Error in AFNI Suma connection

AFNI Message Board
1

I was following the DTI analysis using FATCAT steps and I have gotten to the step where you could view the tracking information in AFNI and SUMA but it is failing to connect. Here is the code/script I am using:

port for AFNI-SUMA communications, and end all other chatter on it

set cport = 12
@Quiet_Talkers -npb_val $cport

set line thickness of SUMA surfaces sent to AFNI

setenv AFNI_SUMA_LINESIZE 0.005

Open talkable AFNI

afni -npb $cport -niml -yesplugouts &

Choose ulay (anat) and olay (FA>0.2) in AFNI

plugout_drive
-npb $cport
-com ‘SWITCH_UNDERLAY dwi_anat.nii.gz’
-com ‘SWITCH_OVERLAY dt_FA.nii.gz’
-com “SEE_OVERLAY +”
-com “SET_PBAR_ALL +99 1.0 Plasma”
-com ‘SET_THRESHNEW 0.2’
-quit

Open talkable SUMA

suma
-npb $cport -niml
-spec indt_std.141.SUBJ_001_both.spec
-sv dwi_anat.nii.gz
-vol dwi_anat.nii.gz
-tract TTT_000.niml.tract &

Drive SUMA to start it ‘talking’ with AFNI; also puts image at

straight-ahead “coronal” view, and hides one hemisphere surface,

so tracts inside are visible

DriveSuma
-npb $cport
-com viewer_cont -key ‘.’ -key ‘t’
-com viewer_cont -key ‘Ctrl+shift+up’ -key ‘]’

This script is exactly what is in the FATCAT instruction step.

AFNI does start up correctly with the DTI information overlaying.

Here is the output of where it goes wrong:
SUMA_niml_call: Contacting on tcp:127.0.0.1:1320 (6), maximum wait 300.000 sec
(You can change max. wait time with env. SUMA_DriveSumaMaxWait)
PO: plugout ‘plugout_drive’ has broken connection!
: iochan_goodcheck: no longer alive
…Error SUMA_Read_SpecFile: File indt_std.141.SUBJ_001_both.spec does not exist or cannot be read.
Error SUMA_Engine: Error in SUMA_Read_SpecFile.
…-- Error SUMA_niml_call (SUMA_niml.c:597):
WriteCheck timed out (> 300000 ms).
– Error SUMA_SendToSuma (SUMA_niml.c:4335):
Failed in SUMA_niml_call
– Error DriveSuma (SUMA_DriveSuma.c:58):
Failed to initialize SUMA_SendToSuma
– Error SUMA_SendToSuma (SUMA_niml.c:4363):
You must call SUMA_SendToSuma with action 0 before action 1.
No Communcation cleanup done.
oo Warning SUMA_ProcessCommand (SUMA_driver.c:628):
Failed in SUMA_SendToSuma
Communication halted.
– Error SUMA_SendToSuma (SUMA_niml.c:4363):
You must call SUMA_SendToSuma with action 0 before action 1.
No Communcation cleanup done.
oo Warning SUMA_ProcessCommand (SUMA_driver.c:628):
Failed in SUMA_SendToSuma
Communication halted.
[1] + Exit 1 suma -npb 12 -niml -spec indt_std.141.SUBJ_001_both.spec -sv dwi_anat.nii.gz -vol dwi_anat.nii.gz -tract TTT_000.niml.tract

Please let me know how to fix this or what I am doing wrong.

Thank you.

2

Hm, are you sure that the “spec” file exists with that name/in that location? There is this error message that makes it seem like it doesn’t:


...Error SUMA_Read_SpecFile: File indt_std.141.SUBJ_001_both.spec does not exist or cannot be read.

It looks like you need to change the “SUBJ_001”, which is the subject ID in the example, to your own?

–pt

3

Such a silly mistake on my part - that is exactly what the problem was. Thank you.

4

Rockin’.

–pt