<div dir="ltr"><div><div>Hi,<br><br></div>I just wanted to forward this exchange we recently had on the support forum for our neuroimaging package C-PAC (which uses AFNI via Nipype). It looks like the AFNI binary in Neurodebian is currently broken.<br><br></div>--John Pellman<br><br><div><div><div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">John Pellman</b> <span dir="ltr"><<a href="mailto:pellman.john@gmail.com">pellman.john@gmail.com</a>></span><br>Date: 2015-11-20 9:52 GMT-05:00<br>Subject: Re: [cpax_forum] Workflow did not execute cleanly<br>To: <a href="mailto:cpax_forum@googlegroups.com">cpax_forum@googlegroups.com</a><br><br><br><div dir="ltr">For future reference for anyone who encounters a similar issue, we determined that the AFNI binary was the source of the problem. The error that the version of 3dSkullstrip (distributed with Neurodebian) was "freeglut (3dSkullStrip): failed to open display ':1'". Therefore, if the Neurodebian AFNI binary does not work, downloading a compiled version of AFNI from the AFNI website would be the next thing to try.<br></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2015-11-06 15:22 GMT-05:00 Kwan Chen <span dir="ltr"><<a href="mailto:kwan.chen@gmail.com" target="_blank">kwan.chen@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Sure I'll give that a try and let you know what happens.</p>
<br><div class="gmail_quote"><div><div><div dir="ltr">On Fri, Nov 6, 2015, 3:21 PM John Pellman <<a href="mailto:pellman.john@gmail.com" target="_blank">pellman.john@gmail.com</a>> wrote:<br></div></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div><div><div>Hi Kwan,<br><br></div>This looks to be an issue with this particular AFNI binary. Could you run 'apt-get remove afni' and then try installing the latest AFNI binary using the instructions in the link below?<br><br><a href="http://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht00_inst/html/linux_inst_basic.html" target="_blank">http://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht00_inst/html/linux_inst_basic.html</a><br><br></div>Best,<br></div>John Pellman<br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-11-06 14:22 GMT-05:00 John Pellman <span dir="ltr"><<a href="mailto:pellman.john@gmail.com" target="_blank">pellman.john@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi Kwan,<br><br></div>Could you send us the crash file located at /home/kchen/temp/cpac-abide/log/crash-20151105-150523-kchen-anat_skullstrip.pklz so that we can take a look at it?<br><br></div>Best,<br></div>John Pellman<br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-11-06 14:22 GMT-05:00 Cameron Craddock <span dir="ltr"><<a href="mailto:cameron.craddock@gmail.com" target="_blank">cameron.craddock@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div>Skullstrip requires some libraries that are not always installed. It doesn't look like that is the problem for you. <br><br>Sent from my iPhone</div><div><div><div><br>On Nov 6, 2015, at 2:17 PM, Kwan Chen <<a href="mailto:kwan.chen@gmail.com" target="_blank">kwan.chen@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">3dSkullStrip is installed (if that's what you were trying to figure out).<br><br>output:<br><br><font size="1"><span style="font-family:courier new,monospace">$ 3dSkullStrip<br>-- Error 3dSkullStrip (/tmp/buildd/afni-0.20141224~dfsg.1/SUMA/SUMA_3dSkullStrip.c:1312):<br>Too few parameters. Use 3dSkullStrip for details<br><br>Usage: A program to extract the brain from surrounding.<br> tissue from MRI T1-weighted images. <br> The simplest command would be:<br> 3dSkullStrip <-input DSET></span></font><br><br><br>When I execute this command:<br><br><font size="1"><span style="font-family:courier new,monospace">$ 3dSkullStrip -input mprage.nii.gz</span></font><br><br>I get two output files with .BRIK and .HEAD.<br><br>Just FYI, the AFNI is from neurodebian.<br>On Friday, November 6, 2015 at 9:01:21 AM UTC-5, Cameron Craddock wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div>Could you type 3dSkullStrip on the command line and see if it give you any errors?<br><br>Sent from my iPhone</div><div><br>On Nov 6, 2015, at 8:57 AM, Kwan Chen <<a rel="nofollow">kwan...@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">Hi everyone,<br><br>I am new to cpac so I'm still learning the ropes. Nonetheless I encountered some errors. Anyone have any suggestions?<br><br>The dataset is "ABIDE", which includes 3 subjects with T1 and resting state fmri. All I am hoping to do is process them and view them. Pipeline tests were okay with the subject files.<br><br>Anyone have any suggestions on how I should go about interpreting this?<br><br>Best,<br><br>Kwan<br><br><br><br><br><br><br>Output:<br><br>++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Dec 26 2014) [64-bit]<br>++ Authored by: KR Hammett & RW Cox<br>++ Output dataset /home/kchen/temp/cpac-abide/working/resting_preproc_session_1/_scan_rest_1_rest/std_dev_0/std_dev.nii.gz<br>151105-15:08:34,1 workflow INFO:<br> [Job finished] jobname: write_log.a0 jobid: 132<br>151105-15:08:34,4 workflow INFO:<br> [Job finished] jobname: std_dev_0.a0 jobid: 133<br>151105-15:08:34,7 workflow INFO:<br> [Job finished] jobname: sinker_38.a0 jobid: 134<br>151105-15:08:34,10 workflow INFO:<br> [Job finished] jobname: func_mask_normalize.a0 jobid: 136<br>151105-15:08:34,13 workflow INFO:<br> [Job finished] jobname: process_outputs_26.a0 jobid: 241<br>151105-15:08:34,17 workflow INFO:<br> [Job finished] jobname: process_outputs_32.a0.a0 jobid: 253<br>151105-15:08:34,23 workflow INFO:<br> Submitting 2 jobs<br>151105-15:08:34,23 workflow INFO:<br> Executing: process_outputs_38.a0 ID: 135<br>151105-15:08:34,27 workflow INFO:<br> Executing: sinker_15.a0 ID: 137<br>151105-15:08:34,33 workflow INFO:<br> Executing node process_outputs_38.a0 in dir: /home/kchen/temp/cpac-abide/working/resting_preproc_session_1/_scan_rest_1_rest/process_outputs_38<br>151105-15:08:34,34 workflow INFO:<br> Executing node sinker_15.a0 in dir: /home/kchen/temp/cpac-abide/working/resting_preproc_session_1/_scan_rest_1_rest/sinker_15<br>_compcor : _compcor_None<br>_csf_threshold : _csf_threshold_0.96<br>_gm_threshold : _gm_threshold_0.7<br>_target_angle_deg : _target_angle_deg_90<br>_threshold : _threshold_0.2<br>_wm_threshold : _wm_threshold_0.96<br>pipeline : pipeline_Abide-preprocess<br>151105-15:08:36,38 workflow INFO:<br> [Job finished] jobname: process_outputs_38.a0 jobid: 135<br>151105-15:08:36,42 workflow INFO:<br> [Job finished] jobname: sinker_15.a0 jobid: 137<br>151105-15:08:36,46 workflow INFO:<br> Submitting 1 jobs<br>151105-15:08:36,46 workflow INFO:<br> Executing: process_outputs_15.a0 ID: 138<br>151105-15:08:36,51 workflow INFO:<br> Executing node process_outputs_15.a0 in dir: /home/kchen/temp/cpac-abide/working/resting_preproc_session_1/_scan_rest_1_rest/process_outputs_15<br>_compcor : _compcor_None<br>_csf_threshold : _csf_threshold_0.96<br>_gm_threshold : _gm_threshold_0.7<br>_target_angle_deg : _target_angle_deg_90<br>_threshold : _threshold_0.2<br>_wm_threshold : _wm_threshold_0.96<br>pipeline : pipeline_Abide-preprocess<br>151105-15:08:38,52 workflow INFO:<br> [Job finished] jobname: process_outputs_15.a0 jobid: 138<br>151105-15:08:40,58 workflow INFO:<br> ***********************************<br>151105-15:08:40,58 workflow ERROR:<br> could not run node: resting_preproc_session_1.anat_preproc_0.anat_skullstrip<br>151105-15:08:40,58 workflow INFO:<br> crashfile: /home/kchen/temp/cpac-abide/log/crash-20151105-150523-kchen-anat_skullstrip.pklz<br>151105-15:08:40,59 workflow INFO:<br> ***********************************<br>Process Process-3:<br>Traceback (most recent call last):<br> File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap<br> self.run()<br> File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run<br> self._target(*self._args, **self._kwargs)<br> File "/usr/local/lib/python2.7/dist-packages/CPAC/pipeline/cpac_pipeline.py", line 5880, in prep_workflow<br> workflow.run(plugin='MultiProc', plugin_args={'n_procs': c.numCoresPerSubject})<br> File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 700, in run<br> runner.run(execgraph, updatehash=updatehash, config=self.config)<br> File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/base.py", line 268, in run<br> report_nodes_not_run(notrun)<br> File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/base.py", line 92, in report_nodes_not_run<br> raise RuntimeError(('Workflow did not execute cleanly. '<br>RuntimeError: Workflow did not execute cleanly. Check log for details<br><br><br><br></div>
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