Sorry for the confusion there, Matthew. I used the GUI, and it was working with 20 stat images, but when I sent the email I removed a bunch of the stats/copeX and stats/zstatX parts from the command line quote in the hopes of making it easier to read. I suppose I should have realized that only I'd be making it more confusing!
I'm using version 4.1.6, from the fsl-4.1.6-centos5_64 build. Also, I'll note that running featquery on otherwise identical but FLIRT-registered feat analyses runs without any problems.
Thanks!
-Jim
On Tue, 23 Aug 2011 11:02:27 +0100, Matthew Webster <[log in to unmask]> wrote:
>Hello James,
> Did you construct the featquery command-line call manually or use the Featquery GUI? Looking at the command line call below it is requesting the processing of 20 stat images, but only 8 are supplied ( cope and zstat 1-4 ). If you did use the GUI, then upload your 4 feat directories and we'll check what is going wrong. Could you also confirm which version of FSL you are using ( number and architecture? )
>
>Many Regards
>
>Matthew
>> Howdy-
>>
>> I'm receiving exactly the same message when I try to run featquery on FNIRT-registered data. It doesn't matter is I supply my own mask image, if I use the atlas functions in featquery to select a standard mask, or if I choose to use XYZ coordinates.
>>
>> I'd like to upload my files if you have the time to look at them. Thanks!
>>
>> -Jim Porter
>>
>>
>> p.s., Here's my error from the standard atlas attempt:
>>
>> /opt/bliss/fsl/bin/featquery 4 fnirt_test/fnirt_Blk1.feat fnirt_test/fnirt_Blk2.feat fnirt_test/fnirt_Blk3.feat fnirt_test/fnirt_Blk4.feat 20 stats/cope1 stats/cope2 stats/cope3 stats/cope4 stats/zstat1 stats/zstat2 stats/zstat3 stats/zstat4 AtlasLeftNAcc_fqtest -a 5 -p -s -w -b /tmp/featquery_vz8eIz
>>
>> expected floating-point number but got "Mask"
>> while executing
>> "format %.4g [ lindex $thevals 0 ] "
>> ("for" body line 243)
>> invoked from within
>> "for { set f 1 } { $f <= $featquery(multiple) } { incr f 1 } {
>>
>> #{{{ setup output dir and logging etc.
>>
>> set mask $origmask
>>
>> cd [ lindex $argv $f ]
>> ..."
>> (file "/opt/bliss/fsl/bin/featquery" line 167)
>>
>>
>>
>> On Mon, 18 Jul 2011 13:36:25 +0200, Cornelius Werner <[log in to unmask]> wrote:
>>
>>> Hi Steve,
>>>
>>> I understood the help output of featquery sucht that if no leading
>>> slash is supplied, featquery will look inside the *.feat directories
>>> for the mask (i.e., relative path). However, I also tried masks
>>> located in the directory I ran featquery from and also tried absolute
>>> paths, to no avail. I will give it another shot, but if that doesn't
>>> work either, I'd be thankful if you could have a look at the data.
>>>
>>> Thanks a lot,
>>> Cornelius
>>>
>>> On Sat, Jul 16, 2011 at 10:12 AM, Stephen Smith <[log in to unmask]> wrote:
>>>> Hi Cornelius - are you sure that reg_standard/mask exists relative to the
>>>> directory you are calling featquery from?
>>>> If you're still stuck, feel free to upload the output featquery directory
>>>> (and a copy of what appears in your terminal when you run it) and email us
>>>> the upload ID and we can take a look.
>>>> Cheers.
>>>>
>>>>
>>>>
>>>> On 15 Jul 2011, at 14:31, Cornelius Werner wrote:
>>>>
>>>> Dear list,
>>>>
>>>> I tried to overcome my previously posted problem by running featquery
>>>> from the command line. But every time I try to run it against FNIRT#ed
>>>> feat directories, it fails. FLIRT'ed ones do not seem to pose a
>>>> problem. However, I really need the FNIRT ones...
>>>>
>>>> This is the call:
>>>> featquery 16 /path-to-data/7511_TTT4-7.feat
>>>> /path-to-data/7441_TTT4-7.feat /path-to-data/7519_TTT4-7.feat
>>>> /path-to-data/7442_TTT4-7.feat /path-to-data/7520_TTT4-7.feat
>>>> /path-to-data/7486_TTT4-7.feat /path-to-data/7521_TTT4-7.feat
>>>> /path-to-data/7487_TTT4-7.feat /path-to-data/7488_TTT4-7.feat
>>>> /path-to-data/7576_TTT4-7.feat /path-to-data/7507_TTT4-7.feat
>>>> /path-to-data/7577_TTT4-7.feat /path-to-data/7718_TTT4-7.feat
>>>> /path-to-data/7508_TTT4-7.feat /path-to-data/7510_TTT4-7.feat
>>>> /path-to-data/7719_TTT4-7.feat 6 stats/pe5 stats/pe7 stats/pe13
>>>> stats/pe15 stats/pe21 stats/pe23 acc_46-75-60 reg_standard/mask -vox
>>>> 46 75 60
>>>>
>>>> And this is the error:
>>>>
>>>> expected floating-point number but got "Mask"
>>>> while executing
>>>> "format %.4g [ lindex $thevals 0 ] "
>>>> ("for" body line 243)
>>>> invoked from within
>>>> "for { set f 1 } { $f <= $featquery(multiple) } { incr f 1 } {
>>>>
>>>> #{{{ setup output dir and logging etc.
>>>>
>>>> set mask $origmask
>>>>
>>>> cd [ lindex $argv $f ]
>>>> ..."
>>>> (file "/usr/lib/fsl/4.1/featquery" line 167)
>>>>
>>>> It does not seem to depend on the actual mask I am using. It crashes
>>>> with all masks tried so far.
>>>> Thanks in advance and best regards,
>>>> Cornelius
>>>> --
>>>> Dr. med. Cornelius J. Werner
>>>> Department of Neurology
>>>> RWTH Aachen University
>>>> Pauwelsstr. 30
>>>> 52074 Aachen
>>>> Germany
>>>>
>>>>
>>>>
>>>> ---------------------------------------------------------------------------
>>>> Stephen M. Smith, Professor of Biomedical Engineering
>>>> Associate Director, Oxford University FMRIB Centre
>>>>
>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>> +44 (0) 1865 222726 (fax 222717)
>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>> ---------------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Dr. med. Cornelius J. Werner
>>> Department of Neurology
>>> RWTH Aachen University
>>> Pauwelsstr. 30
>>> 52074 Aachen
>>> Germany
>>
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