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Can someone please provide further instruction on how I would manual register my problem subjects? 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 Mon, Aug 15, 2016 at 7:53 PM, Amanda Rodrigue <[log in to unmask]> wrote: > 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 > -- Amanda Rodrigue Doctoral Candidate Franklin Foundation Neuroimaging Fellow Psychology: Brain and Behavior Sciences University of Georgia