Hi Antonios - Constantine,
what is the output in your shell when you're trying to run this command:
/usr/share/fsl/bin/fsl_reg 01_CON_002_S_0295_M06_struc_GM template_GM_init 01_CON_002_S_0295_M06_struc_GM_to_T_init -fnirt "--config=GM_2_MNI152GM_2mm.cnf"
Cheers,
Gwenaelle
--- En date de : Sam 13.9.08, 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: Samedi 13 Septembre 2008, 18h01
> Hi Gwenaelle,
> Indeed subtracting these two images gave me a blank image.
> (so we're talking
> about the same image)
> Find attached the folowing files:
> fslvbm2d.e25560.1.txt.tar.gz ,
> fnirt.txt.tar.gz and
> log_files.tar.gz (contains all the log files of the
> analysis)
>
> Thank you
>
>
> On Fri, 12 Sep 2008 15:59:28 +0000, Gwenaëlle DOUAUD
> <[log in to unmask]> wrote:
>
> >Hi Antonios,
> >
> >the second pass of your template hasn't worked
> (.msf files are empty and
> _to_T_init.nii.gz not created). The template_GM and
> template_GM_init should
> then basically look the same when template_GM should look
> much more refined...
> >
> >Could you please send me one fslvbm2d.e25560 file?
> >
> >and also, what do you get when you type
> "fnirt" in your shell?
> >
> >Cheers,
> >Gwenaelle
> >
> >
> >--- En date de : Ven 12.9.08, 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: Vendredi 12 Septembre 2008, 9h16
> >> Yes Gwenaelle,
> >> These files are not created in my struc folder,
> only some
> >> blank msf files
> >> for each subject with the names
> >> *XXX*_struc_GM_to_T_init_warp.msf
> >> Though the analysis continued and templates were
> created
> >> which looked quite
> >> normal.
> >> The ls-al txt file is attached for your
> consideration.
> >>
> >> Thank you Gwenaelle
> >>
> >> On Thu, 11 Sep 2008 12:06:15 +0000, Gwenaëlle
> DOUAUD
> >> <[log in to unmask]> wrote:
> >>
> >> >Hi Antonios - Constantine,
> >> >
> >> >could you please copy/paste in a text file the
> output
> >> of a ls -al in your
> >> struc directory?
> >> >
> >> >Cheers,
> >> >Gwenaelle
> >> >
> >> >
> >> >--- En date de : Mer 10.9.08, 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: Mercredi 10 Septembre 2008, 10h39
> >> >> Hi Gwenaelle,
> >> >> Yes you are right, I'm sorry for
> wasting your
> >> time with
> >> >> such a silly mistake
> >> >> of mine.
> >> >> I run correctly this time the
> fslvbm_2_template
> >> and it
> >> >> created the template
> >> >> which looks ok (template_4D_GM through
> fslview).
> >> Though
> >> >> some of the log
> >> >> files showed some errors and i'm not
> sure if
> >> >> they're important and can
> >> >> affect my results.Can you take a look at
> them
> >> please and
> >> >> tell me your opinion?
> >> >>
> >> >> The error files are: fslvbm2d.e25560
> >> >>
> fslvbm2e.e29568
> >> >> and a warning message in: fslvbm2e.o29568
> >> >>
>
> >> fslvbm2c.o23932
> >> >>
> >> >> For once more thank you
> >> >>
> >> >> On Tue, 9 Sep 2008 12:56:39 +0000,
> Gwenaëlle
> >> DOUAUD
> >> >> <[log in to unmask]> wrote:
> >> >>
> >> >> >Hi,
> >> >> >
> >> >> >the problem is coming from what
> you've
> >> entered in
> >> >> your template_list: you
> >> >> entered (first line) the name of this
> image that
> >> does not
> >> >> exist.
> >> >> Subsequently, the first-pass template is
> not
> >> created, then
> >> >> the second one...
> >> >> >
> >> >> >Try rerunning fslvbm_2 with the
> correct names
> >> in the
> >> >> template_list, it
> >> >> should be fine...
> >> >> >
> >> >> >Cheers,
> >> >> >Gwenaelle
> >> >> >
> >> >> >PS: The two versions I mentioned were
> of the
> >> >> template_list, not of fslvbm_2.
> >> >> >
> >> >> >
> >> >> >--- En date de : Mar 9.9.08, 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: Mardi 9 Septembre 2008,
> 14h28
> >> >> >> Hello again Gwenaelle,
> >> >> >>
> >> >> >> I've modifed the
> fslvbm_2_template as
> >> >> you've
> >> >> >> proposed and the run was more
> >> >> >> normal this time.Though the
> >> template_GM_4D image
> >> >> was not
> >> >> >> created.I've
> >> >> >> noticed the following errors:
> >> >> >> 1st) Even though my template
> list
> >> contains 36 (out
> >> >> of the
> >> >> >> 38 files,since
> >> >> >> according to the guides the same
> amount
> >> of
> >> >> controls and
> >> >> >> patients should be
> >> >> >> used) ,it seems that the script
> processes
> >> all the
> >> >> files
> >> >> >> (i've seen that the
> >> >> >> same issue has been reported in
> the fsl
> >> list with
> >> >> the
> >> >> >> title: "VBM template
> >> >> >> creation with selected
> images")
> >> >> >>
> >> >> >> 2nd) an error fslvbm2e.e10389
> report
> >> which is very
> >> >> strange
> >> >> >> for the following
> >> >> >> reason: It mentions that:
> >> >> >> ** ERROR (nifti_image_read):
> failed to
> >> find header
> >> >> file for
> >> >> >>
> >> '01_CON_002_S_0295_SC_struc_GM_to_T_init'
> >> >> >> ** ERROR:
> >> >> >>
> >> >>
> >>
> nifti_image_open(01_CON_002_S_0295_SC_struc_GM_to_T_init):
> >> >> >> bad
> >> >> >> header info
> >> >> >>
> >> >> >> and the strange thing is that
> >> 01_CON_002_S_0295_SC
> >> >> file
> >> >> >> does not exist.This
> >> >> >> file actually is the
> >> 20_CON_002_S_0295_SC.
> >> >> >>
> >> >> >> In order for this to be more
> clarified
> >> find
> >> >> attached the
> >> >> >> .txt files that
> >> >> >> were created during the analysis
> + the
> >> structure
> >> >> of my
> >> >> >> folder were the
> >> >> >> analysis took place.
> >> >> >> Thank you
> >> >> >>
> >> >> >>
> >> >> >> On Mon, 8 Sep 2008 14:30:24
> +0100,
> >> Antonios -
> >> >> Constantine
> >> >> >> Thanellas
> >> >> >> <[log in to unmask]>
> wrote:
> >> >> >>
> >> >> >> >Yes Gwenaelle,
> >> >> >> >I work with an AMD athlon 64
> ,3200+,
> >> with 1GB
> >> >> RAM and a
> >> >> >> SATA hard disk. My
> >> >> >> >platform is Ubuntu 7.10
> (gutsy) and i
> >> use the
> >> >> FSL 4.1.0
> >> >> >> version. All my data
> >> >> >> > (brain images) come though
> from a
> >> previous
> >> >> version of
> >> >> >> fsl (FSL 4.0) and
> >> >> >> >ubuntu (7.04).
> >> >> >> >As i've already
> mentioned i
> >> bypassed the
> >> >> first step
> >> >> >> of VBM analysis since i
> >> >> >> >had already my brain images
> >> extracted and i
> >> >> confronted
> >> >> >> this problem when i
> >> >> >> >was trying to run the script
> >> fslvbm_2_template
> >> >> -n.
> >> >> >> >Find attached an
> fslerroreport that
> >> may give
> >> >> you some
> >> >> >> more info regarding my
> >> >> >> >system and my environmental
> >> variables.
> >> >> >> >In case you need some more
> >> information ,just
> >> >> inform me
> >> >> >> >Thank you
> >> >> >> >
> >> >> >> >
> >> >> >> >On Mon, 8 Sep 2008 12:30:56
> +0000,
> >> Gwenaëlle
> >> >> DOUAUD
> >> >> >>
> ><[log in to unmask]>
> >> wrote:
> >> >> >> >
> >> >> >> >>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
> >> >> >> >>
> >> >> >> >>
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