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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