Hi Darren,
To clarify - featquery only uses dim1-3 to check for matching size.
In your call to featquery it looks like there is a space within the
filename of the mask image - is that just from pasting into the email or
could that explain the problem?
Cheers :)
On Wed, 2 Jul 2003, Darren Schreiber wrote:
> I was able to create an ROI file from the AFNI TTatlas finally. I
> created it in the space of the avg152T1 brain and it looks fine on top
> of that brain when I view it in AFNI. I have changed that file from
> AFNI to Analyze format and then tried to use it with FeatQuery. This
> is the error that I got:
>
> /usr/local/fsl3/bin/featquery 1
> /sig/iacoboni/schreiber/QuestionsFSL/ACLMRTUcontrasts8.gfeat/cope1.feat
> 1 filtered_func_data
> /sig/iacoboni/schreiber/ QuestionsFSL/ACLMRTUcontrasts8.gfeat/
> LeftAmygdalaROI_0000.hdr
> child process exited abnormally
>
> Since the error message isn't verbose, I went looking at the report.txt
> file and found:
>
> Processing FEAT directory 1 :
> /offsite/sig/iacoboni/schreiber/QuestionsFSL/ACLMRTUcontrasts8.gfeat/
> cope1.feat
> Error - mask size doesn't match any of the images in the FEAT directory
>
> The images looked to be of the same size in AFNI (I use zstat2 below,
> but the results are the same for filter_func_data.) So, I verified
> this using AFNI's 3dinfo tool:
>
> Dataset File: LeftAmygdalaROI.hdr+orig
> Identifier Code: ANLZ409oQf4y0OMSdghqxfR1Eg Creation Date: Wed Jul 2
> 11:58:18 2003
> Dataset Type: MRI Anatomy (-anat)
> Byte Order: MSB_FIRST {assumed} [this CPU native = MSB_FIRST]
> Storage Mode: ANALYZE files
> Data Axes Orientation:
> first (x) = Right-to-Left
> second (y) = Posterior-to-Anterior
> third (z) = Inferior-to-Superior [-orient RPI]
> R-to-L extent: 1.000 [L] -to- 181.000 [L] -step- 2.000 mm [
> 91 voxels]
> A-to-P extent: -217.000 [A] -to- -1.000 [A] -step- 2.000 mm
> [109 voxels]
> I-to-S extent: 1.000 [S] -to- 181.000 [S] -step- 2.000 mm [
> 91 voxels]
> Number of values stored at each pixel = 1
> -- At sub-brick #0 '?' datum type is float
>
> Dataset File: zstat2.hdr+orig
> Identifier Code: ANLZAUGnkqYH2qx_MDerJjN9YQ Creation Date: Wed Jul 2
> 11:59:11 2003
> Dataset Type: Intensity (-fim)
> Byte Order: MSB_FIRST {assumed} [this CPU native = MSB_FIRST]
> Storage Mode: ANALYZE files
> Data Axes Orientation:
> first (x) = Right-to-Left
> second (y) = Posterior-to-Anterior
> third (z) = Inferior-to-Superior [-orient RPI]
> R-to-L extent: 1.000 [L] -to- 181.000 [L] -step- 2.000 mm [
> 91 voxels]
> A-to-P extent: -217.000 [A] -to- -1.000 [A] -step- 2.000 mm
> [109 voxels]
> I-to-S extent: 1.000 [S] -to- 181.000 [S] -step- 2.000 mm [
> 91 voxels]
> Number of values stored at each pixel = 1
> -- At sub-brick #0 '?' datum type is float
> statcode = fim
>
> They look to be in the same orientation and same dimensions (I haven't
> altered zstat2.hdr from when it came out of FSL). I looked at them
> both using avwhd:
>
> filename LeftAmygdalaROI.hdr
> sizeof_hdr 348
> data_type
> db_name LeftAmygdalaROI
> extents 0
> session_error 0
> regular r
> hkey_un0
> dim0 3
> dim1 91
> dim2 109
> dim3 91
> dim4 1
> dim5 1
> dim6 1
> dim7 1
>
> filename zstat2.hdr
> sizeof_hdr 348
> data_type
> db_name
> extents 16384
> session_error 0
> regular r
> hkey_un0
> dim0 4
> dim1 91
> dim2 109
> dim3 91
> dim4 1
> dim5 0
> dim6 0
> dim7 0
>
> My assumption is that dim means dimension and is some indication of
> size (infering that from the numbers in the AFNI output). The
> differences seem to be in the "extents" and in dim0, dim5-7. Am I
> looking at the right indicators? Any ideas how I get featquery to see
> these files as the same size?
>
> On Mark Cohen's suggestion, I tried to duplicated the header from
> zstat2.hdr onto a file I called LeftAmygdalaROI.hdr (I made a backup of
> the original). I tried featquery again and got the same results.
>
> Any other ideas? I have pasted the entire results of the avwhd output
> below for both files. Any other ways of working around this or
> figuring out what is wrong?
>
> filename zstat2.hdr
> sizeof_hdr 348
> data_type
> db_name
> extents 16384
> session_error 0
> regular r
> hkey_un0
> dim0 4
> dim1 91
> dim2 109
> dim3 91
> dim4 1
> dim5 0
> dim6 0
> dim7 0
> vox_units mm
> cal_units
> unused1 0
> datatype 16
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 -2.0000000000
> pixdim2 2.0000000000
> pixdim3 2.0000000000
> pixdim4 0.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 0.0000
> funused1 1.0000
> funused2 0.0000
> funused3 0.0000
> cal_max 0.0000
> cal_min 0.0000
> compressed 0
> verified 0
> glmax 5
> glmin -6
> descrip Externally created avw->header
> aux_file
> orient 0
> originator
> origin1 46
> origin2 64
> origin3 37
> generated
> scannum
> patient_id
> exp_date
> exp_time
> hist_un0
> views 0
> vols_added 0
> start_field 0
> field_skip 0
> omax 0
> omin 0
> smin 0
> smin 0
>
>
> filename LeftAmygdalaROI.hdr
> sizeof_hdr 348
> data_type
> db_name LeftAmygdalaROI_0
> extents 0
> session_error 0
> regular r
> hkey_un0
> dim0 3
> dim1 91
> dim2 109
> dim3 91
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units
> cal_units
> unused1 0
> datatype 16
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 2.0000000000
> pixdim2 2.0000000000
> pixdim3 2.0000000000
> pixdim4 1.0000000000
> pixdim5 1.0000000000
> pixdim6 1.0000000000
> pixdim7 1.0000000000
> vox_offset 0.0000
> funused1 1.0000
> funused2 0.0000
> funused3 0.0000
> cal_max 0.0000
> cal_min 0.0000
> compressed 0
> verified 0
> glmax 1
> glmin 0
> descrip
> aux_file
> orient 0
> originator
> origin1 0
> origin2 0
> origin3 0
> generated
> scannum
> patient_id
> exp_date
> exp_time
> hist_un0
> views 0
> vols_added 0
> start_field 0
> field_skip 0
> omax 0
> omin 0
> smin 0
> smin 0
>
Stephen M. Smith MA DPhil CEng MIEE
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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