Resting State Proc 3dpc Error

AFNI Message Board
1

Dear AFNI experts,

I encountered the following error during resting state analysis (example 11) when their proc scripts reached 3dpc.

3dpc -mask follow_ROI_FSvent+tlrc -pcsave 3 -prefix rm.ROIPC.FSvent rm.det_pcin_rall+tlrc
++ 3dpc: AFNI version=AFNI_17.1.10 (Jun 6 2017) [64-bit]
** ERROR: covariance diagonal (1,1) = 0
** ERROR: covariance diagonal (2,2) = 0
** ERROR: covariance diagonal (3,3) = 0
** ERROR: covariance diagonal (4,4) = 0
** ERROR: covariance diagonal (5,5) = 0
** ERROR: covariance diagonal (6,6) = 0
** ERROR: covariance diagonal (7,7) = 0
** ERROR: covariance diagonal (8,8) = 0
** ERROR: covariance diagonal (9,9) = 0
** ERROR: covariance diagonal (10,10) = 0
** ERROR: covariance diagonal (11,11) = 0
** ERROR: covariance diagonal (12,12) = 0
** ERROR: covariance diagonal (13,13) = 0
** ERROR: covariance diagonal (14,14) = 0
** ERROR: covariance diagonal (15,15) = 0
** ERROR: covariance diagonal (16,16) = 0
** ERROR: covariance diagonal (17,17) = 0
** ERROR: covariance diagonal (18,18) = 0
** ERROR: covariance diagonal (19,19) = 0
** ERROR: covariance diagonal (20,20) = 0
** ERROR: covariance diagonal (21,21) = 0
** ERROR: covariance diagonal (22,22) = 0
** ERROR: covariance diagonal (23,23) = 0
** ERROR: covariance diagonal (24,24) = 0
** ERROR: covariance diagonal (25,25) = 0
** ERROR: covariance diagonal (26,26) = 0
** ERROR: covariance diagonal (27,27) = 0
** ERROR: covariance diagonal (28,28) = 0
** ERROR: covariance diagonal (29,29) = 0
** ERROR: covariance diagonal (30,30) = 0
** ERROR: covariance diagonal (31,31) = 0
** ERROR: covariance diagonal (32,32) = 0
** ERROR: covariance diagonal (33,33) = 0
** ERROR: covariance diagonal (34,34) = 0
** ERROR: covariance diagonal (35,35) = 0
** ERROR: covariance diagonal (36,36) = 0
** ERROR: covariance diagonal (37,37) = 0
** ERROR: covariance diagonal (38,38) = 0
** ERROR: covariance diagonal (39,39) = 0
** ERROR: covariance diagonal (40,40) = 0
** ERROR: covariance diagonal (41,41) = 0
** ERROR: covariance diagonal (42,42) = 0
** ERROR: covariance diagonal (43,43) = 0
** ERROR: covariance diagonal (44,44) = 0
** ERROR: covariance diagonal (45,45) = 0
** ERROR: covariance diagonal (46,46) = 0
** ERROR: covariance diagonal (47,47) = 0
** ERROR: covariance diagonal (48,48) = 0
** ERROR: covariance diagonal (49,49) = 0
** ERROR: covariance diagonal (50,50) = 0
** ERROR: covariance diagonal (51,51) = 0
** ERROR: covariance diagonal (52,52) = 0
** ERROR: covariance diagonal (53,53) = 0
** ERROR: covariance diagonal (54,54) = 0
** ERROR: covariance diagonal (55,55) = 0
** ERROR: covariance diagonal (56,56) = 0
** ERROR: covariance diagonal (57,57) = 0
** ERROR: covariance diagonal (58,58) = 0
** ERROR: covariance diagonal (59,59) = 0
** ERROR: covariance diagonal (60,60) = 0
** ERROR: covariance diagonal (61,61) = 0
** ERROR: covariance diagonal (62,62) = 0
** ERROR: covariance diagonal (63,63) = 0
** ERROR: covariance diagonal (64,64) = 0
** ERROR: covariance diagonal (65,65) = 0
** ERROR: covariance diagonal (66,66) = 0
** ERROR: covariance diagonal (67,67) = 0
** ERROR: covariance diagonal (68,68) = 0
** ERROR: covariance diagonal (69,69) = 0
** ERROR: covariance diagonal (70,70) = 0
** ERROR: covariance diagonal (71,71) = 0
** ERROR: covariance diagonal (72,72) = 0
** ERROR: covariance diagonal (73,73) = 0
** ERROR: covariance diagonal (74,74) = 0
** ERROR: covariance diagonal (75,75) = 0
** ERROR: covariance diagonal (76,76) = 0
** ERROR: covariance diagonal (77,77) = 0
** ERROR: covariance diagonal (78,78) = 0
** ERROR: covariance diagonal (79,79) = 0
** ERROR: covariance diagonal (80,80) = 0
** ERROR: covariance diagonal (81,81) = 0
** ERROR: covariance diagonal (82,82) = 0
** ERROR: covariance diagonal (83,83) = 0
** ERROR: covariance diagonal (84,84) = 0
** ERROR: covariance diagonal (85,85) = 0
** ERROR: covariance diagonal (86,86) = 0
** ERROR: covariance diagonal (87,87) = 0
** ERROR: covariance diagonal (88,88) = 0
** ERROR: covariance diagonal (89,89) = 0
** ERROR: covariance diagonal (90,90) = 0
** ERROR: covariance diagonal (91,91) = 0
** ERROR: covariance diagonal (92,92) = 0
** ERROR: covariance diagonal (93,93) = 0
** ERROR: covariance diagonal (94,94) = 0
** ERROR: covariance diagonal (95,95) = 0
** ERROR: covariance diagonal (96,96) = 0
** ERROR: covariance diagonal (97,97) = 0
** ERROR: covariance diagonal (98,98) = 0
** ERROR: covariance diagonal (99,99) = 0
** ERROR: covariance diagonal (100,100) = 0
** ERROR: covariance diagonal (101,101) = 0
** ERROR: covariance diagonal (102,102) = 0
** ERROR: covariance diagonal (103,103) = 0
** ERROR: covariance diagonal (104,104) = 0
** ERROR: covariance diagonal (105,105) = 0
** ERROR: covariance diagonal (106,106) = 0
** ERROR: covariance diagonal (107,107) = 0
** ERROR: covariance diagonal (108,108) = 0
** ERROR: covariance diagonal (109,109) = 0
** ERROR: covariance diagonal (110,110) = 0
** ERROR: covariance diagonal (111,111) = 0
** ERROR: covariance diagonal (112,112) = 0
** ERROR: covariance diagonal (113,113) = 0
** ERROR: covariance diagonal (114,114) = 0
** ERROR: covariance diagonal (115,115) = 0
** ERROR: covariance diagonal (116,116) = 0
** ERROR: covariance diagonal (117,117) = 0
** ERROR: covariance diagonal (118,118) = 0
** ERROR: covariance diagonal (119,119) = 0
** ERROR: covariance diagonal (120,120) = 0
** ERROR: covariance diagonal (121,121) = 0
** ERROR: covariance diagonal (122,122) = 0
** ERROR: covariance diagonal (123,123) = 0
** ERROR: covariance diagonal (124,124) = 0
** ERROR: covariance diagonal (125,125) = 0
** ERROR: covariance diagonal (126,126) = 0
** ERROR: covariance diagonal (127,127) = 0
** ERROR: covariance diagonal (128,128) = 0
** ERROR: covariance diagonal (129,129) = 0
** ERROR: covariance diagonal (130,130) = 0
** ERROR: covariance diagonal (131,131) = 0
** ERROR: covariance diagonal (132,132) = 0
** ERROR: covariance diagonal (133,133) = 0
** ERROR: covariance diagonal (134,134) = 0
** ERROR: covariance diagonal (135,135) = 0
** ERROR: covariance diagonal (136,136) = 0
** ERROR: covariance diagonal (137,137) = 0
** ERROR: covariance diagonal (138,138) = 0
** ERROR: covariance diagonal (139,139) = 0
** ERROR: covariance diagonal (140,140) = 0
** ERROR: covariance diagonal (141,141) = 0
** ERROR: covariance diagonal (142,142) = 0
** ERROR: covariance diagonal (143,143) = 0
** ERROR: covariance diagonal (144,144) = 0
** ERROR: covariance diagonal (145,145) = 0
** ERROR: covariance diagonal (146,146) = 0
** ERROR: covariance diagonal (147,147) = 0
** ERROR: covariance diagonal (148,148) = 0
** ERROR: covariance diagonal (149,149) = 0
** ERROR: covariance diagonal (150,150) = 0
** ERROR: covariance diagonal (151,151) = 0
** ERROR: covariance diagonal (152,152) = 0
** ERROR: covariance diagonal (153,153) = 0
** ERROR: covariance diagonal (154,154) = 0
** ERROR: covariance diagonal (155,155) = 0
** ERROR: covariance diagonal (156,156) = 0
** ERROR: covariance diagonal (157,157) = 0
** ERROR: covariance diagonal (158,158) = 0
** ERROR: covariance diagonal (159,159) = 0
** ERROR: covariance diagonal (160,160) = 0
** ERROR: covariance diagonal (161,161) = 0
** ERROR: covariance diagonal (162,162) = 0
** ERROR: covariance diagonal (163,163) = 0
** ERROR: covariance diagonal (164,164) = 0
** ERROR: covariance diagonal (165,165) = 0
** ERROR: covariance diagonal (166,166) = 0
** ERROR: covariance diagonal (167,167) = 0
** ERROR: covariance diagonal (168,168) = 0
** ERROR: covariance diagonal (169,169) = 0
** ERROR: covariance diagonal (170,170) = 0
** ERROR: covariance diagonal (171,171) = 0
** ERROR: covariance diagonal (172,172) = 0
** ERROR: covariance diagonal (173,173) = 0
** ERROR: covariance diagonal (174,174) = 0
** ERROR: covariance diagonal (175,175) = 0
** ERROR: covariance diagonal (176,176) = 0
** ERROR: covariance diagonal (177,177) = 0
** ERROR: covariance diagonal (178,178) = 0
** ERROR: covariance diagonal (179,179) = 0
** ERROR: covariance diagonal (180,180) = 0
** ERROR: covariance diagonal (181,181) = 0
** ERROR: covariance diagonal (182,182) = 0
** ERROR: covariance diagonal (183,183) = 0
** ERROR: covariance diagonal (184,184) = 0
** ERROR: covariance diagonal (185,185) = 0
** ERROR: covariance diagonal (186,186) = 0
** ERROR: covariance diagonal (187,187) = 0
** ERROR: covariance diagonal (188,188) = 0
** ERROR: covariance diagonal (189,189) = 0
** ERROR: covariance diagonal (190,190) = 0
** ERROR: covariance diagonal (191,191) = 0
** ERROR: covariance diagonal (192,192) = 0
** ERROR: covariance diagonal (193,193) = 0
** ERROR: covariance diagonal (194,194) = 0
** ERROR: covariance diagonal (195,195) = 0
** ERROR: covariance diagonal (196,196) = 0
** ERROR: covariance diagonal (197,197) = 0
** ERROR: covariance diagonal (198,198) = 0
** ERROR: covariance diagonal (199,199) = 0
** ERROR: covariance diagonal (200,200) = 0
** ERROR: covariance diagonal (201,201) = 0
** ERROR: covariance diagonal (202,202) = 0
** ERROR: covariance diagonal (203,203) = 0
** ERROR: covariance diagonal (204,204) = 0
** ERROR: covariance diagonal (205,205) = 0
** ERROR: covariance diagonal (206,206) = 0
** ERROR: covariance diagonal (207,207) = 0
** ERROR: covariance diagonal (208,208) = 0
** ERROR: covariance diagonal (209,209) = 0
** ERROR: covariance diagonal (210,210) = 0
** ERROR: covariance diagonal (211,211) = 0
** ERROR: covariance diagonal (212,212) = 0
** ERROR: covariance diagonal (213,213) = 0
** ERROR: covariance diagonal (214,214) = 0
** ERROR: covariance diagonal (215,215) = 0
** ERROR: covariance diagonal (216,216) = 0
** ERROR: covariance diagonal (217,217) = 0
** ERROR: covariance diagonal (218,218) = 0
** ERROR: covariance diagonal (219,219) = 0
** ERROR: covariance diagonal (220,220) = 0
** ERROR: covariance diagonal (221,221) = 0
** ERROR: covariance diagonal (222,222) = 0
** ERROR: covariance diagonal (223,223) = 0
** ERROR: covariance diagonal (224,224) = 0
** ERROR: covariance diagonal (225,225) = 0
** ERROR: covariance diagonal (226,226) = 0
** ERROR: covariance diagonal (227,227) = 0
** ERROR: covariance diagonal (228,228) = 0
** ERROR: covariance diagonal (229,229) = 0
** ERROR: covariance diagonal (230,230) = 0
** ERROR: covariance diagonal (231,231) = 0
** ERROR: covariance diagonal (232,232) = 0
** ERROR: covariance diagonal (233,233) = 0
** ERROR: covariance diagonal (234,234) = 0
** ERROR: covariance diagonal (235,235) = 0
** ERROR: covariance diagonal (236,236) = 0
** ERROR: covariance diagonal (237,237) = 0
** FATAL ERROR: *** program exiting right here and now!
** Program compile date = Jun 6 2017

When running 3dmaskave -mask follow_ROI_FSvent+tlrc rm.det_pcin_rall+tlrc, I got the following.

++ 3dmaskave: AFNI version=AFNI_17.1.10 (Jun 6 2017) [64-bit]
+++ 1132 voxels survive the mask
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]
0 [1132 voxels]

Also, when checking anat and epi registration, epi image was not aligned to anat image. Could you please suggest how to solve this?

Thank you in advance for your help,
Jun

2

Hi Jun,

Sorry for being slow on this.

Yes, it looks like your entire dataset is zero. It seems likely
that the most original data is not in close enough alignment,
between the EPI, anat and template, meaning that some of
it probably does not have accurate spatial information.

Consider running @Align_Centers with a template for the
-base parameter. You might verify both the EPI and anat.

  • rick
3

Hi Rick,

Thank you so much for the reply. Just have a quick question regarding your suggestion. I am not sure how to use @Align_Centers.

AFNI instruction says it should be @Align_Centers <-base BASE> <-dset DSET>. I am confused how to place anat and epi data using this script. Could you please advise?

Have a good weekend,
Jun

4

Hi Jun,

It might be useful to run 3dinfo on each and look at the extents. Feel free to post that.

But without knowing, it might be just as safe to align everything to whichever standard space template you are using. That would mean running @Align_Centers on each dataset (EPI and anat), using -base TEMPLATE+tlrc, for whichever template you are using.

Does that seem reasonable?

  • rick
5

Hi Rick,

Thanks for the reply. Yes, I have run @Align_Centers for both EPI and anat (@Align_Centers -base MNI152_T1_2009c+tlrc -dset anat+orig). It created EPI.shift.1D and anat.shift.1D. Can I rerun proc using these files?

Thanks,
Jun

6

Hi Jun,

Run it on the shifted datasets. The .1D files might just be informational.

  • rick
7

Hi Rick,

Thanks, it works well!

Best,
Jun

8

Hi Rick,

Thanks again for your help. Just faced an another issue when running resting state proc py for other participant’s data. It showed the message below and stopped running.

+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
echo – GCOR = cat out.gcor.1D
cat out.gcor.1D
– GCOR = 0.0541623
3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr ab -prefix rm.DP
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
3dTstat -sum -prefix corr_brain rm.DP+tlrc
++ 3dTstat: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
3dcalc -a follow_ROI_aeseg+tlrc -b full_mask.AES131.Ex+tlrc -expr ab -prefix rm.fm.aeseg
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
3dmaskave -q -mask rm.fm.aeseg+tlrc rm.errts.unit+tlrc
++ 3dmaskave: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
+++ 6461 voxels survive the mask
3dcalc -a rm.errts.unit+tlrc -b mean.unit.aeseg.1D -expr ab -prefix rm.DP.aeseg
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
3dTstat -sum -prefix corr_af_aeseg rm.DP.aeseg+tlrc
++ 3dTstat: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
3dcalc -a follow_ROI_FSvent+tlrc -b full_mask.AES131.Ex+tlrc -expr a*b -prefix rm.fm.FSvent
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
3dmaskave -q -mask rm.fm.FSvent+tlrc rm.errts.unit+tlrc
++ 3dmaskave: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
*** No voxels survive the masking operation

Could you advise why it shows ‘*** No voxels survive the masking operation’ and how to resolve it?

Thanks,
Jun

9

Hi Jun,

Look at the rm.fm.VSfent+tlrc dataset, along with follow_ROI_FSvent+tlrc, and see what they show as the ventricles. Maybe they are very small, and the final dataset ends up with no voxels in it. Perhaps FreeSurfer was not able to define them well. You should be sure of why it comes up empty.

There is currently no login for what to do in the proc script if such a mask comes up empty. Since there is nothing to regress, and assuming the mask was made in a reasonable way, but is small enough to disappear, there might be no happy choices going forward (drop subject, more gently erode the mask, substitute your own mask, do not regress from the ventricles).

  • rick