Hi Antonios - Constantine,
this is exactly the problem, you're right. I know about this script (since I've written it with Steve), this is why I asked you the output of imglob as it was the only problem I could think of :-).
It would be interesting for us to know why you've got such problem. So could you please give me as much details as possible: e.g., on which machine are you working, with which kind of environment etc.?
To solve your problem for the moment, try replacing `$FSLDIR/bin/imglob *_struc.*` by `$FSLDIR/bin/remove_ext *_struc.*` throughout the fslvbm_2_template and fslvbm_3_proc scripts. It should work fine...
Cheers,
Gwenaelle
--- En date de : Lun 8.9.08, Antonios - Constantine Thanellas <[log in to unmask]> a écrit :
> De: Antonios - Constantine Thanellas <[log in to unmask]>
> Objet: Re: [FSL] following different order on VBM analysis steps+in addition
> À: [log in to unmask]
> Date: Lundi 8 Septembre 2008, 14h05
> Gwenaelle, according to the fslvbm_2_template code from line
> 39:
>
> ### segmentation
> /bin/rm -f fslvbm2a
> for g in `$FSLDIR/bin/imglob *_struc.*` ; do
> echo $g
> echo "$FSLDIR/bin/fast -R 0.3 -H 0.1 ${g}_brain ;
> \
> $FSLDIR/bin/immv ${g}_brain_pve_1 ${g}_GM"
> >> fslvbm2a
> done
>
> When the creation of the fslvbm2a file will start it will
> start including
> images that will have an extra extension ( _brain ) since
> the code is: echo
> "$FSLDIR/bin/fast -R 0.3 -H 0.1 ${g}_brain ; \) .
> Of course such an image
> does not exist and this is i guess the reason why the
> errors start appearing
> (** ERROR (nifti_image_read): failed to find header file
> for
> '01_CON_002_S_0295_M06_struc.nii.gz_brain')
>
> This part of code is different in your version of
> fslvbm_2_template?What do
> you recommend me to do?Is this ${g}_brain part necessary?
> If i modify it to
> $g then the file will look "more correct" but i
> don't know if this will
> affect negatively the following parts of the script. Also
> the
> $FSLDIR/bin/immv ${g}_brain_pve_1 ${g}_GM will create
> similar problems since
> it will try to move a file
> 01_CON_002_S_0295_M06_struc.nii.gz_brain_pve_1
> that does not exist.
>
> This is the output after listing the images in the /struc:
>
> dinos@Spartan:~/Desktop/FSL-VBM-new/GE/M06/struc$ for g in
> `$FSLDIR/bin/imglob *_struc.*` ; do echo $g ; done
> 01_CON_002_S_0295_M06_struc.nii.gz
> 02_CON_014_S_0519_M06_struc.nii.gz
> 03_CON_014_S_0548_M06_struc.nii.gz
> 04_CON_014_S_0558_M06_struc.nii.gz
> 05_CON_027_S_0074_M06_struc.nii.gz
> 06_CON_027_S_0120_M06_struc.nii.gz
> 07_CON_029_S_0845_M06_struc.nii.gz
> 08_CON_029_S_0866_M06_struc.nii.gz
> 09_CON_033_S_0516_M06_struc.nii.gz
> 10_CON_033_S_0734_M06_struc.nii.gz
> 11_CON_033_S_0923_M06_struc.nii.gz
> 12_CON_033_S_1016_M06_struc.nii.gz
> 13_CON_052_S_0951_M06_struc.nii.gz
> 14_CON_094_S_0692_M06_struc.nii.gz
> 15_CON_094_S_0711_M06_struc.nii.gz
> 16_CON_098_S_0896_M06_struc.nii.gz
> 17_CON_126_S_0680_M06_struc.nii.gz
> 18_CON_127_S_0684_M06_struc.nii.gz
> 19_CON_130_S_0232_M06_struc.nii.gz
> 20_CON_130_S_0886_M06_struc.nii.gz
> 21_CON_133_S_0525_M06_struc.nii.gz
> 22_PAT_002_S_0816_M06_struc.nii.gz
> 23_PAT_002_S_0938_M06_struc.nii.gz
> 24_PAT_002_S_1018_M06_struc.nii.gz
> 25_PAT_006_S_0547_M06_struc.nii.gz
> 26_PAT_014_S_0356_M06_struc.nii.gz
> 27_PAT_014_S_1095_M06_struc.nii.gz
> 28_PAT_024_S_1171_M06_struc.nii.gz
> 29_PAT_027_S_0850_M06_struc.nii.gz
> 30_PAT_029_S_0836_M06_struc.nii.gz
> 31_PAT_033_S_0724_M06_struc.nii.gz
> 32_PAT_033_S_0739_M06_struc.nii.gz
> 33_PAT_094_S_1090_M06_struc.nii.gz
> 34_PAT_126_S_0606_M06_struc.nii.gz
> 35_PAT_127_S_0431_M06_struc.nii.gz
> 36_PAT_130_S_0956_M06_struc.nii.gz
> 37_PAT_131_S_0497_M06_struc.nii.gz
> 38_PAT_136_S_0299_M06_struc.nii.gz
> dinos@Spartan:~/Desktop/FSL-VBM-new/GE/M06/struc$
>
>
>
>
> On Mon, 8 Sep 2008 10:51:32 +0000, Gwenaëlle DOUAUD
> <[log in to unmask]> wrote:
>
> >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
|
