Sorry, but I have just now gotten back to this problem.  Ran fslorient2standard on all images and still had images come back flipped.  When you say "manual" registration do you mean with FLIRT outside of the automated template creating process?  If so, there doesn't seem to be a GM ICBM-152 (what the segmented images are registered to in the regular automated template pipeline)  listed in the standards folder.  Also would I run that registration on the skull stripped file or segment it first as in the automated pipeline and then register?  Finally, how does it work when I put  registered files in with others that are unregistered into the automated template generation process?  Sorry I don't have much experience using FSL.

On Wed, Jul 13, 2016 at 10:55 AM, Matthew Webster <[log in to unmask]> wrote:

Hi Amanda,
                    I’ve been able to reproduce the issue locally. A fix that worked for the two “bad” files was to run fslreorient2std on the input structural ( and manually regenerate their registrations ) which gave good registrations for each step ( non-flipped )! It might be worth running fslreorient2std on all the “bad” structurals ( and maybe even the “good” ones, since it shouldn’t make anything worse ) and then re-running fslvbm_2_template from scratch - if you try this and the new merged output still contains flipped images, you may need to manually register the few bad files, and then regenerate the final template.

Hope this helps,
Kind Regards
Matthew

> On 13 Jul 2016, at 15:18, Amanda Rodrigue <[log in to unmask]> wrote:
>
> Hi Matthew, any luck?
>
> On Friday, July 8, 2016, Amanda Rodrigue <[log in to unmask]> wrote:
> Ok, it looks like it worked.  It's called Rodrigue_VBM.  HCC_1213 and LCC_1118 are the bad ones.  Also in my struc directory there are also a ton of files that start with fslvbm2a.e4 followed by a bunch of numbers.  Almost all these files (all but 2 or 3) have a file size of 0.  I'm not sure if this matters or not but it seemed odd.  Thanks for your help!
>
> On Fri, Jul 8, 2016 at 7:16 AM, Matthew Webster <[log in to unmask]> wrote:
> Hello,
>          I’m afraid the tar file didn’t appear on our server - maybe it might be easier to upload a subset, e.g. for two “good” and two “bad” subjects, tar up all the files referring to that subject, and all the template_<blah> files?
>
> Kind Regards
> Matthew
>
>
>
>> On 7 Jul 2016, at 18:17, Amanda Rodrigue <[log in to unmask]> wrote:
>>
>> Can you let me know if it has uploaded. It was taking a really long time and I am not sure it went through.  It should be named Rodrigue_struc,tar.gz.  Thanks!
>>
>> On Wed, Jul 6, 2016 at 3:58 PM, Amanda Rodrigue <[log in to unmask]> wrote:
>> Hi, I'm in the process of uploading.  Her are the subjects that had the orientation issue:
>> FSL #/Subid
>> 25/HCC_1213
>> 50/LCC_1118
>> 51/LCC_1121
>> 66/LCC_1191
>> 84/SZ_1107
>> 85/SZ_1111
>> 89/SZ_1187
>> 100/SZ_1254
>> 112/SZ_1310
>>
>> On Tue, Jul 5, 2016 at 9:54 AM, Matthew Webster <[log in to unmask]> wrote:
>> Hello,
>>       This sounds quite odd, I think we need to have a look at all the files - can you tar and upload the whole directory to the oxfile link ( https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF )?
>>
>> Kind Regards
>> Matthew
>>
>>> On 5 Jul 2016, at 14:15, Amanda Rodrigue <[log in to unmask]> wrote:
>>>
>>> Hi Matthew any thoughts on what might be wrong?
>>>
>>> On Wed, Jun 29, 2016 at 4:56 PM, Amanda Rodrigue <[log in to unmask]> wrote:
>>> So the <blah>_GM_to_T_init is not oriented correctly when overlaid on the template_GM_init but the <blah>_GM_to_T is correctly oriented when overlaid on  template_GM_init.
>>>
>>> On Wed, Jun 29, 2016 at 10:44 AM, Matthew Webster <[log in to unmask]> wrote:
>>> Hello,
>>>          The registered outputs created during VBM may change orientation, this is fine providing the registration is correct. For one of the problematic subjects, can you check if the first-pass registration has worked - e.g.
>>>
>>> compare <blah>_GM_to_T_init to template_GM_init in FSLview
>>>
>>> and let me know if the two are registered?
>>>
>>> Kind Regards
>>> Matthew
>>>
>>> > On 29 Jun 2016, at 14:30, Amanda Rodrigue <[log in to unmask]> wrote:
>>> >
>>> > Hello,
>>> > I am following the instructions for FSL's VBM analysis and  having some difficulties with the fslvbm_2_template step.  The script runs fine but when I look at the results (the template_4D_GM.nii.gz in fsl view there are about 8 or 9 subjects that are misoriented.  I have looked at them all in fsl view and the labels are correct and all are in the same orientation as those subs that are correctly oriented as reported by fslorient.  The brain image is in the correct orientation in all the files produced by the template script until the Sub#_anat_struc_GM_to_T_init.gz.  Consequently this is when the orientation switches from neurological to radiological.  I have also tried fslorient2standard on these subjects, as suggested by some comments on the message board but it does not seem to make a difference. Any input would be appreciated.
>>> > Amanda
>>>
>>>
>>>
>>> --
>>> Amanda Rodrigue
>>> Doctoral Candidate
>>> Franklin Foundation Neuroimaging Fellow
>>> Psychology: Brain and Behavior Sciences
>>> University of Georgia
>>>
>>>
>>>
>>> --
>>> Amanda Rodrigue
>>> Doctoral Candidate
>>> Franklin Foundation Neuroimaging Fellow
>>> Psychology: Brain and Behavior Sciences
>>> University of Georgia
>>
>>
>>
>>
>> --
>> Amanda Rodrigue
>> Doctoral Candidate
>> Franklin Foundation Neuroimaging Fellow
>> Psychology: Brain and Behavior Sciences
>> University of Georgia
>>
>>
>>
>> --
>> Amanda Rodrigue
>> Doctoral Candidate
>> Franklin Foundation Neuroimaging Fellow
>> Psychology: Brain and Behavior Sciences
>> University of Georgia
>
>
>
>
> --
> Amanda Rodrigue
> Doctoral Candidate
> Franklin Foundation Neuroimaging Fellow
> Psychology: Brain and Behavior Sciences
> University of Georgia
>
>
> --
> Amanda Rodrigue
> Doctoral Candidate
> Franklin Foundation Neuroimaging Fellow
> Psychology: Brain and Behavior Sciences
> University of Georgia
>

--

Amanda Rodrigue

Doctoral Candidate

Franklin Foundation Neuroimaging Fellow

Psychology: Brain and Behavior Sciences

University of Georgia