Hi Rick and guys,
I'm from Porto Alegre/Brazil and I'm implementing the real time fmri using afni. I was looking for a solution to an error and I found this topic.
So, my error is similar. I developed a script that detect the new patient folder when the exam start and then I start Dimon with the script below:
Dimon -rt \
-infile_prefix $PATIENTDIR/i \
-host $RTFMRI_AFNI_HOST \
-tr $TR_TIME \
-nt $VOLUMES_PER_RUN \
-num_slices $NUMBER_OF_SLICES \
-quit
I'm using a GE 3T Scanner.
I am able to detect the DICOM images from the folder and send to afni in real time only if I use 3 slices. If I set any other slice number Dimon give's me the same error that John describe or this other:
***********************************************
Error: slice missing!
current file : e13384396/s13386501/i13386548.MRDC.48
expected z-offset : -9.2044
actual z-offset : -5.6045
current run : 16
slice number : 2 (of 5)
***********************************************
I get the same error also when I use Dimon in offline mode with a folder without using -dicom_org command, so maybe I think the problem is the order that the images arrived in the folder or something like,...
I made an scan sequency with debug and you can see details below:
Brain Institute
Porto Alegre-RS-Brazil
Description: This script will help you to Send the images to AFNI in real time.
-->Scanner Base Directory: home1/sdc_image_pool/images
--> To send the images in real time is necessary run the localizer exam before.
--> Press Enter only if you have executed the localizer exam from this patient.
--> home1/sdc_image_pool/images/p13384395/ is the Patient created for this exam at Wed Apr 8 21:20:45 BRT 2015. Is this correct? (yes/no):
--> Please insert TR in the form [2.0 or 3.0 or 5.0]:--> TR was sucessfully changed to: 2.0
--> Please insert the number of volumes:--> Number of volumes was sucessfully changed to: 30
--> Please insert the number of slices:--> Number of slices was sucessfully changed to: 5
-->Searching for the new images from the Scanner. Start the Exam now!
..
..
..
..
..
..
..
..
..
..
home1/sdc_image_pool/images/p13384395/e13384396/s13386501 is now the current Patient.
Dimon running, use <ctrl-c> to quit...
-- starting I/O to afni
Opening control channel tcp:10.63.183.78:7961 to AFNI.
Entering AFNI_WAIT_CONTROL_MODE.
Control channel connected to AFNI. Entering AFNI_OPEN_DATA_MODE.
Sending control information to AFNI:
tcp:10.63.183.78:7960
Opening data channel tcp:10.63.183.78:7960 to AFNI.
Can't connect? tcp_connect[connect]: Connection refused
Entering AFNI_CATCHUP_MODE.
Entering AFNI_CONTINUE_MODE.
++ comm link to afni established at <10.63.183.78>
-- scanning for first volume
-- n2scan = 5, max = 40
++ allocating 5 image pointers (was 0)
-- not a Siemens Mosaic
-- used process_siemens_mosaic...
++ Data detected to be oblique
end init_options : opts_t struct at 0x94d3f0 :
start_file = (NULL)
start_dir = (NULL)
dicom_glob = e13384396/s13386501/i*
infile_list = (NULL)
sp = (NULL)
gert_outdir = (NULL)
(argv, argc) = (0x7fffa4cb3948, 17)
tr, ep = 2, 0.01
nt, num_slices = 30, 5
nice, pause = 0, 0
sleep_frac = 1.5
sleep_init = 0
sleep_vol = 0
debug = 3
quit, use_dicom = 1, 1
use_last_elem = 0
show_sorted_list = 0
gert_reco = 0
gert_filename = (NULL)
gert_prefix = (NULL)
gert_nz = 0
gert_format = 0
gert_exec = 0
gert_quiterr = 0
dicom_org = 0
sort_num_suff = 0
sort_acq_time = 0
rev_org_dir = 0
rev_sort_dir = 0
flist_file = (NULL)
(rt, swap, rev_bo) = (1, 0, 0)
host = 10.63.183.78
drive_list(u,a,p) = 0, 0, (nil)
wait_list (u,a,p) = 0, 0, (nil)
rt_list (u,a,p) = 0, 0, (nil)
end init_options : param_t struct at 0x94d3a0 :
ftype = 4
(nused, nalloc) = (0, 0)
flist = (nil)
glob_dir = e13384396/s13386501/i*
nfiles = 0
fnames = (nil)
++ realloc of flist : param_t struct at 0x94d3a0 :
ftype = 4
(nused, nalloc) = (0, 40)
flist = 0x953680
glob_dir = e13384396/s13386501/i*
nfiles = 5
fnames = 0x953560
-- is_oblique = 1, is_mosaic = 0
++ allocating 8192 bytes for is->x_im
++ allocated image 0 at address 0x954fc0
-- not a Siemens Mosaic
-- used process_siemens_mosaic...
post mri_read_dicom_get_obliquity -- oblique info = 2
3.4375 0.0000 0.0000 -108.2810
0.0000 3.4375 -0.0159 -125.8070
0.0000 0.0152 3.6000 -12.8044
0.0000 0.0000 0.0000 1.0000
++ allocated image 1 at address 0x95b400
++ allocated image 2 at address 0x95d410
++ allocated image 3 at address 0x95f420
++ allocated image 4 at address 0x961430
++ updating delta (3.599960) to mean dz (3.599960)
+d cov: returning first, last, delta = 0, 1, 3.59996
.-d computed nap_time is 3000 ms (TR = 2.00)
++ allocating 10 image pointers (was 5)
++ allocated image 5 at address 0x963440
++ allocated image 6 at address 0x967e20
++ allocated image 7 at address 0x969e30
++ allocated image 8 at address 0x96be40
++ allocated image 9 at address 0x96de50
++ updating delta (3.599960) to mean dz (3.599960)
+d cov: returning first, last, delta = 0, 1, 3.59996
*************************************************
Error: missing slice in first volume!
detected at file: e13384396/s13386501/i13386504.MRDC.5
re-starting at file: e13384396/s13386501/i13386507.MRDC.6
*************************************************
.++ allocating 15 image pointers (was 10)
++ allocated image 10 at address 0x96fe60
++ allocated image 11 at address 0x971e70
++ allocated image 12 at address 0x973e80
++ allocated image 13 at address 0x975e90
++ allocated image 14 at address 0x977ea0
++ updating delta (3.599960) to mean dz (3.599963)
+d cov: returning first, last, delta = 0, 4, 3.59996
-- num_slices_ok (same location): checking 5 against 5...
+d (same location) num_slices found matches option, 5
+d found first slice of second volume
-- data is oblique
-- first volume found (5 slices)
-- scanned 5 image files, from <e13384396/s13386501/i13386502.MRDC.1> to <e13384396/s13386501/i13386506.MRDC.4>
end read_ge_files : param_t struct at 0x94d3a0 :
ftype = 4
(nused, nalloc) = (5, 40)
flist = 0x953680
glob_dir = e13384396/s13386501/i*
nfiles = 5
fnames = 0x953560
-- scanned 10 image files, from <e13384396/s13386501/i13386502.MRDC.1> to <e13384396/s13386501/i13386511.MRDC.10>
end read_ge_files : param_t struct at 0x94d3a0 :
ftype = 4
(nused, nalloc) = (10, 40)
flist = 0x953680
glob_dir = e13384396/s13386501/i*
nfiles = 10
fnames = 0x95b210
-- scanned 15 image files, from <e13384396/s13386501/i13386507.MRDC.6> to <e13384396/s13386501/i13386521.MRDC.20>
end read_ge_files : param_t struct at 0x94d3a0 :
ftype = 4
(nused, nalloc) = (15, 40)
flist = 0x953680
glob_dir = e13384396/s13386501/i*
nfiles = 20
fnames = 0x965450
+d first volume : vol_t struct at 0x7fffa4cb35f0 :
nim = 5
(fl_1, fn_1, fn_n) = (0, 5, 9)
first_file = e13384396/s13386501/i13386507.MRDC.6
last_file = e13384396/s13386501/i13386511.MRDC.10
(z_first, z_last) = (-12.8044, 1.59545)
z_delta, image_dz = (3.59996, 3.6)
oblique = 1
(seq_num, run) = (-1, 16)
+d first volume : ge_header_info at 0x7fffa4cb35f0 :
good = 1
(nx,ny) = (64,64)
uv17 = 16
index = 6
im_index = -1
atime = 212359.000000
(dx,dy,dz) = (3.4375,3.4375,3.6)
zoff = -12.8044
(tr,te) = (2,0)
orients = RLAPIS
+d first volume : ge_extras at 0x7fffa4cb362c :
bpp = 2
cflag = 0
hdroff = -1
skip = -1
swap = 0
kk = 0
xorg = -108.281
yorg = -125.807
(xyz0,xyz1,xyz2) = (0,0,0)
(xyz3,xyz4,xyz5) = (0,0,0)
(xyz6,xyz7,xyz8) = (0,0,0)
+d first volume : mosaic_info at 0x7fffa4cb3670 :
is_mosaic = 0
nslices = 0
mos_nx, ny = 0, 0
-d first vol - new params : param_t struct at 0x94d3a0 :
ftype = 4
(nused, nalloc) = (15, 40)
flist = 0x953680
glob_dir = e13384396/s13386501/i*
nfiles = 20
fnames = 0x965450
-d ftype: DICOM
completing orients from 'RLAPIS' to'RLAPIS'
-- system order is LSB_FIRST, image order is LSB_FIRST
++ dataset control info for afni:
ACQUISITION_TYPE 2D+zt
ZORDER alt
TR 2.000000
XYFOV 220.000000 220.000000 18.000000
XYMATRIX 64 64 5
DATUM short
XYZAXES R-L A-P I-S
XYZFIRST 108.280998R 125.806999A 12.804400I
BYTEORDER LSB_FIRST
OBLIQUE_XFORM 3.437500 0.000000 0.000000 -108.280998 0.000000 3.437500 -0.015931 -125.806999 0.000000 0.015211 3.600000 -12.804400 0.000000 0.000000 0.000000 1.000000
DRIVE_AFNI OPEN_WINDOW axialimage
DRIVE_AFNI OPEN_WINDOW axialgraph pinnum=30
NOTE created remotely via real-time afni starting with file : 'e13384396/s13386501/i13386507.MRDC.6' creation command : Dimon -rt -infile_prefix e13384396/s13386501/i -host 10.63.183.78 -tr 2.0 -nt 30 -num_slices 5 -zorder alt -debug 3 -quit
++ sent images from volume (16:-1) to host 10.63.183.78
-- first vol ART_comm struct at 0x94d500 :
(state, mode) = (3, 5)
(use_tcp, swap) = (1, 0)
byte_order = 1
is_oblique = 1
zorder = alt
host = 10.63.183.78
ioc_name = tcp:10.63.183.78:7960
(ioc, param) = (0x0x952030, 0x0x94d3a0)
oblique_xform:
3.4375 0.0000 0.0000 -108.2810
0.0000 3.4375 -0.0159 -125.8070
0.0000 0.0152 3.6000 -12.8044
0.0000 0.0000 0.0000 1.0000
-d computed nap_time is 3000 ms (TR = 2.00)
-d computed nap_time is 3000 ms (TR = 2.00)
-- scanning for additional volumes...
-- run 16: 1 ++ nap time = 3000, tr_naps = 1
-- svs: init alloc - vol 1, run 16, file e13384396/s13386501/i13386507.MRDC.6
-- svs: run 16, seq_num 1
2
-- svs: run 16, seq_num 2
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:2) to host 10.63.183.78
. (volume retry test for warning 'slice out of order'...)
-d computed nap_time is 3000 ms (TR = 2.00)
***********************************************
Error: slice out of order!
current file : e13384396/s13386501/i13386523.MRDC.24
expected z-offset : -9.2044
actual z-offset : -2.0045
current run : 16
slice number : 2 (of 5)
***********************************************
***********************************************
Error: slice out of order!
current file : e13384396/s13386501/i13386525.MRDC.22
expected z-offset : -2.0045
actual z-offset : -9.2044
current run : 16
slice number : 4 (of 5)
***********************************************
3
-- svs: run 16, seq_num 3
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:3) to host 10.63.183.78
4
-- svs: run 16, seq_num 4
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:4) to host 10.63.183.78
(volume retry test for warning 'slice out of order'...)
-d computed nap_time is 3000 ms (TR = 2.00)
***********************************************
Error: slice out of order!
current file : e13384396/s13386501/i13386533.MRDC.34
expected z-offset : -9.2044
actual z-offset : -2.0045
current run : 16
slice number : 2 (of 5)
***********************************************
***********************************************
Error: slice out of order!
current file : e13384396/s13386501/i13386535.MRDC.32
expected z-offset : -2.0045
actual z-offset : -9.2044
current run : 16
slice number : 4 (of 5)
***********************************************
5
-- svs: run 16, seq_num 5
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:5) to host 10.63.183.78
(volume retry test for warning 'slice missing'...)
-d computed nap_time is 3000 ms (TR = 2.00)
***********************************************
Error: slice missing!
current file : e13384396/s13386501/i13386539.MRDC.39
expected z-offset : -5.6045
actual z-offset : -2.0045
current run : 16
slice number : 3 (of 5)
***********************************************
***********************************************
Error: Volume severely toasted!
current file : e13384396/s13386501/i13386540.MRDC.38
expected z-offset : 1.5955
actual z-offset : -5.6045
current run : 16
slice number : 5 (of 5)
***********************************************
6
-- svs: run 16, seq_num 6
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:6) to host 10.63.183.78
(volume retry test for warning 'slice missing'...)
-d computed nap_time is 3000 ms (TR = 2.00)
++ allocating 19 image pointers (was 15)
++ allocated image 15 at address 0x980c60
++ allocated image 16 at address 0x982c70
++ allocated image 17 at address 0x984c80
++ allocated image 18 at address 0x986c90
***********************************************
Error: slice missing!
current file : e13384396/s13386501/i13386543.MRDC.43
expected z-offset : -9.2044
actual z-offset : -5.6045
current run : 16
slice number : 2 (of 5)
***********************************************
***********************************************
Error: Volume severely toasted!
current file : e13384396/s13386501/i13386545.MRDC.42
expected z-offset : 1.5955
actual z-offset : -9.2044
current run : 16
slice number : 5 (of 5)
***********************************************
7
-- svs: run 16, seq_num 7
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:7) to host 10.63.183.78
(volume retry test for warning 'slice missing'...)
-d computed nap_time is 3000 ms (TR = 2.00)
++ allocating 20 image pointers (was 19)
++ allocated image 19 at address 0x98a2f0
***********************************************
Error: slice missing!
current file : e13384396/s13386501/i13386548.MRDC.48
expected z-offset : -9.2044
actual z-offset : -5.6045
current run : 16
slice number : 2 (of 5)
***********************************************
***********************************************
Error: Volume severely toasted!
current file : e13384396/s13386501/i13386550.MRDC.47
expected z-offset : 1.5955
actual z-offset : -9.2044
current run : 16
slice number : 5 (of 5)
***********************************************
8
-- svs: run 16, seq_num 8
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:8) to host 10.63.183.78
(volume retry test for warning 'slice missing'...)
-d computed nap_time is 3000 ms (TR = 2.00)
++ allocating 25 image pointers (was 20)
++ allocated image 20 at address 0x98d5f0
++ allocated image 21 at address 0x98f600
++ allocated image 22 at address 0x991610
++ allocated image 23 at address 0x993620
++ allocated image 24 at address 0x995630
***********************************************
Error: slice missing!
current file : e13384396/s13386501/i13386554.MRDC.54
expected z-offset : -5.6045
actual z-offset : -2.0045
current run : 16
slice number : 3 (of 5)
***********************************************
***********************************************
Error: Volume severely toasted!
current file : e13384396/s13386501/i13386555.MRDC.53
expected z-offset : 1.5955
actual z-offset : -5.6045
current run : 16
slice number : 5 (of 5)
***********************************************
9
-- svs: run 16, seq_num 9
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:9) to host 10.63.183.78
(volume retry test for warning 'slice missing'...)
-d computed nap_time is 3000 ms (TR = 2.00)
***********************************************
Error: slice missing!
current file : e13384396/s13386501/i13386558.MRDC.58
expected z-offset : -9.2044
actual z-offset : -5.6045
current run : 16
slice number : 2 (of 5)
***********************************************
***********************************************
Error: Volume severely toasted!
current file : e13384396/s13386501/i13386560.MRDC.57
expected z-offset : 1.5955
actual z-offset : -9.2044
current run : 16
slice number : 5 (of 5)
***********************************************
10
-- svs: run 16, seq_num 10
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:10) to host 10.63.183.78
11
-- svs: run 16, seq_num 11
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:11) to host 10.63.183.78
12
-- svs: run 16, seq_num 12
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:12) to host 10.63.183.78
13
-- svs: run 16, seq_num 13
completing orients from 'RLAPIS' to'RLAPIS'
++ sent images from volume (16:13) to host 10.63.183.78
(volume retry test for warning 'slice missing'...)
-d computed nap_time is 3000 ms (TR = 2.00)
***********************************************
Error: slice missing!
current file : e13384396/s13386501/i13386578.MRDC.78
expected z-offset : -9.2044
actual z-offset : -5.6045
current run : 16
slice number : 2 (of 5)
***********************************************
Any idea??
Thanks a lot.
