Hi,
I've just got back from holidays and tried the files you sent.
They all worked fine for me on my machine.
One possibility is that you have a problem with the settings for decimal points and commas, as governed by the country settings on your Mac. Try the following in a terminal just before running fdt_rotate_bvecs:
LC_NUMERIC=en_GB.UTF-8
If this fixes it then one solution is to export this in your .bash_profile (or equivalent) but be warned that this may interfere with the behaviour of other programs (e.g. excel) that use numerical data.
If this does not fix it then let us know.
All the best,
Mark
On 26 Aug 2013, at 03:03, Vincent Koppelmans <[log in to unmask]> wrote:
> Hi Mark,
>
> I have uploaded two sets of (bvec + ecclog) files to the website.
>
> Thanks for your help,
>
> Vincent
>
>
> Op 19 aug. 2013, om 04:04 heeft Mark Jenkinson <[log in to unmask]> het volgende geschreven:
>
>> Hi,
>>
>> I don't understand this as I conducted my test on a MacBook Pro running 10.8.4 and using FSL version 5.0.4. Can you please upload the files to the link I sent, so that we can investigate it here on the Mac.
>>
>> All the best,
>> Mark
>>
>>
>> On 18 Aug 2013, at 03:06, Vincent Koppelmans <[log in to unmask]> wrote:
>>
>>> Hi Mark,
>>>
>>> I tried running fdt_rotate_bvec on a couple of machines, and it turned out the problem seems restricted to the set up:
>>>
>>> The problem I initially encountered was on a MacBook Pro running FSL 5.0.4 under OSX 10.8.4
>>>
>>> fdt_rotate_bvec ran fine on FSL 5.0.1 under Red Hat Linux 6.4 (I copied the script from a later version) and on FSL 5.0.4 on Ubuntu 12.04 LTS (I had to change the first line from #!/bin/sh to #!/bin/bash).
>>>
>>> I still haven't been able to get fdt_rotate_bvec working on OSX. Do you have any suggestions for me?
>>>
>>> Thanks,
>>>
>>> Vincent
>>>
>>>
>>>
>>> Op 17 aug. 2013, om 04:18 heeft Mark Jenkinson <[log in to unmask]> het volgende geschreven:
>>>
>>>> Hi,
>>>>
>>>> This looks fine, so I've no idea why you are getting all zeros.
>>>> Can you please upload the bvec and ecclog files to this site:
>>>> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
>>>> and we'll see if we can track down the problem at this end.
>>>>
>>>> All the best,
>>>> Mark
>>>>
>>>>
>>>> On 16 Aug 2013, at 12:42, Vincent Koppelmans <[log in to unmask]> wrote:
>>>>
>>>>> Hi Mark,
>>>>>
>>>>> Like I said, I have two datasets, so here are the outputs for one bvec matrix of each set:
>>>>>
>>>>> Data set 1)
>>>>> file: ASCII text, with very long lines
>>>>> wc: 3 186 3107 <name_oiginal_bvec_file>.bvec
>>>>>
>>>>> Data set 2)
>>>>> file: ASCII text
>>>>> wc: 3 48 430 <name_oiginal_bvec_file>.bvec
>>>>>
>>>>> Thanks for your help,
>>>>>
>>>>> Vincent
>>>>>
>>>>>
>>>>>
>>>>> Op 16 aug. 2013, om 04:00 heeft Mark Jenkinson <[log in to unmask]> het volgende geschreven:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> It sounds like you are running it correctly.
>>>>>> My only suggestion is that the bvec file might not have a standard unix format.
>>>>>> Can you run the following:
>>>>>> file original_bvec_file.bvec
>>>>>> and
>>>>>> wc original_bvec_file.bvec
>>>>>> and let us know what the outputs are?
>>>>>>
>>>>>> All the best,
>>>>>> Mark
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 15 Aug 2013, at 19:55, Vincent <[log in to unmask]> wrote:
>>>>>>
>>>>>>> Hi FSL users,
>>>>>>>
>>>>>>> I have two different datasets of DWI images (different resoution, directions, NSA, etc.) that I corrected for motion and eddy current using eddy_current.
>>>>>>>
>>>>>>> I tried using fdt_rotate_bvecs (FSL 5.0.4) on subjects of both data sets, but the script always outputs a matrix of zeros.
>>>>>>>
>>>>>>> The syntax I use is:
>>>>>>> fdt_rotate_bvec original_bvec_file.bvec output_name_new_bvec_file.txt ecc_log.ecclog
>>>>>>>
>>>>>>> An example of a bvec file is:
>>>>>>> 0 -0.216002 0.444561 0.635186 -0.500549 0.22123 0.891941 0.169316 0.263966 -0.598524 0.899631 -0.985305 -0.627905 0.350119 -0.527048 -0.420617
>>>>>>> 0 -0.898615 -0.418727 -0.770066 -0.192538 0.53117 0.079143 0.513429 -0.440254 0.00692 0.223429 -0.166405 0.62708 0.93647 0.773124 -0.804161
>>>>>>> 0 0.381882 0.791854 -0.059474 0.844026 -0.817873 -0.445171 0.841262 -0.858195 -0.801075 0.375157 0.038505 0.460984 0.020968 -0.352844 -0.420008
>>>>>>>
>>>>>>> An example of the ecclog file is:
>>>>>>> processing ecc_DWI_tmp0000
>>>>>>>
>>>>>>> Final result:
>>>>>>> 1.000000 0.000000 0.000000 0.000000
>>>>>>> 0.000000 1.000000 0.000000 0.000000
>>>>>>> 0.000000 0.000000 1.000000 0.000000
>>>>>>> 0.000000 0.000000 0.000000 1.000000
>>>>>>>
>>>>>>> processing ecc_DWI_tmp0001
>>>>>>>
>>>>>>> Final result:
>>>>>>> 1.013296 0.001221 -0.000585 -1.589181
>>>>>>> -0.000941 1.018853 -0.003931 -1.686168
>>>>>>> 0.001744 -0.003690 1.030896 -1.585792
>>>>>>> 0.000000 0.000000 0.000000 1.000000
>>>>>>>
>>>>>>> processing ecc_DWI_tmp0002
>>>>>>>
>>>>>>> Final result:
>>>>>>> 1.012999 0.000073 -0.000476 -1.460119
>>>>>>> 0.001104 1.017430 -0.010545 -1.262310
>>>>>>> -0.000546 0.001471 1.029328 -1.436947
>>>>>>> 0.000000 0.000000 0.000000 1.000000
>>>>>>> (etc...)
>>>>>>>
>>>>>>> fdt_rotate_bvec does not output an error. It just shows me the count of all the slices/directions being processed.
>>>>>>>
>>>>>>> Where do I go wrong?
>>>>>>>
>>>>>>> Thanks, Vincent
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