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Hi Hoi fong, Mark Jenkinson clarified to me that the order in which robustfov and fslreorient2std are applied does not matter, so you can run them in either order. Cheers, Pau; On 26 August 2015 at 12:24, Chan Hoi Fong <[log in to unmask]> wrote: > Dear Paul, > I can't believe I made such mistakes! > Is it better to run fslreorient2std before robustfov ? What is the > difference? > Thanks > Hoi fong > 2015/8/26 下午4:05於 "paul mccarthy" <[log in to unmask]>寫道： > >> Hi Hoifong, >> >> Aah, you need to provide a second argument to fslreorient2std. The usage >> is: >> >> fslreorient2std <input> <output> >> >> If you don't provide an output file, it will just print the estimated >> transformation, which is what you are seeing. >> >> Also, I suspect that you would want to run fslreorient2std after running >> robustfov, although others may have a different opinion on this. >> >> Cheers, >> >> Paul >> >> On 26 August 2015 at 01:11, Chan Hoi Fong <[log in to unmask]> wrote: >> >>> Dear Paul, >>> I have tried to run fslreorient2std "file name" before robustfov to >>> remove neck. It showed >>> >>> 218-174-67-179:vbmfm201508 chanhoifong$ fslreorient2std rFM01.nii.gz >>> >>> 0.000000 0.000000 -1.000000 174.993317 >>> >>> -1.000000 0.000000 0.000000 231.500000 >>> >>> 0.000000 1.000000 0.000000 0.000000 >>> >>> 0.000000 0.000000 0.000000 1.000000 >>> Is my way to orientation is correct? >>> the Slicer showed the orientation in the axial view column (4,5,6th )is >>> not the same . Is that the reason for the poor alignment? >>> >>> oritent.png >>> <https://drive.google.com/file/d/0Bww6QcZ1f46rUGpuNDliamdFbGs/view?usp=drive_web> >>> >>> orient2.png >>> <https://drive.google.com/file/d/0Bww6QcZ1f46rR3hua0dPTUUxZE0/view?usp=drive_web> >>> >>> thanks >>> hoifong >>> >>> On Tue, Aug 25, 2015 at 4:10 PM, paul mccarthy <[log in to unmask]> >>> wrote: >>> >>>> Hi Hoifong, >>>> >>>> It really looks to me like most of your input images have not been >>>> re-oriented to standard space - looking at template_4D_GM in FSLView, only >>>> volumes 10, 19, and 21 are oriented to standard space - the rest are >>>> flipped along the A-P axis. >>>> >>>> Could you double check that your input images were re-oriented >>>> correctly? If they have been, maybe you could try modifying the call to >>>> fsl_reg, which is on line 110 of fslvbm_2_template (in FSL 5.0.8), reducing >>>> the degrees of freedom and/or the search range. >>>> >>>> Cheers, >>>> >>>> Paul >>>> >>>> On 24 August 2015 at 23:21, Chan Hoi Fong <[log in to unmask]> >>>> wrote: >>>> >>>>> Paul >>>>> The template_4d_GM and Template_GM_init looked fine to me. >>>>> template_4D_GM.nii.gz >>>>> <https://drive.google.com/file/d/0Bww6QcZ1f46rUVhaSXpuQkExUm8/view?usp=drive_web> >>>>> >>>>> template_GM_init.nii.gz >>>>> <https://drive.google.com/file/d/0Bww6QcZ1f46rV19IeDZ6UDdOd1k/view?usp=drive_web> >>>>> since my control and patient number is different. I make the template >>>>> list as the user guide , using the same number for both groups. >>>>> If the alignment to the standard space is not good so do you mean i >>>>> should run fslvbm_2_template -n? >>>>> >>>>> thanks! >>>>> hoifong >>>>> >>>>> On Mon, Aug 24, 2015 at 5:44 PM, paul mccarthy < >>>>> [log in to unmask]> wrote: >>>>> >>>>>> Hi Hoifong, >>>>>> >>>>>> I just re-read your first email, and realised that you have already >>>>>> run fslreorient2std on your images. >>>>>> >>>>>> It looks like the registration to the ICBM-152 standard space, in >>>>>> fslvbm_2_template, has gone wrong - you can see this for yourself if you >>>>>> look at template_GM overlaid on the MNI152_T1_2mm reference image - >>>>>> template_GM is flipped along the A-P axis. >>>>>> >>>>>> This is probably causing the subsequent registrations in >>>>>> fslvbm_3_proc to fail. >>>>>> >>>>>> Could you check template_GM_4D again, and also template_GM_init, to >>>>>> see whether they look good or bad? >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Paul >>>>>> >>>>>> On 24 August 2015 at 09:39, paul mccarthy <[log in to unmask]> >>>>>> wrote: >>>>>> >>>>>>> Hi Hoifong, >>>>>>> >>>>>>> It looks like registration failed for all of your subjects - try >>>>>>> running 'fslreorient2std' on all of your images, and start the VBM pipeline >>>>>>> from the beginning again. >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Paul >>>>>>> >>>>>>> On 21 August 2015 at 01:48, Chan Hoi Fong <[log in to unmask]> >>>>>>> wrote: >>>>>>> >>>>>>>> >>>>>>>> Dear Mark & paul >>>>>>>> I have tried the robustfov and the neck was removed as attacment >>>>>>>> 1-3(jpeg). Then i ran fslvbm_1_bet-N, fslvbm_2_template -a, the template >>>>>>>> _4d_ is ok. >>>>>>>> >>>>>>>> 螢幕快照 2015-08-21 上午8.27.56.png >>>>>>>> <https://drive.google.com/file/d/0Bww6QcZ1f46rM0hOTDZBeHFEZTg/view?usp=drive_web> >>>>>>>> >>>>>>>> 螢幕快照 2015-08-21 上午8.27.42.png >>>>>>>> <https://drive.google.com/file/d/0Bww6QcZ1f46rZFQ0M0hUTE1Ed28/view?usp=drive_web> >>>>>>>> >>>>>>>> >>>>>>>> 螢幕快照 2015-08-21 上午8.27.28.png >>>>>>>> <https://drive.google.com/file/d/0Bww6QcZ1f46rSl9qQ1dOR2RVSlk/view?usp=drive_web> >>>>>>>> >>>>>>>> >>>>>>>> However, fslvbm_3_proc results a poor aligned GM_mod_merg. Any >>>>>>>> steps i was wrong ? >>>>>>>> GM_mod_merg.nii.gz >>>>>>>> <https://drive.google.com/file/d/0Bww6QcZ1f46rdnc4eDlDVWkyWEU/view?usp=drive_web> >>>>>>>> >>>>>>>> >>>>>>>> GM_mask.nii.gz >>>>>>>> <https://drive.google.com/file/d/0Bww6QcZ1f46rZ0hLUEpOeGtYM0E/view?usp=drive_web> >>>>>>>> >>>>>>>> template_GM.nii.gz >>>>>>>> <https://drive.google.com/file/d/0Bww6QcZ1f46rdWR3X2NwcTdJSUk/view?usp=drive_web> >>>>>>>> >>>>>>>> Thanks >>>>>>>> Chan >>>>>>>> >>>>>>>> On Thu, Aug 13, 2015 at 10:51 PM, Mark Jenkinson < >>>>>>>> [log in to unmask]> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> You need to use the -r option as well, in order to specify an >>>>>>>>> output name. >>>>>>>>> >>>>>>>>> All the best, >>>>>>>>> Mark >>>>>>>>> >>>>>>>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on >>>>>>>>> behalf of Chan Hoi Fong <[log in to unmask]> >>>>>>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> >>>>>>>>> Date: Thursday, 13 August 2015 15:39 >>>>>>>>> To: "[log in to unmask]" <[log in to unmask]> >>>>>>>>> Subject: Re: [FSL] extra-Brain tissue "circled" in BET >>>>>>>>> >>>>>>>>> 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 >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> 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 >>>>> >>>> >>>> >>> >>> >>> -- >>> Hoi Fong, Chan, MD >>> En Chu Kong hospital, Department of neurology >>> National Taiwan University , Department of anatomy and cell biology >>> Taipei >>> >> >>