2.1107.5.2.19.45407.2017120111250036157300193
-- writing file list to dimon.list...
** have 688 unprocessed image(s)
I assume this has something to do with the files not being named and/or sorted correctly, but I'm not really sure how to go about fixing the issue. I've tried dicom_hdr MR*, which gives me a whole lot of info on the dicoms, but I don't know what to do with that to create a sorting/name rule, or if there is a simpler solution.
Any help would be greatly appreciated!
Thanks!
Samantha
