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Also the most common misorientation is that they are upside down, not just simply flipped along the vertical axis. I will check the link provided to see if there are any other options but this doesn't seem to be a problem with the files themselves since the subjects that are a problem now were not a problem in the previous iteration. [image: Inline image 1][image: Inline image 2] On Tue, Aug 30, 2016 at 11:55 AM, Amanda Rodrigue <[log in to unmask]> wrote: > When I first encountered this problem, I viewed the images in fsl view > and all labels are correct and the images are oriented correctly. The > labels are also correct in all the previous steps of the VBM pipeline. I > have already submitted data to someone and the two suggestions were the > ones I have already attempted. This was the response to my data submission. > > "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." > > On Tue, Aug 30, 2016 at 11:15 AM, Rosalia Dacosta Aguayo < > [log in to unmask]> wrote: > >> Hi Amanda, >> >> I know perfectly what is waiting until a month to get a solution to your >> problem. Do not worry. The solution to your problem depends whether your >> images are just flipped, or have any other problems: it would be nice if >> you could open the problematic ones with fslview and see if they conserve >> the labels (A-P, R-L, I-F). Also, did you use any marker during the scanner >> in order to have information about R-L orientation, this could also help. >> Finally, fslreorient2std is not the only option, because the option >> depends on the real problem you have with your images. I would recommend >> you read carefully this link: http://fsl.fmrib.ox.ac.uk/fsl/ >> fslwiki/Orientation%20Explained?highlight=%28fslreorient2std%29 and try >> to see which is the best option for your images. >> >> Also, if you still can not cope with those images it should be nice you >> share some of them with a link to any place where you save them and so >> others can see where it could be the problem. >> >> Hope this helps, >> >> Rosalia >> >> >> >> 2016-08-30 16:59 GMT+02:00 Amanda Rodrigue <[log in to unmask]>: >> >>> Hello again, I have tried running fslreorient2std on all my images and >>> ran the whole analysis from scratch, still getting flipped images during >>> template generation (fslvbm_2_template -a). >>> >>> I have also tried registering the problem subjects (n=9) before hand to >>> the MNI152_T1_2mm_brain.nii.gz using FLIRT and putting the registered files >>> into the template process. It worked for all but 1 subject, but now I have >>> a completely different set of subjects (n=5) that are now in the incorrect >>> orientation in the template. I don't think this is a problem with >>> individual subjects but a problem in the template generation itself. When >>> looking at the files generated from the template building command, for 4/5 >>> of the subjects the file ending in *_GM_to_T is in the correct >>> orientation but the file *_GM_to_T_init is not. The reaming subject >>> has correctly oriented data but is flipped for both *_GM_to_T and *_GM_to_T_init >>> files. >>> >>> I have been trying to resolve this problem for a month and I am at a >>> loss of what else to try. >>> >>> On Fri, Aug 19, 2016 at 4:44 AM, Mark Jenkinson < >>> [log in to unmask]> wrote: >>> >>>> Hi, >>>> >>>> >>>> >>>> You can do "manual" registrations with either the GUI or the >>>> command-line in a place outside of your VBM analysis folder. Then, when >>>> you are happy with them, you can replace the appropriate files in the >>>> folder and start the analysis from the appropriate point. The precise >>>> details depend on whether it is the creation of the template or the >>>> subsequent registrations to the template. However, if you are not >>>> confident with this then it is a lot easier just to run fslreorient2std on >>>> all of your images and restart the whole VBM process from scratch. >>>> >>>> >>>> >>>> All the best, >>>> >>>> Mark >>>> >>>> >>>> >>>> >>>> >>>> *From: *FSL - FMRIB's Software Library <[log in to unmask]> on behalf >>>> of Amanda Rodrigue <[log in to unmask]> >>>> *Reply-To: *FSL - FMRIB's Software Library <[log in to unmask]> >>>> *Date: *Thursday, 18 August 2016 at 16:28 >>>> *To: *"[log in to unmask]" <[log in to unmask]> >>>> *Subject: *Re: [FSL] fslvbm_2_template orientation problem >>>> >>>> >>>> >>>> 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 >>>> >>>> >>> >>> >>> -- >>> Amanda Rodrigue >>> Doctoral Candidate >>> Franklin Foundation Neuroimaging Fellow >>> Psychology: Brain and Behavior Sciences >>> University of Georgia >>> >> >> >> >> -- >> Rosalía Dacosta-Aguayo, Post-Doctoral Researcher. >> Biomedicine, PhD >> Clinical Neuropsychologist >> >> Department of Neurosciences. >> Group of Neurodegenerative Diseases >> Gaixotasun Neuroendekapenezko Taldea >> Neurozientziak Arloa >> >> [log in to unmask] >> T. +34 943 006 128 >> >> IIS BIODONOSTIA - OSI DONOSTIALDEA >> Pº Dr. Beguiristain s/n * 20014 Donostia-San Sebastián SPAIN * T.+34 943 >> 006 012 * F. +34 943 006 250 * [log in to unmask] * >> www.biodonostia.org >> > > > > -- > 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