Hi Paul,
Please, upload the complete data for one random subject to the web address
I just sent you. I'll try to have a look in the next days. Thanks
All the best,
Anderson
On 11 September 2014 20:40, Paul Beach <[log in to unmask]> wrote:
> Correct. Under standard space I selected nonlinear and put in the required
> '_brain' files under "main structural image".
>
> Looking in the "reg" subdirectory of the resultant .feat directory I found
> no highres2standard_jac.nii.gz file. What's extra funny, though, is that
> neither the filtered_func_data.nii.gz or the melodic_IC.nii.gz files are
> registered to MNI152. They're all still in subject space. I don't know if
> this means something failed, but I don't see any striking error messages in
> the overall FEAT reports.
>
> The only "error" I can find under the 'Registration' portion is:
> did not find file: example_func2highres.mat. Generating transform.
> did not find file: highres2standard.mat. Generating transform.
>
> I've since found a way (through various google searches) to produce the
> highres2standard_jac.nii.gz. However, that doesn't fix the other problem I
> have of all my output files being in subject space rather than MNI152.
>
> With respect to that problem, I've tried using featregapply, as per Steve
> Smith's suggestion earlier, but I'm getting some error message I don't
> understand:
>
> *echo 'set fmri(inmelodic) 1' >> RestState_1_FSL_LAS.feat/design.fsf*
> *featregapply RestState_1_FSL_LAS.feat -f*
> *wrong # args: should be "set varName ?newValue?"*
> * while executing*
> *"set fmri(inmelodic) 1 featregapply denoised_data.nii.gz -f"*
> * (file "design.fsf" line 916)*
> * invoked from within*
> *"source ${filename}"*
> * (procedure "feat5:load" line 58)*
> * invoked from within*
> *"feat5:load -1 1 design.fsf"*
> * (file "/extern/soft/tools/fsl-5.0.4/bin/featregapply" line 164)*
>
>
>
>
>
>
> On Thu, Sep 11, 2014 at 3:14 PM, Anderson M. Winkler <
> [log in to unmask]> wrote:
>
>> Hi Paul,
>>
>> Are you sure you are looking in the right place or in the outputs for
>> subject that had indeed undergone non-linear registration? By this I mean:
>> in the 'Registration' tab in FEAT or in Melodic GUI you specified the 'Main
>> structural image' (you T1 in native space), and you marked the checkbox
>> 'Non-linear' in the 'Standard space' box. Then you made sure that it ran
>> successfully for that subject, and you are looking into the subdirectory
>> 'reg' of the *.feat or *.ica directory of that same subject. There should
>> be a highres2standard_jac.nii.gz file there. That is the Jacobian that
>> you'd use for the modulation of GM.
>>
>> All the best,
>>
>> Anderson
>>
>>
>> On 11 September 2014 16:20, Paul Beach <[log in to unmask]> wrote:
>>
>>> Hi Anderson,
>>>
>>> It looks as though I actually don't have the highres2standard_jac.nii.gz
>>> file in my reg directory. How do I go about making this file?
>>>
>>> Thanks
>>>
>>>
>>> On Thu, Sep 4, 2014 at 10:37 AM, Anderson M. Winkler <
>>> [log in to unmask]> wrote:
>>>
>>>> Hi Paul,
>>>>
>>>> Have a look if you don't have already the file
>>>> highres2standard_jac.nii.gz in the 'reg' directory (along with the
>>>> highres2standard_warp.nii.gz). It's probably there, then you won't need to
>>>> run the fnirtfileutils, and it's one step less to do. :-)
>>>>
>>>> The highres2standard_pve_1.nii.gz is the GM partition. This is the file
>>>> you need to modulate.
>>>>
>>>> All the best,
>>>>
>>>> Anderson
>>>>
>>>>
>>>>
>>>> On 3 September 2014 16:50, Paul Beach <[log in to unmask]> wrote:
>>>>
>>>>> Anderson,
>>>>>
>>>>> After getting all my subjects re-ran through FEAT and using non-linear
>>>>> registration. I then ran a test subject's MNI152 transformed brain through
>>>>> FAST, as we previously discussed.
>>>>> /extern/soft/tools/fsl-5.0.4/bin/fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 -o
>>>>> /extern/research/PI/training/beachpau/FSL/SUBJECTS/HS_001/RestState_1_FSL_LAS.feat/reg/highres2standard
>>>>> /extern/research/PI/training/beachpau/FSL/SUBJECTS/HS_001/RestState_1_FSL_LAS.feat/reg/highres2standard
>>>>>
>>>>> I obtained the following files:
>>>>> highres2standard_pve_0.nii.gz
>>>>> highres2standard_pve_1.nii.gz
>>>>> highres2standard_pve_2.nii.gz
>>>>> highres2standard_pveseg.nii.gz
>>>>> highres2standard_seg.nii.gz
>>>>> highres2standard_mixeltype.nii.gz
>>>>>
>>>>> Looking at the fnirtfileutils command
>>>>> <http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fnirt/warp_utils.html>,
>>>>> which I need to use to produce the jacobian map, I see that I need to have
>>>>> an input fnirtcoefs file as well as a refvolume. I'm not really sure which
>>>>> of the above output qualifies for either of those. Is it one of these or
>>>>> could they include one of the previously existing files in the 'reg'
>>>>> directory - such as the highres2standard_warp.nii.gz file?
>>>>>
>>>>> Thanks for your help
>>>>>
>>>>>
>>>>> On Thu, Aug 28, 2014 at 10:40 AM, Anderson M. Winkler <
>>>>> [log in to unmask]> wrote:
>>>>>
>>>>>> Hi Paul,
>>>>>> Yes... it looks like it run with linear (affine) only...
>>>>>> All the best,
>>>>>> Anderson
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 28 August 2014 14:18, Paul Beach <[log in to unmask]> wrote:
>>>>>>
>>>>>>> Thank you Anderson.
>>>>>>>
>>>>>>> A quick follow-up as I start the process. The files in the "reg"
>>>>>>> subdirectory have the following contents:
>>>>>>> example_func.nii.gz highres2example_func.mat highres.nii.gz
>>>>>>>
>>>>>>> I'm thinking these (mainly the middle .mat file) might not be the
>>>>>>> correct files for step 2 as, looking at my design.fsf file, I have "set
>>>>>>> fmri(regstandard_nonlinear_yn)" at '0'.
>>>>>>>
>>>>>>> So I guess I have to re-run things from the beginning, feat-wise?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Aug 28, 2014 at 7:29 AM, Anderson M. Winkler <
>>>>>>> [log in to unmask]> wrote:
>>>>>>>
>>>>>>>> Hi Paul,
>>>>>>>>
>>>>>>>> Almost:
>>>>>>>> 1. Yes, that's it.
>>>>>>>> 2. Take the warps that should be in the "reg" subdirectory of the
>>>>>>>> .feat directory, and use fnirtfileutils to produce the Jacobian map. Of
>>>>>>>> course, they will only be there if you used non-linear registration when
>>>>>>>> running the preprocessing.
>>>>>>>> 3. Use fslmaths to modulate the GM maps by the Jacobian, that is,
>>>>>>>> multiply the GM maps by the Jacobian.
>>>>>>>> 4. Take the modulated maps and merge them into a 4D file.
>>>>>>>>
>>>>>>>> That's it. This 4D output goes as a voxelwise EV in randomise.
>>>>>>>>
>>>>>>>> All the best,
>>>>>>>>
>>>>>>>> Anderson
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 27 August 2014 17:52, Paul Beach <[log in to unmask]> wrote:
>>>>>>>>
>>>>>>>>> Anderson,
>>>>>>>>>
>>>>>>>>> I *think *I understand (some of) what you're saying here.
>>>>>>>>>
>>>>>>>>> 1. Take T1 images for each subject that are *already* MNI152
>>>>>>>>> registered and run them through FAST.
>>>>>>>>> 2. take the resultant GM masks and run them through fslmaths to
>>>>>>>>> produce the Jacobian map ... so, fnirtfileutils --cout on each of those
>>>>>>>>> masks?
>>>>>>>>> 3. do "something" with those jacobian maps to produce a final 4D
>>>>>>>>> file...this is the most confusing part. Are you referring to the final
>>>>>>>>> FSLVBM 4D file? I'm not really sure what I would be doing with fslmerge,
>>>>>>>>> the jacobian maps, and whatever other inputs to get the final 4D file.
>>>>>>>>> 4. Would this be the final 4D file I run through randomise? or
>>>>>>>>> would step 3 be performed after completing FSLVBM steps?
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Paul
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, Aug 26, 2014 at 5:37 PM, Anderson M. Winkler <
>>>>>>>>> [log in to unmask]> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Paul,
>>>>>>>>>>
>>>>>>>>>> It's probably a bit more complicated than that. To have the GM in
>>>>>>>>>> the same common space as the functionals you need to use the same warps
>>>>>>>>>> that were used to align the fMRI maps to that space, to then align the GM.
>>>>>>>>>> To align the fMRI, the default in FEAT and in the Melodic GUI is a T1-w
>>>>>>>>>> template, whereas for VBM, it's a GM template. This means you'd have to
>>>>>>>>>> tweak the alignment of one of these.
>>>>>>>>>>
>>>>>>>>>> Maybe a quick strategy could be to get, for each subject, the
>>>>>>>>>> T1-w image that is already in the common space (it's used to drive the
>>>>>>>>>> registration of the fMRI in the 1st level FEAT and in the Melodic GUI) and
>>>>>>>>>> segment that image using FAST, then modulate the resulting GM partition
>>>>>>>>>> with fslmaths (you can produce the Jacobian map with fnirtfileutils) and
>>>>>>>>>> finally produce the 4D file with fslmerge.
>>>>>>>>>>
>>>>>>>>>> All the best,
>>>>>>>>>>
>>>>>>>>>> Anderson
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 26 August 2014 20:44, Paul Beach <[log in to unmask]> wrote:
>>>>>>>>>>
>>>>>>>>>>> Thanks for your response, Anderson.
>>>>>>>>>>>
>>>>>>>>>>> So basically just the output file from fslvbm_3_proc?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Aug 25, 2014 at 4:04 PM, Anderson M. Winkler <
>>>>>>>>>>> [log in to unmask]> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Paul,
>>>>>>>>>>>>
>>>>>>>>>>>> For this, you'd need the GM maps (modulated and merged as a 4D
>>>>>>>>>>>> file) in the same common space as the functional maps used with randomise
>>>>>>>>>>>> in the dual regression. In randomise, use then the options --vxl and --vxf.
>>>>>>>>>>>>
>>>>>>>>>>>> All the best,
>>>>>>>>>>>>
>>>>>>>>>>>> Anderson
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 25 August 2014 17:10, Paul Beach <[log in to unmask]> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> FSL folks,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I'm interested in using VBM-based results as a regressor of no
>>>>>>>>>>>>> interest in my ICA analyses (such as in: Werner et al., 2013. *Human
>>>>>>>>>>>>> Brain Mapping*) . I want to make sure I have the process
>>>>>>>>>>>>> straight, though.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Specifically, my questions are: which VBM output file should
>>>>>>>>>>>>> be used as a voxel-wise EV? Then, how do I set that as a confound
>>>>>>>>>>>>> regressor, as voxel-wise EVs don't have the typical EV box for each subject?
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Paul Beach
>>>>>>>>>>>>> DO/PhD candidate - Year VI
>>>>>>>>>>>>> Michigan State University
>>>>>>>>>>>>> - College of Osteopathic Medicine
>>>>>>>>>>>>> - Neuroscience Program
>>>>>>>>>>>>> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (
>>>>>>>>>>>>> *CoGeNT*)
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Paul Beach
>>>>>>>>>>> DO/PhD candidate - Year VI
>>>>>>>>>>> Michigan State University
>>>>>>>>>>> - College of Osteopathic Medicine
>>>>>>>>>>> - Neuroscience Program
>>>>>>>>>>> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Paul Beach
>>>>>>>>> DO/PhD candidate - Year VI
>>>>>>>>> Michigan State University
>>>>>>>>> - College of Osteopathic Medicine
>>>>>>>>> - Neuroscience Program
>>>>>>>>> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Paul Beach
>>>>>>> DO/PhD candidate - Year VI
>>>>>>> Michigan State University
>>>>>>> - College of Osteopathic Medicine
>>>>>>> - Neuroscience Program
>>>>>>> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Paul Beach
>>>>> DO/PhD candidate - Year VI
>>>>> Michigan State University
>>>>> - College of Osteopathic Medicine
>>>>> - Neuroscience Program
>>>>> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Paul Beach
>>> DO/PhD candidate - Year VI
>>> Michigan State University
>>> - College of Osteopathic Medicine
>>> - Neuroscience Program
>>> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
>>>
>>
>>
>
>
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
>
