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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