Thanks very much Mark. No I don't have NaNs.
________________________________
From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
Sent: Fri 6/18/2010 6:15 PM
To: [log in to unmask]
Subject: Re: [FSL] invwarp error
Hi,
As you have higher-resolution images then it is fine
to ignore the warning message from invwarp, as
the results of the fslstats -w clearly show that you
have performed brain extraction correctly.
So just use --force in your invwarp command.
For the fnirt warnings, just make sure that:
1. You didn't forget to specify a valid affine starting guess for the
--aff parameter.
2. You don't have any strange values in your data (e.g. NaNs)
and then if that is the case and the registration looks
OK then you can ignore the warnings.
All the best,
Mark
On 18 Jun 2010, at 19:22, Rajagopalan, Venkateswaran wrote:
> Thanks very much Mark
>
> fslhd t1_brain
>
> filename t1_brain.nii.gz
>
> sizeof_hdr 348
> data_type FLOAT32
> dim0 3
> dim1 512
> dim2 512
> dim3 160
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 0.5000000000
> pixdim2 0.5000000000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 352
> cal_max 784.0000
> cal_min 0.0000
> scl_slope 1.000000
> 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 Unknown
> intent_code 0
> intent_name
> intent_p1 0.000000
> intent_p2 0.000000
> intent_p3 0.000000
> qform_name Scanner Anat
> qform_code 1
> qto_xyz:1 -0.499999 0.000000 0.001827 132.945801
> qto_xyz:2 0.000000 0.500000 -0.000000 -97.717926
> qto_xyz:3 0.000913 0.000000 0.999998 -55.025944
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 -0.499999 0.000000 0.001745 132.945801
> sto_xyz:2 0.000000 0.500000 0.000000 -97.717926
> sto_xyz:3 0.000873 0.000000 0.999998 -55.025944
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip FSL4.0
> aux_file
>
> fslstats t1_brain -w
>
> 112 290 71 322 9 144 0 1
>
> There is one thing i noticed now when i tried to run same commands
> in another subjects where this invwarp failed. FNIRT gives me the
> following warning but it runs and gives me good output
>
> "SpMat::SolveForx: Warning requested tolerence not obtained.
> Requested tolerance was 0.001, and achieved tolerance was 1.5044
> This may or may not be a problem in your application, but you should
> look into it"
>
> Is this serious warning which i should take care of if so how?
>
> Thanks very much
>
> venkat
>
>
>
>
>
>
>
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
> Sent: Fri 6/18/2010 1:40 PM
> To: [log in to unmask]
> Subject: Re: [FSL] invwarp error
>
> Hi,
>
> This looks all correct to me.
> Can you run both:
> fslhd t1_brain
> and
> fslstats t1_brain -w
> and send us the output.
>
> It is possible that you are just over the
> automatic checking threshold and that it
> isn't serious, in which case the --force
> flag with invwarp would solve the problem.
> However, it is worth checking the above
> output first.
>
> All the best,
> Mark
>
>
> On 18 Jun 2010, at 18:37, Rajagopalan, Venkateswaran wrote:
>
>>
>> Hi All,
>>
>> I used the following to commands to do non-linreg between my T1 and
>> MNI space and i would like to now bring MNI to my t1 space where i
>> encountered the problem with invwarp (i saw archives about this but
>> my case is different from the one in the archive)
>>
>> flirt -ref MNI152_T1_2mm_brain.nii.gz -in t1_brain.nii.gz -out
>> T1_in_MNI_space_linreg -omat T1_2_MNI_linreg.mat
>>
>> fnirt --ref=MNI152_T1_2mm --in=t1.nii --aff=T1_2_MNI_linreg.mat --
>> iout=T1_in_MNI_space_nonlinreg --cout=T1_2_MNI_nonlin --
>> config=T1_2_MNI152_2mm.cnf
>>
>> invwarp -w T1_2_MNI_nonlin.nii.gz -o MNI_2_T1_space_inversewarp -r
>> t1_brain.nii.gz
>>
>> WARNING!! Reference image has large non-zero ROI. Check that BET has
>> run successfully on this
>>
>> i have used the same t1_brain in both the cases after BET (and some
>> manual edits to the brain to remove left over non-brain regions).
>> The same commands (invwarp too) ran without any problem in another
>> subject which is processed identically like the one above
>>
>> What am i doing wrong here.
>>
>> Thanks
>>
>> venkat
>>
>>
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> P Please consider the environment before printing this e-mail
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> Cleveland Clinic is ranked one of the top hospitals
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> a complete listing of our services, staff and
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> Confidentiality Note: This message is intended for use
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===================================
P Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2009).
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.
Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law. If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited. If
you have received this communication in error, please
contact the sender immediately and destroy the material in
its entirety, whether electronic or hard copy. Thank you.
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