Hi Chan,
I would strongly recommend that you spend some time learning about
Unix. Understanding how file systems work, and how to organise,
rename, and move files and folders/directories is an absolute
pre-requisite to using FSL, and you won't get far without having at
least a basic understanding.
MJ and Janine have prepared a very good youtube introduction to Unix -
you can find the link under the "Unix section" here:
http://fsl.fmrib.ox.ac.uk/fslcourse/
You should also go through the FSL course practicals, as they will
give you a more hands-on introduction to using FSL within a Unix
environment: http://fsl.fmrib.ox.ac.uk/fslcourse/
Cheers,
Paul
On 24/07/2019, Chan Hyuk Park <[log in to unmask]> wrote:
> dear christina
>
> thank you for your comment
>
> I tried to rename files,bvecs or bvals, according to paul'recommend
>
> bvecs--> mv bvecs.bvec
> bvals--> mv bvals.bval
>
> However, yet 'bvecs not found' was shown
>
> Is the files strange?
>
> I have confused due to this problem for several days.
>
> thanks
>
> 2019년 7월 24일 (수) 오후 3:02, Christina Roßmanith <
> [log in to unmask]>님이 작성:
>
>> bvecs and bvals are files not folders.
>>
>> Regards,
>> Christina
>>
>> On Mi, 2019-07-24 at 06:32 +0900, Chan Hyuk Park wrote:
>>
>> Dear expert
>>
>> I tried to perform FSL.
>>
>> However, continuously "0 slices processed"
>>
>> Please referred to attached file.
>>
>> For bedpostx, I had data.nii.gz, nodif_mask_brain.nii.gz, bvecs and bvals
>>
>> Is this right ?
>>
>> thanks
>>
>> 2019년 7월 23일 (화) 오후 4:45, paul mccarthy <[log in to unmask]>님이 작성:
>>
>> Hi Chan,
>>
>> The input directory for bedpostx needs to contain these files, named
>> exactly as listed:
>>
>> data.nii.gz
>> nodif_brain_mask.nii.gz
>> bvecs
>> bvals
>>
>> Paul
>>
>> On 22/07/2019, Chan Hyuk Park <[log in to unmask]> wrote:
>> > thank you for your reply
>> > However, although I tried to rename the files, in betpostx process I
>> showed
>> > the following
>> > "bedpostx /mnt/hgfs/DTIsample/My_book_1 -n 2 -w 1 -b 1000
>> > /usr/local/fsl/bin/bedpostx /mnt/hgfs/DTIsample/My_book_1 -n 2 -w 1 -b
>> > 1000
>> > subjectdir is /mnt/hgfs/DTIsample/My_book_1
>> > Making bedpostx directory structure
>> > Queuing preprocessing stages
>> > Queuing parallel processing stage
>> > 0 slices processed
>> > 0 slices processed
>> > "
>> > 0 slices processed was shown continuously.
>> >
>> > My processes were
>> > 1. make the folder for bvec and bval
>> > 2. "bvecs" folder --> enclosed mv_bvecs.bvec
>> > "bvals: folder--> enclosed mv_bvals.bval
>> >
>> > Is it right?
>> >
>> > If there were no folders for bvec and bval, continuously
>> > "subjectdir is
>> > /mnt/hgfs/DTIsample/My_book_1/mnt/hgfs/DTIsample/My_book_1/bvecs not
>> found
>> > " was shown.
>> >
>> > I am sorry to be so basic.
>> >
>> > Thnaks and regard
>> >
>> > CH Park
>> >
>> > 2019년 7월 22일 (월) 오후 4:49, paul mccarthy <[log in to unmask]>님이 작성:
>> >
>> >> Hi Chan,
>> >>
>> >> No, the first format is correct. You just need to rename the files.
>> >>
>> >> Paul
>> >>
>> >> On 22/07/2019, Chan Hyuk Park <[log in to unmask]> wrote:
>> >> > Dear expert
>> >> >
>> >> > Thank you for your comment
>> >> >
>> >> > I knew that bvecs file was rotate.
>> >> >
>> >> > if bvecs files was shown the follwing
>> >> > 0 -1 -0.643 -0.258 -0.745 -0.164
>> >> > 0 0 0.766 0.307 -0.594 -0.507
>> >> > 0 0 0.916 0.303 0.846 0.513
>> >> >
>> >> > we rotate file? the following
>> >> > 0, 0, 0
>> >> > -1, 0, 0
>> >> > -0.643, 0.766, 0
>> >> > -0.258, 0.307, 0.916
>> >> > -0.745, -0.594, 0.303
>> >> > -0.164, -0.507, 0.846
>> >> > 0.796, -0.321, 0.513
>> >> >
>> >> > If this is correct, is there comma?
>> >> >
>> >> > thanks and regards
>> >> >
>> >> >
>> >> > 2019년 7월 19일 (금) 오후 4:58, paul mccarthy <[log in to unmask]>님이
>> 작성:
>> >> >
>> >> >> Howdy,
>> >> >>
>> >> >> Try renaming your bvals and bvals files like so - run these
>> >> >> commands
>> >> >> in a terminal:
>> >> >>
>> >> >> mv bvals.bval bvals
>> >> >> mv bvecs.bvec bvec
>> >> >>
>> >> >> and then try running bedpostx again.
>> >> >>
>> >> >> Cheers,
>> >> >>
>> >> >> Paul
>> >> >>
>> >> >> On 18/07/2019, Chan Hyuk Park <[log in to unmask]> wrote:
>> >> >> > sorry one more question
>> >> >> >
>> >> >> > In bedpostx processing, 0 slices processed was shown.
>> >> >> >
>> >> >> > Is it error?
>> >> >> >
>> >> >> > 2019년 7월 18일 (목) 오전 8:39, Chan Hyuk Park <[log in to unmask]>님이
>> 작성:
>> >> >> >
>> >> >> >> Dear sir
>> >> >> >> I am doctor. my major is rehabilitioan medicine
>> >> >> >> I would like to use tractograpy using FSL for finding progrnosis
>> in
>> >> >> >> patients with stroke.
>> >> >> >>
>> >> >> >> I have some questions about FSL.
>> >> >> >>
>> >> >> >> I try to use FSL for tractograpy.
>> >> >> >>
>> >> >> >> However, the error was shown. " bvecs not found"
>> >> >> >> My files for FSL were
>> >> >> >> data.nii.gz, nodif_brain_mask.nii.gz, bvecs.bvec, bvals.bval f
>> >> >> >>
>> >> >> >> My sequnece was the following
>> >> >> >> 1. eddy current correction--> .hdr file convert
>> >> >> >> 2. BET brain extraction--> input image: data.nii.gz, output
>> >> >> >> image:
>> >> >> >> data_brain changed to nodif_brain
>> >> >> >> 3. brain outline extimates--> 0.3
>> >> >> >> 4. output binary brain mas image
>> >> >> >> 5. after above process, I confirmed nodif_brain_mask.nii file
>> >> >> >> 6. BEDpostx extimation of diffuction parameters click
>> >> >> >> --> In input directory, select fold
>> >> >> >>
>> >> >> >>
>> >> >> >> I found " bvec not found."
>> >> >> >>
>> >> >> >> I will wait for you reply
>> >> >> >>
>> >> >> >> thanks and regard
>> >> >> >> --
>> >> >> >> Thanks and Best Regards
>> >> >> >> CH Park(TEL: 010-8860-7994)
>> >> >> >>
>> >> >> >
>> >> >> >
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>> >
>> >
>> > --
>> > Thanks and Best Regards
>> > CH Park(TEL: 010-8860-7994)
>> >
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