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 fong2015/8/26 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,PaulOn 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 showed218-174-67-179: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?thankshoifongOn 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,PaulOn 24 August 2015 at 23:21, Chan Hoi Fong <[log in to unmask]> wrote:PaulThe template_4d_GM and Template_GM_init looked fine to me. 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!hoifongOn 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,PaulOn 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,PaulOn 21 August 2015 at 01:48, Chan Hoi Fong <[log in to unmask]> wrote:Dear Mark & paulI 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.
However, fslvbm_3_proc results a poor aligned GM_mod_merg. Any steps i was wrong ?ThanksChanOn 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 showsFinal 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!!
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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, MDEn Chu Kong hospital, Department of neurologyNational Taiwan University , Department of anatomy and cell biologyTaipei
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Hoi Fong, Chan, MDEn Chu Kong hospital, Department of neurologyNational Taiwan University , Department of anatomy and cell biologyTaipei--Hoi Fong, Chan, MDEn Chu Kong hospital, Department of neurologyNational Taiwan University , Department of anatomy and cell biologyTaipei--Hoi Fong, Chan, MDEn Chu Kong hospital, Department of neurologyNational Taiwan University , Department of anatomy and cell biologyTaipei--Hoi Fong, Chan, MDEn Chu Kong hospital, Department of neurologyNational Taiwan University , Department of anatomy and cell biologyTaipei
