Concatenating multiple runs

[harshk95]

Hi, We had an issue with concatenating recordings from different triggers with data acquired with SpikeGLX from a NP1.0 probe. We followed the inline comments in 'sglx_multi_run_pipeline.py' using the fork for SpikeGLX data and had 5 different triggers to concatenate. However, it does not seem that we get the concatenated file from all the runs since the duration is much shorter than expected and we get the following log from catGT.

[Thd 15236 CPU 15 4/04/22 14:24:57.529] Cmdline: CatGT -dir=W:/nobackup/group/user/AH/043_01 -run=concat220327_220401 -g=0 -t=0,5 -prb_fld -prb=0 -ap -lf -ni -apfilter=butter,12,300,10000 -lffilter=butter,12,1,500 -gblcar -SY=0,-1,6,500 -XA=0,0.8,0.2,0 -XA=7,1,0.2,0 -XD=-1,2,500 -XD=-1,4,5 -XD=-1,5,0 -XD=-1,7,5 -BF=0,5,1,5 -dest=W:/nobackup/garber/kanohars/HA/043_01 -out_prb_fld [Thd 15236 CPU 15 4/04/22 14:25:05.387] Skipping tiny content (olap: 204583110, rem: -7417422, bps: 6) file 'concat220327_220401_g0_t1.nidq.bin'. [Thd 15236 CPU 15 4/04/22 14:25:05.467] Skipping tiny content (olap: 205072890, rem: -23291088, bps: 6) file 'concat220327_220401_g0_t2.nidq.bin'. [Thd 15236 CPU 15 4/04/22 14:25:05.547] Skipping tiny content (olap: 205012470, rem: -7134180, bps: 6) file 'concat220327_220401_g0_t3.nidq.bin'. [Thd 15236 CPU 15 4/04/22 14:25:07.937] Skipping tiny content (olap: 216751854, rem: -67511592, bps: 6) file 'concat220327_220401_g0_t5.nidq.bin'. [Thd 15236 CPU 15 4/04/22 15:00:58.431] Skipping tiny content (olap: 74353845720, rem: -2695779240, bps: 770) file 'concat220327_220401_g0_t1.imec0.ap.bin'. [Thd 15236 CPU 15 4/04/22 15:00:58.578] Skipping tiny content (olap: 74531854320, rem: -8464914150, bps: 770) file 'concat220327_220401_g0_t2.imec0.ap.bin'. [Thd 15236 CPU 15 4/04/22 15:00:58.669] Skipping tiny content (olap: 74509896230, rem: -2592825620, bps: 770) file 'concat220327_220401_g0_t3.imec0.ap.bin'. [Thd 15236 CPU 15 4/04/22 15:03:28.883] Skipping tiny content (olap: 78776493950, rem: -24536489670, bps: 770) file 'concat220327_220401_g0_t5.imec0.ap.bin'. [Thd 15236 CPU 15 4/04/22 15:06:30.597] Skipping tiny content (olap: 6196154580, rem: -224648270, bps: 770) file 'concat220327_220401_g0_t1.imec0.lf.bin'. [Thd 15236 CPU 15 4/04/22 15:06:30.688] Skipping tiny content (olap: 6210988630, rem: -705409320, bps: 770) file 'concat220327_220401_g0_t2.imec0.lf.bin'. [Thd 15236 CPU 15 4/04/22 15:06:30.757] Skipping tiny content (olap: 6209159110, rem: -216068930, bps: 770) file 'concat220327_220401_g0_t3.imec0.lf.bin'. [Thd 15236 CPU 15 4/04/22 15:06:40.864] Skipping tiny content (olap: 6564708150, rem: -2044707280, bps: 770) file 'concat220327_220401_g0_t5.imec0.lf.bin'.

This is what the folder with the run looks like -

We noticed in the documentation of CatGT there is a mention of supercat and were wondering if this is the command that is run. Thanks!

[jsiegle]

@jenniferColonell any advice on this?

[jenniferColonell]

Hi @harshk95 Sorry it took me so long to get around to answering this question! These errors show that the start times in the metadata files are not consistent with consecutive trials -- the negative values for 'rem' indicate that the calculated end time of the concatenated file comes AFTER the end of the file it is trying to add. I'm guessing from the errors that these were actually just independent recordings (that is, not collected as trials) that you need to concatenate. Indeed, supercat, which just concatenates recordings end to end is the correct CatGT command.