Ahhh, here I am trying to check the reg before moving on ... and indeed 
the _hr files appear after tbss_3_reg. Sorry for the noise.

Gary

On Mon, 14 Jan 2008, Gwenaëlle DOUAUD wrote:

> Dear Hima and Gary,
>
> your memory serves you right indeed. Mine, not really
> obviously :-)...
> tbss_3_postreg applies all the nonlinear
> transformations and creates the mean_FA and the
> mean_FA_skeleton (see
> http://www.fmrib.ox.ac.uk/fsl/tbss/index.html for more
> details).
>
> Cheers,
> Gwenaelle
>
>
> --- Himachandra Chebrolu <[log in to unmask]> a
> écrit :
>
>> Gary-
>>
>>   If my memory serves right, the _hr.nii.gz files
>> are created after you run the tbss_3_postreg. Hope
>> this helps. Let me know if you cannot find the files
>> even after running tbss_3_postreg,
>>
>>   Cheers,
>>   Hima
>>
>> Gary Strangman <[log in to unmask]> wrote:
>>
>> I'm afraid I have never gotten any _hr.nii.gz files
>> as output. (I had seen
>> mention to them in the archives, but never saw them
>> in person, so to
>> speak.) Is something silently not finishing? The
>> last line in my
>> tbss_2_reg.o#### file is "Final Transformation" ...
>>
>> Gary
>>
>> On Mon, 14 Jan 2008, Gwenaëlle DOUAUD wrote:
>>
>>> Hi Gary,
>>>
>>> this is not the first time I come up with this
>> problem
>>> with the "new" tbss: you are actually looking at
>> the
>>> wrong output, *_to_target_nonlinear.nii.gz. This
>> is
>>> the warpfield derived from the nonlinear
>> registration
>>> and its size is indeed bigger as it's a 4D file
>> with
>>> three components in the fourth dimension (one for
>> the
>>> deformations along the x-axis, one for y and one
>> for z
>>> -once again with my own, improper words).
>> Everything
>>> seems to have gone fine but the output you want to
>>> look at is *_to_target_nonlinear_hr.nii.gz.
>>> In case you do not have these outputs in your FAi
>>> directory, just let me know...
>>>
>>> Hope tis helps,
>>> Gwenaëlle
>>>
>>>
>>> --- Gary Strangman a
>>> écrit :
>>>
>>>> Hi all,
>>>>
>>>> I used to use FSL3.3 version of TBSS
>> (successfully)
>>>> on my centos4 linux
>>>> box. This past Tues I downloaded & installed
>>>> fsl-4.0.2-centos4_32.tar.gz.
>>>> I must be doing something seriously wrong, since
>>>> every attempt at making
>>>> it through tbss_2_reg results in a super-smooth
>>>> output file (as if a 100mm
>>>> smoothing kernel was passed over the entire trio
>> of
>>>> volumes in the
>>>> tbss_2_reg output file). I've tried data DTI from
>>>> three different Siemens
>>>> machines (1.5 Sonata, 3.0 Trio, 3.0 Tim Trio),
>> all
>>>> with the same result. I
>>>> didn't see anything in the archives, but I'm
>> hoping
>>>> this is just a "duh" on
>>>> my part. The command sequence below, using all
>>>> defaults except for bet -f,
>>>> reproduces the problem:
>>>>
>>>>> cd dicom_datadir
>>>>> mri_convert 610000-8-1.dcm c8_dti.nii # raw
>> dicom
>>>> data --> nii
>>>>> eddy_correct c8_dti.nii c8_dti_eddy.nii 0 # no
>>>> probs, 10 B0, 60 angles
>>>>> bet vol0000.nii.gz c8_nodif_brain -f 0.2 -m #
>>>> gives a rounded frontal lobe
>>>>> dtifit -k c8_dti_eddy -o c8 -m
>> c8_nodif_brain_mask
>>>> -r bvecs -b bvals
>>>> [output from dtifit looks fine, FA included]
>>>>
>>>> # re-orient our Siemens data to match the
>> FMRIB58_FA
>>>> template
>>>>> fslswapdim c8_FA x -y z c8_FA_swap
>>>>> fslorient -forceradiological c8_FA_swap
>>>>
>>>> # set up filesystem
>>>>> mkdir tbss
>>>>> mv c8_FA_swap.nii.gz tbss/
>>>>> cd tbss/
>>>>> fslstats c8_FA_swap.nii.gz -R
>>>> [output = 0 1.2247] ... so use scaling of 10000
>>>>> tbss_1_preproc -f 10000 c8_FA_swap.nii.gz
>>>>> tbss_2_reg -T
>>>>
>>>> The output of the last command,
>>>> c8_FA_swap_FAi_to_target_nonlinear.nii.gz,
>>>> is hyper-smooth (doesn't look like an FA image at
>>>> all). It's also 73Mb,
>>>> which seems rather larger than the template (at
>>>> 14Mb). If create the affine
>>>> transofrm volume using ...
>>>>
>>>> ${FSLDIR}/bin/DR/transformation
>> c8_FA_swap_FAi.hdr
>>>> c8_FA_sw_FAi_affine.hdr \
>>>> -dofin c8_FA_swap_FAi_to_target_affine.dof
>>>> -target target.hdr
>>>>
>>>> the affine-reg result nicely co-registers with
>> the
>>>> FMRIB58_FA template, so
>>>> it's not tbss_2_reg, tbss_reg, or areg ... pretty
>>>> much leaving nreg to
>>>> blame. If I use the affine-aligned output as the
>>>> source volume for
>>>> registration, as in "tbss_reg
>> c8_FA_sw_affine.nii.gz
>>>> target" I get the same
>>>> hyper-smooth output after the nreg step.
>>>>
>>>> What am I missing?
>>>>
>>>> -best
>>>> Gary
>>>>
>>>
>>>
>>>
>>>
>>
> _____________________________________________________________________________
>>> Ne gardez plus qu'une seule adresse mail ! Copiez
>> vos mails vers Yahoo! Mail http://mail.yahoo.fr
>>>
>>>
>>>
>>
>>
>> ---------------------------------
>> Be a better friend, newshound, and know-it-all with
>> Yahoo! Mobile.  Try it now.
>
>
>
>      _____________________________________________________________________________
> Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail http://mail.yahoo.fr
>
>
>