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Thank you Mark for the response! I was trying to remove neck part using robustfov, however, the neck part was still there after I run robustfov. I guess I can try other options as you suggested. Thanks again, Lili On Thu, Aug 13, 2015 at 12:27 PM, Mark Jenkinson < [log in to unmask]> wrote: > Hi, > > Did you mean that when you ran brain extraction on both images you saw the > same quality of result? Or were you just talking about the output of > robustfov before running brain extraction? All robustfov does is remove > part of the image, so there should not be any differences in the latter. > However, if you are still having trouble with brain extraction after using > robustfov correctly then it would indicate that the problem is not caused > by the amount of neck in the image and you'll need to try other options > (e.g. -f and -g and -R) to see if you can improve your BET results. > > All the best, > Mark > > > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > Lili He <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Thursday, 13 August 2015 16:25 > To: "[log in to unmask]" <[log in to unmask]> > Subject: Re: [FSL] extra-Brain tissue "circled" in BET > > I came across the same problem. I did specified file name for the output, > while the neck was still there, no difference was noticed between input and > output... Anything else am I missing? > Thank you, > Lili > On Thu, Aug 13, 2015 at 10:44 AM, paul mccarthy <[log in to unmask]> > wrote: > >> Hi Hoifong, >> >> You can use the '-r' option to robustfov to output a cropped version of >> the image, i.e.: >> >> 'robustfov -i input.nii.gz -r cropped_input.nii.gz' >> >> Cheers, >> >> Paul >> >> On 13 August 2015 at 15:39, Chan Hoi Fong <[log in to unmask]> wrote: >> >>> Paul, >>> Is it correct to key robustfov -i "file name" ? however, it just shows >>> >>> Final FOV is: >>> >>> 0.000000 464.000000 154.000000 340.000000 0.000000 176.000000 >>> >>> and i check the file with fslview, the neck is not removed. I thought i >>> must miss some steps. >>> >>> thanks! >>> >>> hoifong >>> >>> On Wed, Aug 12, 2015 at 11:23 PM, paul mccarthy <[log in to unmask] >>> > wrote: >>> >>>> Hi Hoifong, >>>> >>>> BET can have trouble with images which have large amounts of neck - try >>>> using the 'robustfov' command to remove the neck area, and re-running BET. >>>> >>>> Cheers, >>>> >>>> Paul >>>> >>>> On 12 August 2015 at 16:09, Chan Hoi Fong <[log in to unmask]> >>>> wrote: >>>> >>>>> I have upload the file to the Google drive, thanks!! >>>>> FM05_struc_to_FM05_struc_brain.png >>>>> <https://drive.google.com/file/d/0Bww6QcZ1f46rN0w3aWJnUXI2X3c/view?usp=drive_web> >>>>> >>>>> >>>>> On Wed, Aug 12, 2015 at 8:58 PM, Mark Jenkinson < >>>>> [log in to unmask]> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> We recommend uploading illustrative pictures (not nifti files) to a >>>>>> third-party website (e.g. a photo sharing site) and including the link in >>>>>> emails to the list if you want to demonstrate something. The limit is >>>>>> imposed to prevent people's inboxes being overwhelmed by people posting >>>>>> nifti files or other large attachments. >>>>>> >>>>>> I'm afraid I can't really comment on how important the brain >>>>>> extraction errors are without seeing any images though. What really >>>>>> matters is whether anything in the extra-brain regions gets segmented as >>>>>> grey matter or not. >>>>>> >>>>>> All the best, >>>>>> Mark >>>>>> >>>>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf >>>>>> of "subscribe FSL Hoi Fong, Chan" <[log in to unmask]> >>>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> >>>>>> Date: Wednesday, 12 August 2015 02:11 >>>>>> To: "[log in to unmask]" <[log in to unmask]> >>>>>> Subject: [FSL] extra-Brain tissue "circled" in BET >>>>>> >>>>>> Dear Experts, >>>>>> I am doing VBM analysis currently . I have run fslreorient2std to >>>>>> reorient all sample. Then i run fslvbm_1_bet –N. However, there are several >>>>>> sampled showing much more extra-brain area circled as the post BET brain >>>>>> area. Will it affect the further analysis? ( i could not upload the image >>>>>> file since it is too large) >>>>>> Thanks!! >>>>>> hoifong >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Hoi Fong, Chan, MD >>>>> En Chu Kong hospital, Department of neurology >>>>> National Taiwan University , Department of anatomy and cell biology >>>>> Taipei >>>>> >>>> >>>> >>> >>> >>> -- >>> Hoi Fong, Chan, MD >>> En Chu Kong hospital, Department of neurology >>> National Taiwan University , Department of anatomy and cell biology >>> Taipei >>> >> >> >