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sotnir / NENAH-BIDS

A collaborate platform for streamlining a BIDS workflow for the NENAH study, on the linux workstation based at University of Southampton.
https://www.southampton.ac.uk/cndng
Creative Commons Zero v1.0 Universal
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Working for NENAHC001 #33

Closed yukaizou2015 closed 7 months ago

yukaizou2015 commented 3 years ago

MRIQC anat sub-NENAHC001_run-1_T1w :+1: sub-NENAHC001_run-2_T1w :-1:

MRIQC func sub-NENAHC001_task-rest_dir-AP_run-1_bold ? sub-NENAHC001_task-rest_dir-AP_run-2_bold :-1:

Rawdata dwi sub-NENAHC001_dir-AP_run-1_dwi.nii.gz :+1: sub-NENAHC001_dir-PA_run-1_dwi.nii.gz :-1: for dir-PA mrinfo: [ERROR] bvecs and bvals files must have same number of diffusion directions as DW-image (gradients: 5, image: 1)

yukaizou2015 commented 3 years ago

running bash code/NENAH-BIDS/bids/DcmSourcedata_to_NiftiRawdata.sh NENAHC001 has not updated rawdata directory

yukaizou2015 commented 3 years ago

The log file preprocessing_logs/sub-NENAHC001/sub-NENAHC001_DcmSourcedata_to_NiftiRawdata.log suggested permission issue again. Ran chown for several folders within /NENAH_BIDS:

(base) [yz23e20@uos-15263 NENAH_BIDS]$ ls -l
total 20
drwxrwxr-x 3 yz23e20 neuropediatrics 4096 May  7 12:42 code
drwxrwxr-x 4 yz23e20 neuropediatrics 4096 May 12 08:52 derivatives
drwxrwxr-x 3 yz23e20 neuropediatrics 4096 Apr  1 11:55 dicomdir
drwxrwxr-x 4 yz23e20 neuropediatrics 4096 May 12 08:52 rawdata
drwxrwxr-x 3 yz23e20 neuropediatrics 4096 May 12 08:47 sourcedata

And then running

(base) [yz23e20@uos-15263 NENAH_BIDS]$ bash code/NENAH-BIDS/bids/DcmSourcedata_to_NiftiRawdata.sh NENAHC001

The issue is fixed. I will close this ticket.

yukaizou2015 commented 3 years ago 
rawdata/sub-NENAHC001/dwi/sub-NENAHC001_dir-AP_run-1_dwi.bval
      1      44     205
rawdata/sub-NENAHC001/dwi/sub-NENAHC001_dir-PA_run-1_dwi.bval
      1       5      19

sub-NENAHC001_dir-PA_run-1_dwi.bval:

0 0 2600 1000 2600

sub-NENAHC001_dir-PA_run-1_dwi.bvec

0 0 -0.504842 -0.166433 -0.0478463
0 0 0.391475 0.895513 -0.945813
0 0 -0.769339 0.412742 -0.321168
yukaizou2015 commented 3 years ago

mrinfo output for image series "ep2d_diff_b2600_iso2p3_phase_PA_42dir (*ep_b2600#9) [28] ORIGINAL PRIMARY DIFFUSION NONE ND":

From raw data - 2752 volumes From Syngo - 424 volumes

See attached for full outputs.

To do:

Try re-downloading this case from Syngo to see whether this issue persists.

yukaizou2015 commented 3 years ago

(On Linux workstation) Number of image volumes in series 25 and 29 are both different from 2752.

Now finding keyval for sub-NENAHC001_dir-PA_run-1_dwi
mrinfo: [done] scanning DICOM folder "dicomdir/NENAHC001"
Select series ('q' to abort):
   0 -    6 MR images 09:26:26 localizer (*fl2d1) [3] ORIGINAL PRIMARY M ND NORM
   1 -  500 MR images 09:28:37 ep2d_bold_moco_p4_3mm_AP_2170 (?) [4] ORIGINAL PRIMARY FMRI NONE ND NORM MOSAIC
   2 -  500 MR images 09:28:37 MoCoSeries (?) [5] DERIVED PRIMARY FMRI ND NORM MOCO MOSAIC
   3 -    2 MR images 09:36:53 Design (*epfid2d1_82) [6] DERIVED PRIMARY FMRI DESIGN ND NORM MOCO
   4 -    2 MR images 09:36:53 EvaSeries_GLM (?) [7] DERIVED PRIMARY FMRI TTEST ND NORM MOCO MOSAIC GLM
   5 -    6 MR images 09:36:53 Mean_&_t-Maps (?) [8] DERIVED PRIMARY FMRI ND NORM MOCO MOSAIC MEAN
   6 -  168 MR images 09:38:42 gre_field_mapping_3mm (*fm2d2r) [9] ORIGINAL PRIMARY M ND
   7 -  168 MR images 09:38:42 gre_field_mapping_3mm (*fm2d2r) [10] ORIGINAL PRIMARY M ND NORM
   8 -   84 MR images 09:38:43 gre_field_mapping_3mm (*fm2d2r) [11] ORIGINAL PRIMARY P ND
   9 -  352 MR images 09:46:01 t1_mprage_sag_p2_iso_1.0 (*tfl3d1_16) [12] ORIGINAL PRIMARY M NORM DIS2D FM3_2 FIL
  10 -  500 MR images 09:47:57 ep2d_bold_moco_p4_3mm_AP_2170 (?) [13] ORIGINAL PRIMARY FMRI NONE ND NORM MOSAIC
  11 -  500 MR images 09:47:57 MoCoSeries (?) [14] DERIVED PRIMARY FMRI ND NORM MOCO MOSAIC
  12 -    2 MR images 09:55:59 Design (*epfid2d1_82) [15] DERIVED PRIMARY FMRI DESIGN ND NORM MOCO
  13 -    2 MR images 09:55:59 EvaSeries_GLM (?) [16] DERIVED PRIMARY FMRI TTEST ND NORM MOCO MOSAIC GLM
  14 -    6 MR images 09:55:59 Mean_&_t-Maps (?) [17] DERIVED PRIMARY FMRI ND NORM MOCO MOSAIC MEAN
  15 -   62 MR images 09:58:15 t2_tse_tra_p3_256 (*tse2d1_26) [18] ORIGINAL PRIMARY M ND NORM
  16 -   70 MR images 10:00:00 t2_tse_dark-fluid_FLAIR_cor_p2_4mm (*tir2d1_25) [19] ORIGINAL PRIMARY M ND NORM
  17 -  728 MR images 10:01:37 ep2d_diff_mddw_12_p2_DFC (*ep_b0) [20] ORIGINAL PRIMARY DIFFUSION NONE ND NORM DFC
  18 -   56 MR images 10:02:31 ep2d_diff_mddw_12_p2_DFC_ADC (*ep_b0_800) [21] DERIVED PRIMARY DIFFUSION ADC ND NORM DFC
  19 -   56 MR images 10:02:31 ep2d_diff_mddw_12_p2_DFC_TRACEW (*ep_b800t) [22] DERIVED PRIMARY DIFFUSION TRACEW ND NORM DFC
  20 -  288 MR images 10:07:33 t2_spc_da-fl_ax_p2 (*spcir_284ns) [23] ORIGINAL PRIMARY M ND NORM
  21 -    6 MR images 10:14:36 localizer (*fl2d1) [24] ORIGINAL PRIMARY M ND NORM
  22 -  352 MR images 10:20:55 t1_mprage_sag_p2_iso_1.0 (*tfl3d1_16) [25] ORIGINAL PRIMARY M NORM DIS2D FM3_2 FIL
  23 - 5632 MR images 10:22:08 ep2d_diff_b2600_iso2p3_phase_AP_43dir (*ep_b2600#43) [26] ORIGINAL PRIMARY DIFFUSION NONE ND NORM
  24 -  256 MR images 10:28:48 ep2d_diff_b2600_iso2p3_phase_AP_43dir_TRACEW (*ep_b1000t) [27] DERIVED PRIMARY DIFFUSION TRACEW ND NORM
  25 - 3009 MR images 10:29:23 ep2d_diff_b2600_iso2p3_phase_PA_42dir (*ep_b0) [28] ORIGINAL PRIMARY DIFFUSION NONE ND NORM
  26 -  128 MR images 10:36:01 ep2d_diff_b2600_iso2p3_phase_PA_42dir_TRACEW (*ep_b1000t) [29] DERIVED PRIMARY DIFFUSION TRACEW ND NORM
  27 -  136 MR images 10:36:36 ep2d_se_phase_PA_2meas (*epse2d1_122) [30] ORIGINAL PRIMARY M ND NORM
  28 -  136 MR images 10:37:28 ep2d_se_phase_AP_2meas (*epse2d1_122) [31] ORIGINAL PRIMARY M ND NORM
  29 - 1806 MR images 10:38:43 ep2d_diff_b2600_iso2p3x3_phase_PA_42dir (*ep_b1000#22) [32] ORIGINAL PRIMARY DIFFUSION NONE ND NORM
  30 -   84 MR images 10:45:13 ep2d_diff_b2600_iso2p3x3_phase_PA_42dir_TRACEW (*ep_b2600t) [33] DERIVED PRIMARY DIFFUSION TRACEW ND NORM
  31 -   38 MR images 09:49:27 sag (*tfl3d1_16) [100] DERIVED SECONDARY MPR CSA MPR  CSAPARALLEL M NORM DIS2D FM3_2 FIL
  32 -    2 MR images 09:49:27 sag (*tfl3d1_16) [100] DERIVED SECONDARY PROJECTION IMAGE CSA MPR  CSAPARALLEL M NORM DIS2D FM3_2 FIL
? 25
mrinfo: [100%] reading DICOM series "ep2d_diff_b2600_iso2p3_phase_PA_42dir"
mrinfo: [ERROR] dimensions mismatch in DICOM series
mrinfo: [ERROR] error opening image "dicomdir/NENAHC001"
yukaizou2015 commented 3 years ago

mrinfo output for image series "ep2d_diff_b2600_iso2p3_phase_PA_42dir (*ep_b2600#9) [28] ORIGINAL PRIMARY DIFFUSION NONE ND":

From raw data - 2752 volumes From Syngo - 424 volumes

See attached for full outputs.

To do:

Try re-downloading this case from Syngo to see whether this issue persists.

Pass DVD to Chris on 26th August. This case is no longer at Syngo and need to be pushed again.

finnlennartsson commented 1 year ago

Has done a re-scan (sMRI+dMRI+fMRI) because of bad first scan

The new scan has been replaced to old one in: