Actually, it seems that a quotation is the wrong style. I re-ran after
fixing this. Also tried unset SGE_ROOT. It still tries to fork over jobs
to somewhere (I think)
Different error messages now:
Traceback (most recent call last):
File "/usr/local/fsl/python/mist/mist_script.py", line 256, in <module>
do_preproc(sys.argv[2])
File "/usr/local/fsl/python/mist/mist_script.py", line 133, in do_preproc
subprocess.check_call(['bet', t1, sdir + '/mist_t1_brain', '-R'])
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.5/subprocess.py", line
581, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bet',
'/Volumes/NIA_R00/mist_06:2017/test_mist/mist/T1',
'/Volumes/NIA_R00/mist_06:2017/test_mist/mist/mist_t1_brain', '-R']'
returned non-zero exit status 1
On Tue, Jun 27, 2017 at 3:34 PM, Anu Venkatesh <[log in to unmask]> wrote:
> Hi Eelke,
>
> Thank you for your quick response! I kept having a suspicion the config
> file was the culprit, I've attached the actual input file (I had to tweek
> the file a few times because I'm not 100% sure what mist is looking for),
> could you help identify this "non-ascii character"?
>
> As for the SGE, I had tried another options, so I will try your suggestion!
>
> Thanks again,
> Anu
>
> On Tue, Jun 27, 2017 at 3:27 PM, Eelke Visser <[log in to unmask]>
> wrote:
>
>> Hi Anu,
>>
>> Looks like you may have a non-ascii character in your mist_filenames file
>> - does that make sense? Feel free to attach the file if you don't see
>> anything wrong with it.
>>
>> If you don't have SGE set up it should automatically run locally - you
>> can type "unset SGE_ROOT" to be sure.
>>
>> Hope that helps!
>>
>> Eelke
>>
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> Behalf Of Anu Venkatesh
>> Sent: 27 June 2017 14:43
>> To: [log in to unmask]
>> Subject: [FSL] MIST questions, new FSL update 5.0.10
>>
>> Dear FSl support,
>>
>> I'm starting to play around with MIST (FSL and python novice here), and
>> I'm having a lot of trouble with it. I saw it's currently in Beta stage-are
>> bugs still being worked out?
>>
>> First I had some issues with the filenames config file, but after that
>> was sorted out, I'm having trouble from the job submissions end. I've
>> gotten error messages (posted an example below) and I'm still trying to
>> work out how to tell MIST to not look for a SGE (not set up) and just run
>> locally.
>>
>> Help would be very much appreciated!
>>
>> All the best,
>> Anu
>>
>> error messages: Traceback (most recent call last):
>> File "/usr/local/fsl/python/mist/mist_script.py", line 256, in <module>
>> do_preproc(sys.argv[2])
>> File "/usr/local/fsl/python/mist/mist_script.py", line 128, in
>> do_preproc
>> mtypes, scans, vsize = read_config()
>> File "/usr/local/fsl/python/mist/mist_script.py", line 93, in
>> read_config
>> for ln in csv.reader(fnf):
>> File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.5/encodings/ascii.py",
>> line 26, in decode
>> return codecs.ascii_decode(input, self.errors)[0]
>> UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 10:
>> ordinal not in range(128)
>>
>
>
