Hello fsl users,
I have the same problem here as it has been reported by Dost,
i run fslvbm_2_template -a for my data set and no template_GM_4D file was
created.More specific my terminal's layout was the following:
dinos@Spartan:~/Desktop/FSL-VBM/GE/M06/brains/processing_folder$
/usr/bin/time fslvbm_2_template -a
01_CON_002_S_0295_M06_FAi
02_CON_014_S_0519_M06_FAi
03_CON_014_S_0548_M06_FAi
04_CON_014_S_0558_M06_FAi
05_CON_027_S_0074_M06_FAi
06_CON_027_S_0120_M06_FAi
07_CON_029_S_0845_M06_FAi
08_CON_029_S_0866_M06_FAi
09_CON_033_S_0516_M06_FAi
10_CON_033_S_0734_M06_FAi
11_CON_033_S_0923_M06_FAi
12_CON_033_S_1016_M06_FAi
13_CON_052_S_0951_M06_FAi
14_CON_094_S_0692_M06_FAi
15_CON_094_S_0711_M06_FAi
16_CON_098_S_0896_M06_FAi
17_CON_126_S_0680_M06_FAi
18_CON_127_S_0684_M06_FAi
19_CON_130_S_0232_M06_FAi
20_CON_130_S_0886_M06_FAi
21_CON_133_S_0525_M06_FAi
22_PAT_002_S_0816_M06_FAi
23_PAT_002_S_0938_M06_FAi
24_PAT_002_S_1018_M06_FAi
25_PAT_006_S_0547_M06_FAi
26_PAT_014_S_0356_M06_FAi
27_PAT_014_S_1095_M06_FAi
28_PAT_024_S_1171_M06_FAi
29_PAT_027_S_0850_M06_FAi
30_PAT_029_S_0836_M06_FAi
31_PAT_033_S_0724_M06_FAi
32_PAT_033_S_0739_M06_FAi
33_PAT_094_S_1090_M06_FAi
34_PAT_126_S_0606_M06_FAi
35_PAT_127_S_0431_M06_FAi
36_PAT_130_S_0956_M06_FAi
37_PAT_131_S_0497_M06_FAi
38_PAT_136_S_0299_M06_FAi
Running segmentation: ID=24546
Running registration: ID=10355
Creating template: ID=14398
Study-specific template will be created, when complete, check
FAi/template_4D_GM as a movie loop in fslview
14040.91user 178.57system 4:03:51elapsed 97%CPU (0avgtext+0avgdata
0maxresident)k
0inputs+0outputs (313major+25543646minor)pagefaults 0swaps
dinos@Spartan:~/Desktop/FSL-VBM/GE/M06/brains/processing_folder$
and the text files that were created are attached. All text files fslvbm2b.e
show
the following error:
/usr/share/fsl/bin/tbss_reg: line 105: /usr/share/fsl/bin/DR/areg: No such
file or directory
/usr/share/fsl/bin/tbss_reg: line 110: /usr/share/fsl/bin/DR/transformation:
No such file or directory
Indeed in these directories do not exist but instead there's :
dinos@Spartan:/usr/share/fsl/bin/DR$ ls -al
total 48
drwxr-xr-x 2 root root 4096 2008-07-31 18:06 .
drwxr-xr-x 3 root root 20480 2008-07-31 18:06 ..
-rw-r--r-- 1 root root 355 2008-04-01 11:59 affineCC.par
-rw-r--r-- 1 root root 356 2008-04-01 11:59 affine.par
-rw-r--r-- 1 root root 356 2008-04-01 11:59 affineSSD.par
-rw-r--r-- 1 root root 355 2008-04-01 11:59 nonlinearCC.par
-rw-r--r-- 1 root root 356 2008-04-01 11:59 nonlinear.par
-rw-r--r-- 1 root root 356 2008-04-01 11:59 nonlinearSSD.par
dinos@Spartan:/usr/share/fsl/bin/DR$
Why these folders do not exist? i have downloaded and installed the latest
fsl version from scratch yesterday. Where can i find these folders?
My outputs consists also of the following files:
fslvbm_2_template -a scipt run i had the following outputs:
controls_XXX_FAi.hdr (0 bytes hdr. doc)
controls_XXX_FAi.img(0 bytes plain text doc)
controls_XXX_FAi_brain.hdr
controls_XXX_FAi_brain.img
controls_XXX_FAi_brain_pve_0.hdr
controls_XXX_FAi_brain_pve_0.img
controls_XXX_FAi_brain_pve_1.hdr
controls_XXX_FAi_brain_pve_1.img
controls_XXX_FAi_brain_pve_2.hdr
controls_XXX_FAi_brain_pve_2.img
controls_XXX_FAi_brain_seg.hdr
controls_XXX_FAi_brain_seg.img
controls_XXX_FAi_GM.hdr
controls_XXX_FAi_GM.img
controls_XXX_FAi_GM_xflipped.hdr
controls_XXX_FAi_GM_xflipped.img
.....
same for the patients group
a T.hdr and T.img files
Thank you once more
Antonios-Konstantinos Thanellas
On Wed, 9 Jul 2008 23:09:46 +0100, Dost Ongur <[log in to unmask]> wrote:
>Hello,
>
>we are intermittently having the same problem: we run fslvbm_2_template with
>the most recent FSL release on a Linux RedHat machine. All the files seem
>to be created except the template_GM_4D. There are no error messages. We
>can't see the commands running on the machine any longer and we waited 2
>days and no change. Our terminal looks exactly the same as Amit pasted below.
>
>This problem arose when we ran 66 subjects in an analysis, but we can
>actually take 2 or 31 subjects from the same dataset and run
>fslvbm_2_template successfully (i.e. we get a template_GM_4D).
>
>
>Any thoughts?
>Thanks,
>Dost
>
>
>
>On Wed, 9 Jul 2008 14:07:44 +0000, Gwenaëlle DOUAUD
><[log in to unmask]> wrote:
>
>>Hi Amit,
>>
>>first you only need to run fslvbm_2_template -a, which is the option
>recommended for this version of FSL-VBM (the option recommended in the
>future version of FSL-VBM using FNIRT will be -n).
>>Then, you need to wait until you get the results and it can take a while,
>that's why you might still have no outcome. You should be able to see the
>various commands involved in the script running on your computer. If nothing
>has been created tomorrow, then let us know...
>>
>>Cheers,
>>Gwenaelle
>>
>>
>>
>>--- En date de : Mer 9.7.08, Amit Raheja <[log in to unmask]> a écrit :
>>
>>> De: Amit Raheja <[log in to unmask]>
>>> Objet: [FSL] Vbm
>>> À: [log in to unmask]
>>> Date: Mercredi 9 Juillet 2008, 15h43
>>> I am having trouble with the fslvbm_2_template command. The
>>> command seems
>>> to run ok, but I do not get the 4D template output file.
>>> Any ideas? Thank you.
>>>
>>> Here is the what is shown on my terminal.
>>>
>>> > bash-3.2$ fsl
>>> > bash-3.2$ fslvbm_2_template -a
>>> > CON10_FAi
>>> > CON1_FAi
>>> > CON2_FAi
>>> > CON3_FAi
>>> > CON4_FAi
>>> > CON5_FAi
>>> > CON6_FAi
>>> > CON7_FAi
>>> > CON8_FAi
>>> > CON9_FAi
>>> > TBI11_FAi
>>> > TBI12_FAi
>>> > TBI13_FAi
>>> > TBI14_FAi
>>> > TBI15_FAi
>>> > TBI16_FAi
>>> > TBI17_FAi
>>> > TBI18_FAi
>>> > TBI19_FAi
>>> > TBI20_FAi
>>> > TBI21_FAi
>>> > TBI22_FAi
>>> > TBI23_FAi
>>> > TBI24_FAi
>>> > TBI25_FAi
>>> > TBI26_FAi
>>> > TBI27_FAi
>>> > Running segmentation: ID=91407
>>> > Running registration: ID=92361
>>> > Creating template: ID=95178
>>> > Study-specific template will be created, when
>>> complete, check
>>> > FAi/template_4D_GM
>>> > as a movie loop in fslview
>>> > bash-3.2$ fslvbm_2_template -n
>>> > CON10_FAi
>>> > CON1_FAi
>>> > CON2_FAi
>>> > CON3_FAi
>>> > CON4_FAi
>>> > CON5_FAi
>>> > CON6_FAi
>>> > CON7_FAi
>>> > CON8_FAi
>>> > CON9_FAi
>>> > TBI11_FAi
>>> > TBI12_FAi
>>> > TBI13_FAi
>>> > TBI14_FAi
>>> > TBI15_FAi
>>> > TBI16_FAi
>>> > TBI17_FAi
>>> > TBI18_FAi
>>> > TBI19_FAi
>>> > TBI20_FAi
>>> > TBI21_FAi
>>> > TBI22_FAi
>>> > TBI23_FAi
>>> > TBI24_FAi
>>> > TBI25_FAi
>>> > TBI26_FAi
>>> > TBI27_FAi
>>> > Running segmentation: ID=96391
>>> > Running registration: ID=97345
>>> > Creating template: ID=8691
>>> > Study-specific template will be created, when
>>> complete, check
>>> > FAi/template_4D_GM
>>> > as a movie loop in fslview
>>> > bash-3.2$
>
>
>
>_____________________________________________________________________________
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>>========================================================================
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