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re-run heudiconv and defacing for sub-40 after increasing memory demand in heudiconv code

Lennart Wittkuhn 3 years ago
parent
commit
2f8992b781
28 changed files with 28 additions and 18 deletions
  1. 1 1
      code/heudiconv/highspeed-heudiconv-cluster.sh
  2. 1 1
      sub-40/ses-01/anat/sub-40_ses-01_rec-prenorm_T1w.nii.gz
  3. 1 0
      sub-40/ses-01/fmap/sub-40_ses-01_rec-prenorm_dir-AP_epi.json
  4. 1 0
      sub-40/ses-01/fmap/sub-40_ses-01_rec-prenorm_dir-AP_epi.nii.gz
  5. 1 0
      sub-40/ses-01/fmap/sub-40_ses-01_rec-prenorm_dir-PA_epi.json
  6. 1 0
      sub-40/ses-01/fmap/sub-40_ses-01_rec-prenorm_dir-PA_epi.nii.gz
  7. 1 1
      sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-01_bold.json
  8. 1 1
      sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-01_bold.nii.gz
  9. 1 0
      sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-02_bold.json
  10. 1 0
      sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-02_bold.nii.gz
  11. 1 0
      sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-03_bold.json
  12. 1 0
      sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-03_bold.nii.gz
  13. 1 0
      sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-04_bold.json
  14. 1 0
      sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-04_bold.nii.gz
  15. 1 1
      sub-40/ses-01/func/sub-40_ses-01_task-rest_rec-prenorm_run-post_bold.nii.gz
  16. 1 1
      sub-40/ses-01/func/sub-40_ses-01_task-rest_rec-prenorm_run-pre_bold.nii.gz
  17. 1 1
      sub-40/ses-01/sub-40_ses-01_scans.tsv
  18. 1 1
      sub-40/ses-02/anat/sub-40_ses-02_rec-prenorm_T1w.nii.gz
  19. 1 1
      sub-40/ses-02/fmap/sub-40_ses-02_rec-prenorm_dir-AP_epi.nii.gz
  20. 1 1
      sub-40/ses-02/fmap/sub-40_ses-02_rec-prenorm_dir-PA_epi.nii.gz
  21. 1 1
      sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-01_bold.json
  22. 1 1
      sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-01_bold.nii.gz
  23. 1 1
      sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-02_bold.nii.gz
  24. 1 1
      sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-03_bold.json
  25. 1 1
      sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-03_bold.nii.gz
  26. 1 1
      sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-04_bold.nii.gz
  27. 1 1
      sub-40/ses-02/func/sub-40_ses-02_task-rest_rec-prenorm_run-post_bold.nii.gz
  28. 1 1
      sub-40/ses-02/func/sub-40_ses-02_task-rest_rec-prenorm_run-pre_bold.nii.gz

+ 1 - 1
code/heudiconv/highspeed-heudiconv-cluster.sh

@@ -52,7 +52,7 @@ fi
 # maximum number of cpus per process:
 N_CPUS=1
 # memory demand in *GB*
-MEM_GB=4
+MEM_GB=5
 # memory demand in *MB*
 MEM_MB="$((${MEM_GB} * 1000))"
 # read subject ids from the list of the text file

+ 1 - 1
sub-40/ses-01/anat/sub-40_ses-01_rec-prenorm_T1w.nii.gz

@@ -1 +1 @@
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+../../../.git/annex/objects/05/Gq/MD5E-s9985608--80116bebe257c27451c4e3ca271a7245.nii.gz/MD5E-s9985608--80116bebe257c27451c4e3ca271a7245.nii.gz

+ 1 - 0
sub-40/ses-01/fmap/sub-40_ses-01_rec-prenorm_dir-AP_epi.json

@@ -0,0 +1 @@
+../../../.git/annex/objects/0Q/3q/MD5E-s6018--11d9e3c6a55c1c83b4ec854d1594de50.json/MD5E-s6018--11d9e3c6a55c1c83b4ec854d1594de50.json

+ 1 - 0
sub-40/ses-01/fmap/sub-40_ses-01_rec-prenorm_dir-AP_epi.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/g8/mP/MD5E-s3977895--bce396085570aadf71fc3e59b451d2cb.nii.gz/MD5E-s3977895--bce396085570aadf71fc3e59b451d2cb.nii.gz

+ 1 - 0
sub-40/ses-01/fmap/sub-40_ses-01_rec-prenorm_dir-PA_epi.json

@@ -0,0 +1 @@
+../../../.git/annex/objects/kW/5q/MD5E-s6016--1b393359dcb1be6fa53de28e6d9c1f0e.json/MD5E-s6016--1b393359dcb1be6fa53de28e6d9c1f0e.json

+ 1 - 0
sub-40/ses-01/fmap/sub-40_ses-01_rec-prenorm_dir-PA_epi.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/vz/3Z/MD5E-s3922844--06668f5fc3e30d265be541d870ddf3f8.nii.gz/MD5E-s3922844--06668f5fc3e30d265be541d870ddf3f8.nii.gz

+ 1 - 1
sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-01_bold.json

@@ -1 +1 @@
-../../../.git/annex/objects/j9/v8/MD5E-s2497--6afefd3feee1e216e4a2344c99d42aed.json/MD5E-s2497--6afefd3feee1e216e4a2344c99d42aed.json
+../../../.git/annex/objects/Ww/6Z/MD5E-s48823--d00327b5663c47b06b346e6dfb278c52.json/MD5E-s48823--d00327b5663c47b06b346e6dfb278c52.json

+ 1 - 1
sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-01_bold.nii.gz

@@ -1 +1 @@
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+../../../.git/annex/objects/F2/zG/MD5E-s353156190--787852612a904e52fbd57c48d25d6de2.nii.gz/MD5E-s353156190--787852612a904e52fbd57c48d25d6de2.nii.gz

+ 1 - 0
sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-02_bold.json

@@ -0,0 +1 @@
+../../../.git/annex/objects/wv/j3/MD5E-s48814--b810b1e016c120a773208fec34c6a825.json/MD5E-s48814--b810b1e016c120a773208fec34c6a825.json

+ 1 - 0
sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-02_bold.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/K6/1w/MD5E-s353554368--968d517eebe61f95c24495cda8bdd842.nii.gz/MD5E-s353554368--968d517eebe61f95c24495cda8bdd842.nii.gz

+ 1 - 0
sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-03_bold.json

@@ -0,0 +1 @@
+../../../.git/annex/objects/6k/fP/MD5E-s48819--2eb0457e222b1cda1b0047870597148a.json/MD5E-s48819--2eb0457e222b1cda1b0047870597148a.json

+ 1 - 0
sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-03_bold.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/wg/VP/MD5E-s353344449--0e954e4f3de6856bde6ec66de8495ea4.nii.gz/MD5E-s353344449--0e954e4f3de6856bde6ec66de8495ea4.nii.gz

+ 1 - 0
sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-04_bold.json

@@ -0,0 +1 @@
+../../../.git/annex/objects/vF/gj/MD5E-s48823--e900575d4a057579be570d59db831a00.json/MD5E-s48823--e900575d4a057579be570d59db831a00.json

+ 1 - 0
sub-40/ses-01/func/sub-40_ses-01_task-highspeed_rec-prenorm_run-04_bold.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Fm/9w/MD5E-s353061389--d414a381cf8f7e0f926d927d9c3c6bb1.nii.gz/MD5E-s353061389--d414a381cf8f7e0f926d927d9c3c6bb1.nii.gz

+ 1 - 1
sub-40/ses-01/func/sub-40_ses-01_task-rest_rec-prenorm_run-post_bold.nii.gz

@@ -1 +1 @@
-../../../.git/annex/objects/fM/X7/MD5E-s155118544--2848e798cdb0aaeae611dd6285ff0531.nii.gz/MD5E-s155118544--2848e798cdb0aaeae611dd6285ff0531.nii.gz
+../../../.git/annex/objects/wW/PV/MD5E-s155118544--ade7f8c4bbfede255a0a8f92c9922812.nii.gz/MD5E-s155118544--ade7f8c4bbfede255a0a8f92c9922812.nii.gz

+ 1 - 1
sub-40/ses-01/func/sub-40_ses-01_task-rest_rec-prenorm_run-pre_bold.nii.gz

@@ -1 +1 @@
-../../../.git/annex/objects/6q/5X/MD5E-s155178148--9311998e873d8e4d3d449a13a4fa9b29.nii.gz/MD5E-s155178148--9311998e873d8e4d3d449a13a4fa9b29.nii.gz
+../../../.git/annex/objects/g4/Fp/MD5E-s155178148--cccb54fb388585d203d8890914802dee.nii.gz/MD5E-s155178148--cccb54fb388585d203d8890914802dee.nii.gz

+ 1 - 1
sub-40/ses-01/sub-40_ses-01_scans.tsv

@@ -1 +1 @@
-../../.git/annex/objects/Pj/xM/MD5E-s426--8b88a50197385af1291c8e68c02b5d4d.tsv/MD5E-s426--8b88a50197385af1291c8e68c02b5d4d.tsv
+../../.git/annex/objects/Wx/6M/MD5E-s919--4edbc95d4cd36ab57ace1456d25e2476.tsv/MD5E-s919--4edbc95d4cd36ab57ace1456d25e2476.tsv

+ 1 - 1
sub-40/ses-02/anat/sub-40_ses-02_rec-prenorm_T1w.nii.gz

@@ -1 +1 @@
-../../../.git/annex/objects/pf/kp/MD5E-s10171078--03b228e4c56984f6661f5b6641c530ef.nii.gz/MD5E-s10171078--03b228e4c56984f6661f5b6641c530ef.nii.gz
+../../../.git/annex/objects/Pq/w9/MD5E-s10171078--125a39e4727a5d3655c99dc70d627b79.nii.gz/MD5E-s10171078--125a39e4727a5d3655c99dc70d627b79.nii.gz

+ 1 - 1
sub-40/ses-02/fmap/sub-40_ses-02_rec-prenorm_dir-AP_epi.nii.gz

@@ -1 +1 @@
-../../../.git/annex/objects/x4/jk/MD5E-s3959837--d2d82ff8e29e544cac3a3fb280c7a15b.nii.gz/MD5E-s3959837--d2d82ff8e29e544cac3a3fb280c7a15b.nii.gz
+../../../.git/annex/objects/V4/fx/MD5E-s3959837--75bea47437dd6f43c15999758035167a.nii.gz/MD5E-s3959837--75bea47437dd6f43c15999758035167a.nii.gz

+ 1 - 1
sub-40/ses-02/fmap/sub-40_ses-02_rec-prenorm_dir-PA_epi.nii.gz

@@ -1 +1 @@
-../../../.git/annex/objects/wx/W3/MD5E-s3922562--0832ff971cf308b05102cbd67c4e5ba9.nii.gz/MD5E-s3922562--0832ff971cf308b05102cbd67c4e5ba9.nii.gz
+../../../.git/annex/objects/g2/v9/MD5E-s3922562--45a4ca8ef3c5a41536a36e722aa94532.nii.gz/MD5E-s3922562--45a4ca8ef3c5a41536a36e722aa94532.nii.gz

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sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-01_bold.json

@@ -1 +1 @@
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+../../../.git/annex/objects/6X/vz/MD5E-s48828--f10367655306b90a882e18172186eed8.json/MD5E-s48828--f10367655306b90a882e18172186eed8.json

+ 1 - 1
sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-01_bold.nii.gz

@@ -1 +1 @@
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+../../../.git/annex/objects/39/KP/MD5E-s351240855--1b7f6d04274660c89f46ef522471bea9.nii.gz/MD5E-s351240855--1b7f6d04274660c89f46ef522471bea9.nii.gz

+ 1 - 1
sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-02_bold.nii.gz

@@ -1 +1 @@
-../../../.git/annex/objects/G7/88/MD5E-s352473454--273899e1b5805ef9dba60cb3b37f4e6e.nii.gz/MD5E-s352473454--273899e1b5805ef9dba60cb3b37f4e6e.nii.gz
+../../../.git/annex/objects/Jg/7k/MD5E-s352473454--b218f47fd2c4b72644639172e02765df.nii.gz/MD5E-s352473454--b218f47fd2c4b72644639172e02765df.nii.gz

+ 1 - 1
sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-03_bold.json

@@ -1 +1 @@
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+ 1 - 1
sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-03_bold.nii.gz

@@ -1 +1 @@
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sub-40/ses-02/func/sub-40_ses-02_task-highspeed_rec-prenorm_run-04_bold.nii.gz

@@ -1 +1 @@
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sub-40/ses-02/func/sub-40_ses-02_task-rest_rec-prenorm_run-post_bold.nii.gz

@@ -1 +1 @@
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