Hello,
The best fix here is to upgrade FSL to version 5.0.9 or greater ( and rerun the analysis ) as pre 5.0.9 versions can output hex values when certain system libraries are updated. The thread https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;eca12e04.1505 has a similar script to Niels’ for converting hex text-files to decimal.
Hope this helps,
Kind Regards,
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
On 21 Nov 2018, at 11:09, Noelia Martinez-Molina <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi Niels,
I tried it again with a new file containing only the hex numbers and I´m still encountering the same error. Please see enclosed the terminal´s output, script and input file I used this time.
Hope you can find out what´s the issue with the conversion.
Thanks for going on helping me with this,
Noelia
El mié., 21 nov. 2018 a las 12:24, Niels Bergsland (<[log in to unmask]<mailto:[log in to unmask]>>) escribió:
Hi Noelia,
Sorry - I should have been clearer - I was assuming that you were going to just give as input a file with each hex number as the input. It's probably easier to just do it that way and then just repack the data in your stats_ file. So basically, you would just need to create a new text file where each hex number is on a separate line. (e.g.:
0x1.dcp+6
0x1.bp+5
0x1.74p+6
0x1.34p+6
etc.
Then run the script to convert the numbers and replace them in your main file with all of the other data.
Hopefully that resolves it for you - if not, let me know!
Niels
On Wed, Nov 21, 2018 at 11:10 AM Noelia Martinez-Molina <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> Hi Niels,
>
> I really appreciate you are giving me a hand with this. I must apologise because I inadvertently introduced a space in the value in my previous email. So the issue persists since there are no spaces in the original values. Please find enclosed the terminal output that I got after running the code. I also attached the script with the code that I used and the original .txt file.
>
> Hope this helps you to guide me out of this issue.
>
> Thanks again,
> Noelia
>
> El mié., 21 nov. 2018 a las 11:06, Niels Bergsland (<[log in to unmask]<mailto:[log in to unmask]>>) escribió:
>>
>> Hi Noelia,
>> It looks like you have a space is somehow splitting up the input (i.e. you have "0x1 dcp+6" rather than "0x1dcp+6") . If you get rid of the space, it should work. Incidentally though, I don't see that value in your original Excel file - or maybe this was from another analysis? Regardless, if you ensure that there are no spaces in the input, it should work. Let me know if you continue to have issues.
>>
>> Best,
>> Niels
>>
>> On Wed, Nov 21, 2018 at 9:26 AM Noelia Martinez-Molina <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>>>
>>> Hi Niels,
>>>
>>> thank you for your prompt reply. I tried your suggestion but, unfortunately, when I run the code the terminal says printf: 0x1 dcp+6: invalid hex number.
>>>
>>> So I´m afraid I was not able to get the numbers in the right format. Do you have any other suggestions?
>>>
>>> All the best,
>>> Noelia
>>>
>>> El mar., 20 nov. 2018 a las 12:11, Niels Bergsland (<[log in to unmask]<mailto:[log in to unmask]>>) escribió:
>>>>
>>>> Hi,
>>>> It looks like you are running an older version of FSL with a relatively newer version of Linux (possibly a recent version of Ubuntu?). If so, this is due an issue with the glibc library. You should be able to covert them to a standard number like this (where list.txt contains your "malformatted" numbers, one per line):
>>>>
>>>> for line in $(cat list.txt); do printf "%f\n" ${line} ; done
>>>>
>>>>
>>>> -Niels
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Nov 20, 2018 at 11:01 AM Noelia Martinez Molina <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>>>>>
>>>>> Dear FSL experts,
>>>>>
>>>>> I´ve performed probabilistic tractography between the superior temporal gyrus and the nucleus accumbens (in both directions and hemispheres). My point is to prove that there are few connections between these regions in the human brain. When I look at the output files from probtrackX, I do not understand the format of the waytotal values, which represent the streamlines. For example, for one subject, I got waytotal=0x1.cp+4.
>>>>>
>>>>> I´d be very grateful if someone could have a look at all waytotal values (N=38) and tell me how this could be interpreted. Here´s the link to the file:
>>>>> https://drive.google.com/open?id=1ij9vQu34bydZm0xgZmprRaTNJibb3Yrt
>>>>>
>>>>> Thank you in advance for your help.
>>>>>
>>>>> Best wishes,
>>>>> Noelia
>>>>>
>>>>> ########################################################################
>>>>>
>>>>> To unsubscribe from the FSL list, click the following link:
>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>>
>>>>
>>>>
>>>> --
>>>> Niels Bergsland
>>>> Integration Director / Research Assistant Professor of Neurology
>>>> Buffalo Neuroimaging Analysis Center / University at Buffalo
>>>> 100 High St. Buffalo NY 14203
>>>> [log in to unmask]<mailto:[log in to unmask]>
>>>>
>>>> ________________________________
>>>>
>>>> To unsubscribe from the FSL list, click the following link:
>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>
>>>
>>>
>>> --
>>>
>>> *****************************************************
>>> Noelia Martínez Molina, PhD
>>> Postdoctoral Researcher
>>> Cognitive Brain Research Unit (CBRU)
>>> Department of Psychology and Logopedics
>>> Faculty of Medicine
>>> University of Helsinki
>>> E-mail: [log in to unmask]<mailto:[log in to unmask]>
>>> Phone1: +358 50 31 88 048 (Finnish)
>>> Phone2: +34 620 15 23 87 (Spanish)
>>>
>>> -------------------------------------------------------------
>>> "Where words fail, music speaks".
>>> H.C. Andersen
>>> ******************************************************
>>>
>>> ________________________________
>>>
>>> To unsubscribe from the FSL list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>
>>
>>
>> --
>> Niels Bergsland
>> Integration Director / Research Assistant Professor of Neurology
>> Buffalo Neuroimaging Analysis Center / University at Buffalo
>> 100 High St. Buffalo NY 14203
>> [log in to unmask]<mailto:[log in to unmask]>
>>
>> ________________________________
>>
>> To unsubscribe from the FSL list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>
>
>
> --
>
> *****************************************************
> Noelia Martínez Molina, PhD
> Postdoctoral Researcher
> Cognitive Brain Research Unit (CBRU)
> Department of Psychology and Logopedics
> Faculty of Medicine
> University of Helsinki
> E-mail: [log in to unmask]<mailto:[log in to unmask]>
> Phone1: +358 50 31 88 048 (Finnish)
> Phone2: +34 620 15 23 87 (Spanish)
>
> -------------------------------------------------------------
> "Where words fail, music speaks".
> H.C. Andersen
> ******************************************************
>
> ________________________________
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
--
Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]<mailto:[log in to unmask]>
________________________________
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--
*****************************************************
Noelia Martínez Molina, PhD
Postdoctoral Researcher
Cognitive Brain Research Unit (CBRU)
Department of Psychology and Logopedics
Faculty of Medicine
University of Helsinki
E-mail: [log in to unmask]<mailto:[log in to unmask]>
Phone1: +358 50 31 88 048 (Finnish)
Phone2: +34 620 15 23 87 (Spanish)
-------------------------------------------------------------
"Where words fail, music speaks".
H.C. Andersen
******************************************************
________________________________
To unsubscribe from the FSL list, click the following link:
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<terminal_output2.txt><CorrectBadFormat.sh><stats_prob01_N38_FDT_nACC2STG_LEFT_FA_midsag_waytotal.txt>
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