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Subject:

Re: FLIRT-Abort

From:

Shruthi Chapkrapani <[log in to unmask]>

Reply-To:

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

Date:

Tue, 25 Apr 2006 11:00:25 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (178 lines)

Oh my God!!! I did not pay much attention to the hd file.Thanks so
much.Ya this is a mask which I want to use in my analysis stream.I
definitely need only one volume for that. Worked out perfect.

Thanks again.

shruthi

On Apr 25, 2006, at 10:32 AM, Mark Jenkinson wrote:

> Dear Shruthi,
>
> The image PNAS.nii.gz has 600 individual volumes in it.
> The flirt call you've done is trying to make an image that is the
> size of
> the average brain (91x109x91) but with 600 individual volumes - hence
> it will require 91*109*91*600 = 541577400 voxels. With the default
> output
> type of 32bit floats, that makes this image 2.02 Gigabytes! This
> is why
> flirt cannot cope.
>
> Are you sure this is what you want to do?
> You have called the image a "Default mode network mask".
> If you only want to work with the first of the 600 images, then I
> suggest
> that you create a single volume from this using avwroi: e.g.
> avwroi PNAS PNAS_mask 0 1
>
> Then if you run the flirt command with PNAS_mask as the input it
> should work fine.
>
> All the best,
> Mark
>
>
>
> Shruthi Chapkrapani wrote:
>
>> Hi
>>
>> Here is the header info of the Default mode network mask
>> (PNAS.nii.gz)
>> filename PNAS.nii.gz
>>
>> sizeof_hdr 348
>> data_type INT16
>> dim0 4
>> dim1 25
>> dim2 64
>> dim3 64
>> dim4 600
>> dim5 1
>> dim6 1
>> dim7 1
>> vox_units mm
>> time_units s
>> datatype 4
>> nbyper 2
>> bitpix 16
>> pixdim0 0.0000000000
>> pixdim1 6.0000000000
>> pixdim2 3.1250000000
>> pixdim3 3.1250000000
>> pixdim4 4.0000000000
>> pixdim5 1.0000000000
>> pixdim6 1.0000000000
>> pixdim7 1.0000000000
>> vox_offset 352
>> cal_max 4.0000
>> cal_min 0.0000
>> scl_slope 0.000000
>> scl_inter 0.000000
>> phase_dim 0
>> freq_dim 0
>> slice_dim 0
>> slice_name Unknown
>> slice_code 0
>> slice_start 0
>> slice_end 0
>> slice_duration 0.000000
>> time_offset 0.000000
>> intent Label index
>> intent_code 1002
>> intent_name
>> intent_p1 0.000000
>> intent_p2 0.000000
>> intent_p3 0.000000
>> qform_name Unknown
>> qform_code 0
>> qto_xyz:1 6.000000 0.000000 0.000000 0.000000
>> qto_xyz:2 0.000000 3.125000 0.000000 0.000000
>> qto_xyz:3 0.000000 0.000000 3.125000 0.000000
>> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
>> qform_xorient Left-to-Right
>> qform_yorient Posterior-to-Anterior
>> qform_zorient Inferior-to-Superior
>> sform_name Scanner Anat
>> sform_code 1
>> sto_xyz:1 6.000000 0.000000 0.000000 -84.000000
>> sto_xyz:2 0.000000 3.125000 0.000000 -98.437500
>> sto_xyz:3 0.000000 0.000000 3.125000 -98.437500
>> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
>> sform_xorient Left-to-Right
>> sform_yorient Posterior-to-Anterior
>> sform_zorient Inferior-to-Superior
>> file_type NIFTI-1+
>> file_code 1
>> descrip FSL3.2beta
>> aux_file Red to yellowsage_typeV
>>
>>
>> and the transformation Matrix
>>
>> 1.11754 -0.010024 -0.0272254 12.2203
>> 0.0202344 1.03806 0.170907 -8.627
>> 0.0260649 -0.170107 1.17068 -41.1035
>> 0 0 0 1
>>
>>
>> Let me know if you need anything else.
>>
>> Thanks so much
>> shruthi
>>
>>
>>
>>
>> On Apr 24, 2006, at 7:04 PM, Mark Jenkinson wrote:
>>
>>> Hi,
>>>
>>> This is probably because the image is very large and flirt cannot
>>> assign enough memory to it. If it is possible to increase swap
>>> space then that may help.
>>>
>>> If you are not sure whether this is the problem or cannot make it
>>> go away, then please send us the output of avwhd run on the images
>>> you are using, plus the contents of the matrix file.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 24 Apr 2006, at 20:36, Shruthi Chapkrapani wrote:
>>>
>>>> Hi All
>>>>
>>>> I am trying to register one of the Masks into the standard
>>>> space and the command line I am using is
>>>>
>>>> flirt -in MASK/PNAS.nii.gz -ref /Applications/fsl/fsl/etc/
>>>> standard/ avg152T1_brain.hdr -out MASK/PNAS.std.nii.gz -applyxfm
>>>> -init 2.MELODIC/VIP/AM-04V/B+E/BPF/AM-04V_B+E-std-bpf.nii.mat
>>>>
>>>> I am trying to apply a transformation matrix which I already
>>>> have.When I run the above command I get the following error
>>>> WARNING: Both reference and input images have an sform matrix set
>>>> The output image will use the transformed sform from the
>>>> reference image
>>>> flirt(2374) malloc: *** vm_allocate(size=3612672) failed (error
>>>> code=3)
>>>> flirt(2374) malloc: *** error: can't allocate region
>>>> flirt(2374) malloc: *** set a breakpoint in szone_error to debug
>>>> Abort
>>>>
>>>>
>>>> I am not sure why this is happening.Any idea????
>>>>
>>>> Thanks in advance.
>>>>
>>>> Shru
>>>
>>>
>>>
>
>

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