Hi Antonios - Constantine,
it's working for me when I'm doing the same thing than you...
What do you have as an output when doing:
for g in `$FSLDIR/bin/imglob *_struc.*` ; do echo $g; done
in your struc directory?
Cheers,
Gwenaelle
--- En date de : Mer 3.9.08, Antonios - Constantine Thanellas <[log in to unmask]> a écrit :
> De: Antonios - Constantine Thanellas <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] following different order on VBM analysis steps
> À: [log in to unmask]
> Date: Mercredi 3 Septembre 2008, 11h37
> Hi Gwenaelle,
> Since i've already had the brain extracted images
> ready, under the main
> folder of my analysis
> /home/dinos/Desktop/FSL-VBM-new/GE/M06 i've created
> two new folders
> the struc/ and the origdata/ ones.
>
> The origdata/ contains all the brain extracted images with
> the ending
> XXX_brain.nii.gz .
>
> The struc/ contains the same data as the origdata/ but
> instead of
> XXX_brain.nii.gz endings, the endings are of
> XXX_struc_brain.nii.gz form.
> This folder also contains empty files of the following form
> XXX_struc.nii.gz
>
> The contents of the struc/ directory are:
>
> dinos@Spartan:~/Desktop/FSL-VBM-new/GE/M06/struc$ ls -al
> total 196204
> drwxr-xr-x 2 dinos dinos 20480 2008-09-03 12:02 .
> drwxr-xr-x 4 dinos dinos 4096 2008-08-30 20:26 ..
> -rw-r--r-- 1 dinos dinos 5349884 2008-01-21 22:06
> 01_CON_002_S_0295_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 01_CON_002_S_0295_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5267604 2008-01-22 16:40
> 02_CON_014_S_0519_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 02_CON_014_S_0519_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5160949 2008-01-22 17:04
> 03_CON_014_S_0548_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 03_CON_014_S_0548_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5555889 2008-01-22 00:00
> 04_CON_014_S_0558_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 04_CON_014_S_0558_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5444221 2008-01-22 01:07
> 05_CON_027_S_0074_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 05_CON_027_S_0074_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5240154 2008-01-22 01:52
> 06_CON_027_S_0120_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 06_CON_027_S_0120_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 6436685 2008-01-24 18:34
> 07_CON_029_S_0845_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 07_CON_029_S_0845_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4813313 2008-01-22 03:11
> 08_CON_029_S_0866_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 08_CON_029_S_0866_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5311464 2008-01-22 03:31
> 09_CON_033_S_0516_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 09_CON_033_S_0516_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5525600 2008-01-22 18:12
> 10_CON_033_S_0734_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 10_CON_033_S_0734_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5198469 2008-01-22 04:18
> 11_CON_033_S_0923_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 11_CON_033_S_0923_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4912015 2008-01-22 05:02
> 12_CON_033_S_1016_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 12_CON_033_S_1016_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5421149 2008-01-22 18:58
> 13_CON_052_S_0951_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 13_CON_052_S_0951_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4932982 2008-01-22 09:17
> 14_CON_094_S_0692_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 14_CON_094_S_0692_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5405229 2008-01-22 09:59
> 15_CON_094_S_0711_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 15_CON_094_S_0711_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 6279207 2008-01-22 10:42
> 16_CON_098_S_0896_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 16_CON_098_S_0896_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4888035 2008-01-22 12:32
> 17_CON_126_S_0680_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 17_CON_126_S_0680_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4944388 2008-01-22 13:14
> 18_CON_127_S_0684_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 18_CON_127_S_0684_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5366795 2008-01-23 02:35
> 19_CON_130_S_0232_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 19_CON_130_S_0232_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4896669 2008-01-22 13:56
> 20_CON_130_S_0886_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 20_CON_130_S_0886_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4336409 2008-01-22 14:39
> 21_CON_133_S_0525_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 21_CON_133_S_0525_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5243439 2008-01-08 15:24
> 22_PAT_002_S_0816_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 22_PAT_002_S_0816_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4740593 2008-01-08 14:02
> 23_PAT_002_S_0938_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 23_PAT_002_S_0938_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4948123 2008-01-08 17:31
> 24_PAT_002_S_1018_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 24_PAT_002_S_1018_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5075067 2008-01-09 18:28
> 25_PAT_006_S_0547_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 25_PAT_006_S_0547_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5429257 2008-01-08 19:59
> 26_PAT_014_S_0356_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 26_PAT_014_S_0356_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5321111 2008-01-08 14:24
> 27_PAT_014_S_1095_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 27_PAT_014_S_1095_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5825273 2008-01-08 21:54
> 28_PAT_024_S_1171_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 28_PAT_024_S_1171_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4854836 2008-01-08 23:27
> 29_PAT_027_S_0850_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 29_PAT_027_S_0850_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5753070 2008-01-09 00:50
> 30_PAT_029_S_0836_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 30_PAT_029_S_0836_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5795313 2008-01-09 02:22
> 31_PAT_033_S_0724_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 31_PAT_033_S_0724_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5320865 2008-01-09 03:07
> 32_PAT_033_S_0739_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 32_PAT_033_S_0739_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5669105 2008-01-09 04:37
> 33_PAT_094_S_1090_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 33_PAT_094_S_1090_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4644646 2008-01-21 21:21
> 34_PAT_126_S_0606_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 34_PAT_126_S_0606_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5438827 2008-01-09 06:46
> 35_PAT_127_S_0431_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 35_PAT_127_S_0431_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4704471 2008-01-21 18:53
> 36_PAT_130_S_0956_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 36_PAT_130_S_0956_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 5971217 2008-01-09 08:14
> 37_PAT_131_S_0497_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 37_PAT_131_S_0497_M06_struc.nii.gz
> -rw-r--r-- 1 dinos dinos 4902489 2008-01-08 16:31
> 38_PAT_136_S_0299_M06_struc_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 0 2008-08-30 20:18
> 38_PAT_136_S_0299_M06_struc.nii.gz
> dinos@Spartan:~/Desktop/FSL-VBM-new/GE/M06/struc$
>
>
> The contents of the origdata/ folder are:
>
> dinos@Spartan:~/Desktop/FSL-VBM-new/GE/M06/origdata$ ls -al
> total 196188
> drwxr-xr-x 2 dinos dinos 4096 2008-08-30 20:03 .
> drwxr-xr-x 4 dinos dinos 4096 2008-08-30 20:26 ..
> -rw-r--r-- 1 dinos dinos 5349884 2008-01-21 22:06
> 01_CON_002_S_0295_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5267604 2008-01-22 16:40
> 02_CON_014_S_0519_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5160949 2008-01-22 17:04
> 03_CON_014_S_0548_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5555889 2008-01-22 00:00
> 04_CON_014_S_0558_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5444221 2008-01-22 01:07
> 05_CON_027_S_0074_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5240154 2008-01-22 01:52
> 06_CON_027_S_0120_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 6436685 2008-01-24 18:34
> 07_CON_029_S_0845_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4813313 2008-01-22 03:11
> 08_CON_029_S_0866_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5311464 2008-01-22 03:31
> 09_CON_033_S_0516_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5525600 2008-01-22 18:12
> 10_CON_033_S_0734_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5198469 2008-01-22 04:18
> 11_CON_033_S_0923_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4912015 2008-01-22 05:02
> 12_CON_033_S_1016_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5421149 2008-01-22 18:58
> 13_CON_052_S_0951_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4932982 2008-01-22 09:17
> 14_CON_094_S_0692_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5405229 2008-01-22 09:59
> 15_CON_094_S_0711_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 6279207 2008-01-22 10:42
> 16_CON_098_S_0896_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4888035 2008-01-22 12:32
> 17_CON_126_S_0680_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4944388 2008-01-22 13:14
> 18_CON_127_S_0684_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5366795 2008-01-23 02:35
> 19_CON_130_S_0232_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4896669 2008-01-22 13:56
> 20_CON_130_S_0886_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4336409 2008-01-22 14:39
> 21_CON_133_S_0525_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5243439 2008-01-08 15:24
> 22_PAT_002_S_0816_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4740593 2008-01-08 14:02
> 23_PAT_002_S_0938_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4948123 2008-01-08 17:31
> 24_PAT_002_S_1018_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5075067 2008-01-09 18:28
> 25_PAT_006_S_0547_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5429257 2008-01-08 19:59
> 26_PAT_014_S_0356_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5321111 2008-01-08 14:24
> 27_PAT_014_S_1095_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5825273 2008-01-08 21:54
> 28_PAT_024_S_1171_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4854836 2008-01-08 23:27
> 29_PAT_027_S_0850_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5753070 2008-01-09 00:50
> 30_PAT_029_S_0836_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5795313 2008-01-09 02:22
> 31_PAT_033_S_0724_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5320865 2008-01-09 03:07
> 32_PAT_033_S_0739_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5669105 2008-01-09 04:37
> 33_PAT_094_S_1090_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4644646 2008-01-21 21:21
> 34_PAT_126_S_0606_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5438827 2008-01-09 06:46
> 35_PAT_127_S_0431_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4704471 2008-01-21 18:53
> 36_PAT_130_S_0956_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 5971217 2008-01-09 08:14
> 37_PAT_131_S_0497_M06_brain.nii.gz
> -rw-r--r-- 1 dinos dinos 4902489 2008-01-08 16:31
> 38_PAT_136_S_0299_M06_brain.nii.gz
>
> The contents of the parent directory are:
>
> dinos@Spartan:~/Desktop/FSL-VBM-new/GE/M06$ ls -al
> total 432
> drwxr-xr-x 4 dinos dinos 4096 2008-08-30 20:26 .
> drwxr-xr-x 4 dinos dinos 4096 2008-08-30 19:16 ..
> -rw-r--r-- 1 dinos dinos 204 2008-08-30 20:26 .fslvbmlog
> -rw-r--r-- 1 dinos dinos 138 2008-07-21 17:37
> GE_M06_design.con
> -rw-r--r-- 1 dinos dinos 481 2008-07-21 17:37
> GE_M06_design_cov.png
> -rw-r--r-- 1 dinos dinos 70965 2008-07-21 17:37
> GE_M06_design_cov.ppm
> -rw-r--r-- 1 dinos dinos 15270 2008-07-21 17:37
> GE_M06_design.fsf
> -rw-r--r-- 1 dinos dinos 111 2008-07-21 17:37
> GE_M06_design.grp
> -rw-r--r-- 1 dinos dinos 1099 2008-07-21 17:37
> GE_M06_design.mat
> -rw-r--r-- 1 dinos dinos 2023 2008-07-21 17:37
> GE_M06_design.png
> -rw-r--r-- 1 dinos dinos 279303 2008-07-21 17:37
> GE_M06_design.ppm
> drwxr-xr-x 2 dinos dinos 4096 2008-08-30 20:03 origdata
> drwxr-xr-x 2 dinos dinos 20480 2008-08-30 20:27 struc
> -rw-r--r-- 1 dinos dinos 748 2008-07-28 17:24
> template_list
>
> Thank you Gwenaelle
>
>
>
> On Tue, 2 Sep 2008 16:15:56 +0000, Gwenaëlle DOUAUD
> <[log in to unmask]> wrote:
>
> >Hi Antonios-Constantine,
> >
> >the problem here is that the extension of the images is
> not removed, but
> it's working fine for me. So what I would actually need
> is the content of
> your struc/ directory.
> >
> >Cheers,
> >Gwenaelle
> >
> >
> >
> >--- En date de : Sam 30.8.08, Antonios - Constantine
> Thanellas
> <[log in to unmask]> a écrit :
> >
> >> De: Antonios - Constantine Thanellas
> <[log in to unmask]>
> >> Objet: Re: [FSL] Re : [FSL] following different
> order on VBM analysis steps
> >> À: [log in to unmask]
> >> Date: Samedi 30 Août 2008, 20h15
> >> Hi Gwenaëlle,
> >>
> >> I have many errors when i'm running
> fslvbm_2_template
> >> -n
> >> The first one is :
> >>
> >> ** ERROR (nifti_image_read): failed to find header
> file for
> >> '01_CON_002_S_0295_M06_struc.nii.gz_brain'
> >>
> >> My files are of this form
> >> 01_CON_002_S_0295_M06_struc.nii.gz
> >>
> >> 02_CON_XXX__XXXXX_XXX_struc.nii.gz
> >> etc
> >> It seems that one of fsl scripts during the
> >> fslvbm_2_template run, adds this
> >> prefix { _brain} in the end of the file that
> should be
> >> read without renaming
> >> the actual file.So the script can't read a
> file that
> >> doesn't exist. Why this
> >> happens?
> >> I've noticed also that the names' files
> of some
> >> new created files are
> >> really strange with added big prefixes in the end
> of the
> >> file's name. For
> >> instance
> >>
> 01_CON_002_S_0295_M06_struc.nii.gz_GM_to_T_init_warp.msf
> >>
> >> I'm sending you the structure of my files in
> the folder
> >> where the analysis
> >> takes place+ the error messages that aroused
> during it.
> >>
> >> I would really appreciate once more your help
> >> Thank you
> >> Antonios-Constantine Thanellas
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Tue, 26 Aug 2008 17:42:44 +0000, Gwenaëlle
> DOUAUD
> >> <[log in to unmask]> wrote:
> >>
> >> >Hi Antonios,
> >> >
> >> >now the pre-processed data are in a directory
> called
> >> struc/ (instead of FAi/).
> >> >You need to do exactly the same thing as
> previously,
> >> apart from the fact
> >> that there is no need for you to run tbss_1
> anymore, and
> >> fnirt can deal with
> >> compressed nifti images (instead of analyze).
> >> >
> >> >
> >> >So it boils down to:
> >> >- rename your betted images:
> exam00X_struc_brain.nii.gz
> >> >- have in your struc/ directory corresponding
> files
> >> *without* the _brain
> >> suffix, so in this case: exam00X_struc.nii.gz (no
> matter
> >> what they are, so
> >> for you, empty files would just be fine: touch
> >> exam00X_struc.nii.gz).
> >> >
> >> >Cheers,
> >> >Gwen
> >> >
> >> >
> >> >--- En date de : Lun 25.8.08, Antonios -
> Constantine
> >> Thanellas
> >> <[log in to unmask]> a écrit :
> >> >
> >> >> De: Antonios - Constantine Thanellas
> >> <[log in to unmask]>
> >> >> Objet: [FSL] following different order on
> VBM
> >> analysis steps
> >> >> À: [log in to unmask]
> >> >> Date: Lundi 25 Août 2008, 17h05
> >> >> Hello fsl users,
> >> >>
> >> >> I want to ask the same question that
> i've done
> >> one
> >> >> month ago, but for the
> >> >> newer version of FSL 4.1 this time.
> >> >>
> >> >> How can I avoid the first step of VBM
> analysis
> >> >> (fslvbm_1_bet) on FSL 4.1
> >> >> since i have my data already
> "beted"
> >> from a
> >> >> previous analysis step?
> >> >>
> >> >> Gwenaelle gave me an answer (it is
> attached in the
> >> end of
> >> >> this e-mail) that
> >> >> worked fine with fsl 4.0.4 but since now
> i've
> >> upgraded
> >> >> fsl to 4.1 i have the
> >> >> same problem again.
> >> >>
> >> >> Thank you once more
> >> >>
> >> >> On Mon, 21 Jul 2008 14:20:23 +0000,
> Gwenaëlle
> >> DOUAUD
> >> >> <[log in to unmask]> wrote:
> >> >>
> >> >> >Hi Antonios,
> >> >> >
> >> >> >absolutely. The only thing that is
> required is
> >> to
> >> >> present the data as if
> >> >> they'd been processed in the right
> order...
> >> >> >
> >> >> >If, say, you've named your
> various brain
> >> extracted
> >> >> exams:
> >> >> exam00X_brain.nii.gz, then after running
> >> tbss_1_preproc,
> >> >> you'll have in your
> >> >> FAi/ directory all your images called
> >> exam00X_brain_FAi.hdr
> >> >> and .img.
> >> >> >
> >> >> >So you then just need to rename them
> >> >> exam00X_FAi_brain.hdr and .img.
> >> >> >
> >> >> >One additional requirement (for
> nomenclature
> >> purposes)
> >> >> is that you need to
> >> >> have in your FAi/ directory corresponding
> files
> >> *without*
> >> >> the _brain suffix,
> >> >> so in this case: exam00X_FAi.hdr and
> .img (no
> >> matter what
> >> >> they are, so for
> >> >> you, empty files would just be fine:
> touch
> >> exam00X_FAi.hdr
> >> >> and .img).
> >> >> >
> >> >> >Hope this makes sense,
> >> >> >Gwenaelle
> >> >> >
> >> >> >
> >> >> >--- En date de : Lun 21.7.08,
> Antonios -
> >> Constantine
> >> >> Thanellas
> >> >> <[log in to unmask]> a écrit
> :
> >> >> >
> >> >> >> De: Antonios - Constantine
> Thanellas
> >> >> <[log in to unmask]>
> >> >> >> Objet: [FSL] following different
> order on
> >> VBM
> >> >> analysis steps
> >> >> >> À: [log in to unmask]
> >> >> >> Date: Lundi 21 Juillet 2008,
> 12h23
> >> >> >> Dear fsl users,
> >> >> >>
> >> >> >> I want to analyse my data
> >> (controls-patients)
> >> >> using
> >> >> >> fsl's VBM.
> >> >> >>
> >> >> >> All my data (whole heads) have
> been brain
> >> >> extracted with
> >> >> >> BET beforehand in
> >> >> >> another analysis part.
> >> >> >>
> >> >> >> So instead of "beting"
> my data
> >> again
> >> >> (2nd step of
> >> >> >> VBM analysis) can i just
> >> >> >> modify the already extracted
> brains with
> >> >> tbss_1_preproc
> >> >> >> (1st step of VBM
> >> >> >> analysis) and omit the second
> step?
> >> >> >>
> >> >> >> Thank you in advance
> >> >> >> Antonios-Konstantinos Thanellas
> >> >>
> >> >>
> >> >>
> >> >>
> >>
> _____________________________________________________________________________
> >> >>
> >> >> Envoyez avec Yahoo! Mail. Une boite mail
> plus
> >> intelligente
> >> >> http://mail.yahoo.fr
> >>
> >>
> >>
> >>
> _____________________________________________________________________________
> >>
> >> Envoyez avec Yahoo! Mail. Une boite mail plus
> intelligente
> >> http://mail.yahoo.fr
|
