Hi Peter,
We've not done anything that is specific to TBSS - but given that all
the final TBSS stages are done in 1x1x1mm MNI152 space, it should be
easy to use any MNI152-based atlases to assign labels, particularly
for the more major tracts.
Cheers, Steve.
On 18 Apr 2006, at 01:17, Peter Kochunov wrote:
> Have you guys come up with any good way to give the skeletonized
> structures labels? Something like Talairach lobar or track labels?
> Thanks
> peter
>
> ----- Original Message ----- From: "Clifford A. Smith, PhD"
> <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Tuesday, April 11, 2006 4:26 PM
> Subject: Re: [FSL] Tbss
>
>
>> Thanks for the quick solution. Currently working away without a
>> problem.
>> Regards, Cliff
>>
>>
>> ------------------
>> Clifford Smith, PhD
>> Assistant Professor of Behavioral Sciences
>> Rush University Medical Center
>> 312.942.2893
>>
>>
>>
>>> From: Steve Smith <[log in to unmask]>
>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>> Date: Mon, 10 Apr 2006 23:09:15 +0100
>>> To: <[log in to unmask]>
>>> Subject: Re: [FSL] Tbss
>>>
>>> Thanks Clifford - turns out it was a problem with tbss_1_preproc
>>> when
>>> the input images had -ve voxel dimensions - if you put the following
>>> in $FSLDIR/bin, making sure it is executable, things should work
>>> fine:
>>>
>>> http://www.fmrib.ox.ac.uk/fsldownloads/tbss_1_preproc
>>>
>>> Thanks, Steve.
>>>
>>>
>>>
>>> On 10 Apr 2006, at 19:18, Clifford A. Smith, PhD wrote:
>>>
>>>> Uploaded a tar.gz file with four dti_FA.nii.gz files. Files
>>>> a_dti_FA and
>>>> b_dti_FA fail tbss_2_reg. The last two files, created in a similar
>>>> fashion
>>>> in FSL, complete tbss_2_reg without a problem. Analysis is
>>>> completed on a
>>>> Mac Dual G5 (or Quad G5 with similar results). All dti_FA files
>>>> were
>>>> generated in dtifit without a problem. Cliff
>>>>
>>>> #265606
>>>>
>>>>
>>>> ------------------
>>>> Clifford Smith, PhD
>>>> Assistant Professor of Behavioral Sciences
>>>> Rush University Medical Center
>>>> 312.942.2893
>>>>
>>>>
>>>>
>>>>> From: Steve Smith <[log in to unmask]>
>>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>> Date: Mon, 10 Apr 2006 13:54:11 +0100
>>>>> To: <[log in to unmask]>
>>>>> Subject: Re: [FSL] Tbss
>>>>>
>>>>> Thanks Clifford - would you mind generating an FAi directory with
>>>>> just two FA volumes in it, that causes problems when one is
>>>>> aligned
>>>>> to the other, and upload that to us to test?
>>>>> What platform are you running, and which binary FSL distribution?
>>>>>
>>>>> Please upload the files in a single compressed tarfile to
>>>>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>>>> and then email me the upload ID.
>>>>>
>>>>> Cheers, Steve.
>>>>>
>>>>>
>>>>>
>>>>> On 10 Apr 2006, at 13:37, Clifford A. Smith, PhD wrote:
>>>>>
>>>>>> Thanks for the follow-up. Am currently running TBSS on FA
>>>>>> volumes
>>>>>> generated
>>>>>> in an in-house program, so far no problems. On the dtifit
>>>>>> generated volumes
>>>>>> avwnvols = 1. The output of a failed tbss_2_reg is followed by a
>>>>>> completed
>>>>>> tbss_2_reg. Both of the dti_FA files used were created with
>>>>>> dtifit. Cliff
>>>>>>
>>>>>>
>>>>>> Output from ailed tbss_2_reg
>>>>>> nifti_type = 'ANALYZE-7.5'
>>>>>> header_filename = '00107_dti_FA_FAi.hdr'
>>>>>> image_filename = '00107_dti_FA_FAi.img'
>>>>>> image_offset = '0'
>>>>>> ndim = '3'
>>>>>> nx = '128'
>>>>>> ny = '128'
>>>>>> nz = '38'
>>>>>> dx = '1.95312'
>>>>>> dy = '1.95312'
>>>>>> dz = '3.00001'
>>>>>> datatype = '4'
>>>>>> datatype_name = 'INT16'
>>>>>> nvox = '622592'
>>>>>> nbyper = '2'
>>>>>> byteorder = 'MSB_FIRST'
>>>>>> cal_min = '0'
>>>>>> cal_max = '12247'
>>>>>> descrip = 'FSL3.3'
>>>>>> sform_code = '2'
>>>>>> sform_code_name = 'Aligned Anat'
>>>>>> sto_xyz_matrix = '-1.95312 0 0 123.047 0 1.95312 0 -121.093 0 0
>>>>>> 3.00001
>>>>>> -6.00002 0 0 0 1'
>>>>>> sto_ijk matrix = '-0.512001 -0 -0 63 0 0.512001 -0 62 -0 -0
>>>>>> 0.333332 2 0 0
>>>>>> 0 1'
>>>>>> sform_i_orientation = 'Right-to-Left'
>>>>>> sform_j_orientation = 'Posterior-to-Anterior'
>>>>>> sform_k_orientation = 'Inferior-to-Superior'
>>>>>>
>>>>>> Output from successful tbss_2_reg
>>>>>> [Clifford-Smiths-Computer:FSL_Analysis/fsl_tbss/FAi] Cliff%
>>>>>> avwhd -x
>>>>>> dti_FA_FAi.hdr
>>>>>> <nifti_image
>>>>>> nifti_type = 'ANALYZE-7.5'
>>>>>> header_filename = 'dti_FA_FAi.hdr'
>>>>>> image_filename = 'dti_FA_FAi.img'
>>>>>> image_offset = '0'
>>>>>> ndim = '3'
>>>>>> nx = '128'
>>>>>> ny = '128'
>>>>>> nz = '38'
>>>>>> dx = '1.95312'
>>>>>> dy = '1.95312'
>>>>>> dz = '3'
>>>>>> datatype = '4'
>>>>>> datatype_name = 'INT16'
>>>>>> nvox = '622592'
>>>>>> nbyper = '2'
>>>>>> byteorder = 'MSB_FIRST'
>>>>>> cal_min = '0'
>>>>>> cal_max = '12230'
>>>>>> descrip = 'FSL3.3'
>>>>>> />
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------
>>>>>> Clifford Smith, PhD
>>>>>> Assistant Professor of Behavioral Sciences
>>>>>> Rush University Medical Center
>>>>>> 312.942.2893
>>>>>>
>>>>>>
>>>>>>
>>>>>>> From: Steve Smith <[log in to unmask]>
>>>>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>>>> Date: Mon, 10 Apr 2006 07:52:57 +0100
>>>>>>> To: <[log in to unmask]>
>>>>>>> Subject: Re: [FSL] Tbss
>>>>>>>
>>>>>>> Hi Clifford, the nonlinear registration is clearly running
>>>>>>> out of
>>>>>>> memory - we've not seen this here - maybe your images are
>>>>>>> very big?
>>>>>>> Could you make sure that all the images in FAi are 3D, and then
>>>>>>> send
>>>>>>> the results of avwhd to us to look at?
>>>>>>> Cheers, Steve.
>>>>>>>
>>>>>>>
>>>>>>> On 9 Apr 2006, at 22:54, Clifford A. Smith, PhD wrote:
>>>>>>>
>>>>>>>> Been running TBSS in new version. Successful with one
>>>>>>>> dti_FA file
>>>>>>>> to create skeleton for viewing in FSLView. On all other
>>>>>>>> attempts
>>>>>>>> with other dti_FA files, I get errors (see below). I am
>>>>>>>> able to
>>>>>>>> complete FDT without error on these files. Running on a Mac
>>>>>>>> G5.
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Cache has 121 entries
>>>>>>>> Cache statistics: 2 % hits (3 out of 124)
>>>>>>>> Resolution level no. 1 (step sizes 5 to 0.625)
>>>>>>>> Iteration = 1 (out of 20), step size = 5
>>>>>>>> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry =
>>>>>>>> 0.0000 rz
>>>>>>>> = 0.0000
>>>>>>>> sx = 100.0000 sy = 100.0000 sz = 100.0000 sxy = 0.0000 syx =
>>>>>>>> 0.0000 syz = 0.0
>>>>>>>> 000
>>>>>>>> szy = 0.0000 szx = 0.0000 sxz = 0.0000
>>>>>>>> Iteration = 1 (out of 20), step size = 2.5
>>>>>>>> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry =
>>>>>>>> 0.0000 rz
>>>>>>>> = 0.0000
>>>>>>>> sx = 100.0000 sy = 100.0000 sz = 100.0000 sxy = 0.0000 syx =
>>>>>>>> 0.0000 syz = 0.0
>>>>>>>> 000
>>>>>>>> szy = 0.0000 szx = 0.0000 sxz = 0.0000
>>>>>>>> Iteration = 1 (out of 20), step size = 1.25
>>>>>>>> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry =
>>>>>>>> 0.0000 rz
>>>>>>>> = 0.0000
>>>>>>>> sx = 100.0000 sy = 100.0000 sz = 100.0000 sxy = 0.0000 syx =
>>>>>>>> 0.0000 syz = 0.0
>>>>>>>> 000
>>>>>>>> szy = 0.0000 szx = 0.0000 sxz = 0.0000
>>>>>>>> Iteration = 1 (out of 20), step size = 0.625
>>>>>>>> tx = 0.0000 ty = 0.0000 tz = 0.0000 rx = 0.0000 ry =
>>>>>>>> 0.0000 rz
>>>>>>>> = 0.0000
>>>>>>>> sx = 100.0000 sy = 100.0000 sz = 100.0000 sxy = 0.0000 syx =
>>>>>>>> 0.0000 syz = 0.0
>>>>>>>> 000
>>>>>>>> szy = 0.0000 szx = 0.0000 sxz = 0.0000
>>>>>>>> Cache has 121 entries
>>>>>>>> Cache statistics: 2 % hits (3 out of 124)
>>>>>>>> Final transformation tx = 0.0000 ty = 0.0000 tz = 0.0000
>>>>>>>> rx =
>>>>>>>> 0.0000 ry = 0
>>>>>>>> .0000 rz = 0.0000
>>>>>>>> sx = 100.0000 sy = 100.0000 sz = 100.0000 sxy = 0.0000 syx =
>>>>>>>> 0.0000 syz = 0.0
>>>>>>>> 000
>>>>>>>> szy = 0.0000 szx = 0.0000 sxz = 0.0000
>>>>>>>> Reading target ... done
>>>>>>>> Reading source ... done
>>>>>>>> nreg(24480) malloc: *** vm_allocate(size=4294963200) failed
>>>>>>>> (error
>>>>>>>> code=3)
>>>>>>>> nreg(24480) malloc: *** error: can't allocate region
>>>>>>>> nreg(24480) malloc: *** set a breakpoint in szone_error to
>>>>>>>> debug
>>>>>>>> /users/cliff/fsl/bin/tbss_reg: line 22: 24480 Abort
>>>>>>>> trap ${D}/nreg
>>>>>>>> ${REFERENCE}.hdr ${INPUT}.hdr -dofin ${I2R}_affine.dof -
>>>>>>>> dofout $
>>>>>>>> {I2R}_nonlinear.
>>>>>>>> dof -ds 20 -Tp 0 -parameter ${D}/nonlinearCC.par
>>>>>>>> itkRigidTransformation::CheckHeader: Can't open file
>>>>>>>> dti_FA_FAi_to_dti_FA_FAi_no
>>>>>>>> nlinear.dof
>>>>>>>> ** ERROR: nifti_image_read(grotNx): can't open header file
>>>>>>>> ** ERROR: nifti_image_open(grotNx): bad header info
>>>>>>>> Error: failed to open file grotNx
>>>>>>>> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
>>>>>>>> ** ERROR: nifti_image_read(grotNy): can't open header file
>>>>>>>> ** ERROR: nifti_image_open(grotNy): bad header info
>>>>>>>> Error: failed to open file grotNy
>>>>>>>> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
>>>>>>>> ** ERROR: nifti_image_read(grotNz): can't open header file
>>>>>>>> ** ERROR: nifti_image_open(grotNz): bad header info
>>>>>>>> Error: failed to open file grotNz
>>>>>>>> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
>>>>>>>> ** ERROR: nifti_image_read(grotSx): can't open header file
>>>>>>>> ** ERROR: nifti_image_open(grotSx): bad header info
>>>>>>>> Error: failed to open file grotSx
>>>>>>>> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
>>>>>>>> ** ERROR: nifti_image_read(grotSS): can't open header file
>>>>>>>> ** ERROR: nifti_image_open(grotSS): bad header info
>>>>>>>> Error: failed to open file grotSS
>>>>>>>> ERROR: Could not open image grotSS
>>>>>>>> Image Exception : #22 :: Failed to read volume grotSS
>>>>>>>> /users/cliff/fsl/bin/tbss_reg: line 44: 24488 Bus
>>>>>>>> error $FSLDIR/bi
>>>>>>>> n/avwstats++ grotSS -M -P 50 >../${I2R}_nonlinear.msf
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------
>>>>>>>> Clifford Smith, PhD
>>>>>>>> Assistant Professor of Behavioral Sciences
>>>>>>>> Rush University Medical Center
>>>>>>>> 312.942.2893
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ----------------------------------------------------------------
>>>>>>> ---
>>>>>>> --
>>>>>>> ---
>>>>>>> ---
>>>>>>> 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
>>>>>>> ----------------------------------------------------------------
>>>>>>> ---
>>>>>>> --
>>>>>>> ---
>>>>>>> ---
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------
>>>>> ---
>>>>> ---
>>>>> ---
>>>>> 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
>>>>> ------------------------------------------------------------------
>>>>> ---
>>>>> ---
>>>>> ---
>>>
>>>
>>> --------------------------------------------------------------------
>>> ----
>>> ---
>>> 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
>>> --------------------------------------------------------------------
>>> ----
>>> ---
------------------------------------------------------------------------
---
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
------------------------------------------------------------------------
---
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