Hi Steve,
Sorry to bother you with this again, but I am currently re-analyzing the
same dataset I talked about below (message attached) and am again running
into the same problem.
The error goes (and is repeated for each cope and each subject):
/usr/local/fsl/bin/featregapply
L:/ANTorient_3T_PhilipsIntera/ANTorient_FSL/19nov04A_01/functional/4D_19nov
04A_01ANTorientcontrol.feat
could not read "reg/highres.hdr": no such file or directory
while executing
"file mtime $filename "
(procedure "runregfiles" line 5)
invoked from within
"runregfiles $inputs "
("foreach" body line 2)
invoked from within
"foreach inputs [ imglob -oneperimage reg/highres.* ] {
if { [ runregfiles $inputs ] } {
fsl:exec "${FSLDIR}/bin/flirt -ref reg/standard -in $inp..."
invoked from within
"if { ! $cleanup } {
#{{{ apply the normalisation
if { ! [ file exists reg/example_func2standard.mat ] } {
puts "Error - registration has not ..."
(file "/usr/local/fsl/bin/featregapply" line 137)
I followed the precise instructions on
www.fmrib.ox.ac.uk/fslfaq/#feat_mixedup since these instructions worked
before on the exact same dataset.
Furthermore, I tried both with manually applying featregapply to the first
level directories and without manually applying featregapply, the error is
the same in both cases.
The only thing I can think of is that it has something to do with the
patch that the above link tells you to download. The link to this patch no
longer works and I just assumed that this patch would have been integrated
in the current version of FSL 3.2....
Is there something silly that I am overlooking here?
Many thanks,
Bianca.
On Wed, 26 Jan 2005 12:37:58 +0000, Stephen Smith <[log in to unmask]>
wrote:
>Hi - yes, we had a similar question on the list recently and I've just
>tried this out myself. The choosing of cope inputs option nearly works,
>there's just a small change needed so that FEAT doesn't look for tdof
>files everywhere. I've written a brief FAQ entry on how to make this work
>now:
>
>http://www.fmrib.ox.ac.uk/fslfaq/#feat_mixedup
>
>Cheers, Steve.
>
>
>On Tue, 25 Jan 2005, Bianca de Haan wrote:
>
>> Dear FSL list,
>>
>> I am trying to run a pretty straightforward analysis; 14 subjects
>> performed a task and I want to know the mean group activation on a
number
>> of contrasts (windows XP + cygwin).
>>
>> One of the subjects, however, was run on 2 sessions while all other
>> subjects were run on 1 session (this was a mistake, but more data can
>> never hurt, right?)
>>
>> All first level analyses on each individual session ran smoothly. I then
>> ran a second level analysis on the 2 sessions of the subjects with 2
>> sessions (resulting in mean for the subject). I also ran featregapply to
>> get all the subjects with only 1 session into standard space as well.
>>
>> Consequently, to get to my group mean, I ran a higher level analysis
>> selecting the .feat directories from all the subjects with 1 session and
>> the .gfeat directory from the subject with 2 sessions. Here I run into
>> problems with registration, Feat keeps telling me that no all the
>> directories are registered and refuses to run. I have checked this
quite a
>> few times now and by the best of my knowledge featregapply ran
perfectly.
>>
>> When the above method did not work, I switched to selecting the cope
files
>> instead of the feat directories. I selected the cope files for the
>> subjects with only 1 session from the directory .feat/stats and the for
>> the subject with 2 sessions I tried both selecting the cope from the
>> directory .gfeat and from the directory .gfeat/cope.feat/stats. Using
this
>> second option, Feat did decide to run, but it tries to do featregapply
and
>> throws up a good amount of errors doing that. It does however continue
to
>> do the stats, but then gives me the error:
>>
>> Metropolis Hasting Sampling
>> Number of voxels=66
>> Percentage done:
>> 1
>>
>>
>> An exception has been thrown
>> Logic error:- detected by Newmat: index error: requested index = 2
>>
>> MatrixType = Rect # Rows = 1; # Cols = 1
>> Trace: Mcmc_Mh::setup; Gsmanager::run.
>>
>>
>> echo 13 > stats/dof
>>
>> /bin/rm -f stats/zem* stats/zols* stats/mask*
>> Rendering using zmin=2.3 zmax=8
>>
>> mkdir tsplot
>>
>> /usr/local/fsl/bin/tsplot . -f filtered_func_data -o tsplot
>> ** ERROR: nifti_image_read(./stats/pe1): can't open header file
>> ** ERROR: nifti_image_open(./stats/pe1): bad header info
>> Error: failed to open file ./stats/pe1
>> ERROR: Could not open image ./stats/pe1
>> Image Exception : #22 :: Failed to read volume ./stats/pe1
>> Signal 6
>>
>>
>> At the moment I am a bit lost. I could always make my life a lot easier
by
>> treating the 2 sessions from 1 subjects as just 2 subjects (so just do a
>> first level analysis on each of the sessions and then just throw them
into
>> a higher level analysis kinda pretending I have 15 instead of 14
subjects
>> and selecting all the first level .feat directories). I however, feel
this
>> might not really be the right way to do it.
>>
>> I apologize for the longwinded e-mail, but would really appreciate it if
>> anyone could help me here.
>>
>> Many thanks,
>>
>> Bianca.
>>
>
>--
> Stephen M. Smith DPhil
> Associate Director, FMRIB and Analysis Research Coordinator
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>=========================================================================
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