Hi,
The use of Analyze does explain the problem on your machine, as it is
incorrectly reading the warp file (being in Analyze format) and so has
to do
a lot more filing of blank area and correcting for problems due to
poorly
constrained Jacobians.
The puzzling thing is that you can get Analyze output from FSL4.1 as
this
should not be possible. Setting my FSLOUTPUTTYPE variable to ANALYZE
(which is what yours is set to) gives me an error of the form:
ERROR:: Unrecognised value (ANALYZE) of environment variable
FSLOUTPUTTYPE
Legal values are: NIFTI, NIFTI_PAIR, NIFTI_GZ, NIFTI_PAIR_GZ
If you are not getting this error it makes me think that you are not
using
FSL4.1. I notice that in your PATH you have both /usr/share/fsl/bin
and /usr/lib/fsl.
I would check what version you are really using. See what you get with
"which invwarp" to see where it is finding the files.
As for your supercomputer - invwarp will not be run in parallel, so it
is
only using one node of your system, and each node seems to be a 1.5GHz
processor, which may not be so fast. Hence 10 hours, although long,
doesn't
seem unreasonable. However, your setup problems here (I don't know what
your fslinit file is or why it is needed) also makes me wonder if you
have
the right version of FSL installed and are using that one.
We really, really strongly recommend using NIFTI for your output format
(in FSL4.1 you just cannot have ANALYZE for output) and for FNIRT it is
essential. It is the warp fields - particular the coeff fields -
which must use
the nifti format and so you cannot use any tools that deal with these
(including
applywarp and invwarp) with ANALYZE. I would change your FSLOUTPUTTYPE
to NIFTI_GZ, check that you are using FSL4.1 (and install it if
necessary) and
then try running the sequence of commands again on your machine and see
if that fixes the problem.
All the best,
Mark
On 24 Oct 2008, at 00:00, Anthony Ang wrote:
> Hi Jesper,
>
> Attached is the angs_set.txt file for our lab computer. Yes, I
> notice that Analyze output files are produced.
> I also notice that the supercomputer that I used produces NIFTI
> files and when I compared the fnirt --iout file and Applywarp file
> generated by the supercomputer, they are identical.
>
> My subject images (1000024 and so on) are in Analyze format. Do I
> need to convert them to NIFTI in order for flirt, fnirt, invertwarp,
> applywarp to work correctly? Does the use of Analyze files also
> affect other FSL tools such as bet and fast?
>
> However, the difference in the file format still does not explain
> the >10 hours taken by the supercomputer to complete invwarp.
> I remembered when I was using invwarp on the supercomputer, it
> doesn't recognize the invwarp command. A fellow colleague helped and
> found an fslinit file somewhere; copied and pasted one of the lines
> (I think it is module load fsl ....) into the terminal and execute
> it. Then the invwarp is working. We have no control over the
> supercomputer. Could this have explained the long time taken even
> for this supercomputer to carry out invwarp, although it uses NIFTI
> files?
>
> Thanks.
>
> Best regards
> Anthony
>
>
>
> On Thu, Oct 23, 2008 at 8:44 PM, Jesper Andersson <[log in to unmask]
> > wrote:
> Hi again Antony,
>
> the files you sent us are in analyze format. I am not really sure
> how that happened. As of FSL 4.0, there shouldn't really be any
> (simple) way of producing analyze files as output.
>
> This also explains the problems you are having. When fnirt produce
> coefficient files (--cout) it uses a number of fields in the nifti
> header to encode various bits of information that is needed for the
> other applications to later decode them. Not all of those fields are
> present in the analyze format, and the files do not get interpreted
> correctly by either applywarp (which explains that mismatch) or
> invwarp.
>
> As a first step, could you please do
>
> set > angs_set.txt
>
> and then email us angs_set.txt?
>
> Best regards Jesper
>
>
> On 23 Oct 2008, at 08:19, Anthony Ang wrote:
>
>> Hi Mark,
>>
>> The ref no is 470181
>> Thanks.
>>
>> Best regards
>> Anthony
>>
>>
>> ---------- Forwarded message ----------
>> From: Jesper Andersson <[log in to unmask]>
>> Date: Thu, Oct 23, 2008 at 5:38 PM
>> Subject: Re: [FSL] Problem with invwarp
>> To: [log in to unmask]
>> Cc: Mark Jenkinson <[log in to unmask]>, [log in to unmask]
>>
>>
>> Hi Antony,
>>
>> >
>> > fslroi x1000024_resize x1000024_roi 29 182 0 186 41 176
>> > fslroi x1000024_n3ed x1000024_roi_n3ed 29 182 0 186 41 176
>> >
>> > flirt -v -ref MNI152_T1_2mm_brain -in x1000024_roi_n3ed -omat
>> > flirted_x1000024_reducedFOV.mat -out
>> flirted_x1000024_reducedFOV.hdr >
>> > flirt_output
>> >
>> > fnirt -v --in=x1000024_roi --aff=flirted_x1000024_reducedFOV.mat
>> > --cout=fnirted_x1000024_cout --iout=fnirted_x1000024_iout
>> > --config=T1_2_MNI152_2mm > fnirt_output
>> > *
>> > applywarp -v --ref=MNI152_T1_2mm --in=x1000024_roi
>> > --warp=fnirted_x1000024_cout --out=warped_x1000024 >
>> applywarp_output
>>
>> the fnirted_x1000024_iout and warped_x1000024 files should
>> definitely be
>> identical. Could you please tar fnirted_x1000024_iout,
>> warped_x1000024 and
>> nirted_x1000024_cout and then go to
>>
>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>
>> and follow the instructions there to upload the file? When you have
>> done
>> that please email me and Mark with the six-digit code that you are
>> given.
>>
>> Best regards Jesper
>>
>>
>>
>>
>
>
> <angs_set.txt>
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