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Subject:

Re: unequal amount of sessions between subjects

From:

Stephen Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 17 Aug 2005 09:07:25 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (341 lines)

Hi Bianca,

Not sure - I still think that it's something related to the filesystems, 
but I'm a little confused now about the different directories involved. 
Can you run

featregapply <featdir> -c

on all first (and combined first) level featdirs, and then try running the 
higher-level analysis again - then send me directly all relevant 
report.log files, and a full ls -R listing of any first-level (or 
combined) featdirs where you think there was a problem.

Cheers, Steve.




On Thu, 11 Aug 2005, Bianca de Haan wrote:

> Hi Steve,
> 
> I'm a bit lost & puzzled now. When I look at my files, they have the 
> correct names. Are you telling me that this is some incompatibility 
> between the filing systems of cygwin and windows?
> 
> I have done quite a few analyses in FSL using the exact same computer (my 
> last succesful analysis was yesterday) and not had this problem yet... The 
> only thing that sets this analysis apart is the unequal amount of sessions 
> between subjects (1 subject has 2 sessions while all other subjects have 
> only 1 session), so I assumed the same problem as before had surfaced...
> 
> *stumped*
> 
> Many thanks,
> 
> Bianca.
> 
> On Thu, 11 Aug 2005 15:17:31 +0100, Stephen Smith <[log in to unmask]> 
> wrote:
> 
> >Hi Bianca, thanks for sending the directory listing. Yes - the problem is
> >that your files have the wrong names - for example:
> >
> >highres.hdr.lnk
> >instead of
> >highres.hdr
> >
> >I'm assuming you're using Windows - this extra ".lnk" has probably arisen
> >due to using some filesystem which doesn't allow Cygwin to create "normal"
> >unix symbolic links. You could try using a more standard/native XP
> >filesystem? Probably best if you get local sysad advice if, like me,
> >you're not a Windows guru.
> >
> >Cheers, Steve.
> >
> >
> >
> >
> >
> >On Thu, 11 Aug 2005, Bianca de Haan wrote:
> >
> >> Hi Christian,
> >>
> >> All the files that FSL complains do not exist, do in fact exist and can 
> be
> >> accessed.
> >>
> >> Bianca.
> >>
> >> On Thu, 11 Aug 2005 11:07:42 +0100, Christian Beckmann
> >> <[log in to unmask]> wrote:
> >>
> >> >Bianca,
> >> >
> >> >it's complaining that the file L:/ANTorient_3T_PhilipsIntera/
> >> >ANTorient_FSL/19nov04A_01/functional/
> >> >4D_19nov04A_01ANTorientcontrol.feat/reg/highres.hdr
> >> >
> >> >does not exist. Is this correct? If so, you need to fix it, either by
> >> >copying the highres data into this directory or by linking the file.
> >> >cheers
> >> >christian
> >> >
> >> >
> >> >On 11 Aug 2005, at 10:15, Bianca de Haan wrote:
> >> >
> >> >> 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
> >> >>> 
> =====================================================================
> >> >>> ====
> >> >>
> >> >
> >> >--
> >> >  Christian F. Beckmann
> >> >  Oxford University Centre for Functional
> >> >  Magnetic Resonance Imaging of the Brain,
> >> >  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> >> >  Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
> >> >  Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
> >> 
> >=========================================================================
> >>
> >
> >--
> > 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
> >=========================================================================
> 

-- 
 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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