Dear Sir, Script can find the files and it runs successfully, but output is distorted.
Thanks Vasudev On 20 August 2016 at 17:08, Glasser, Matthew <[email protected]> wrote: > As long as the script can find the files you can do whatever you want > regarding input names. > > Peace, > > Matt. > > From: Dev vasu <[email protected]> > Date: Saturday, August 20, 2016 at 10:07 AM > > To: Matt Glasser <[email protected]> > Cc: "<[email protected]>" <[email protected]> > Subject: Re: Images appear to be distorted and cut after Preprocessing > > Dear Sir, > > I would like to ask one thing, is it important that i should use the > folder structure and naming conventions as highlighted in the original code > : unprocessed/3T/T1w_MPR2/${Subject}_3T_T1w_MPR2.nii.gz, or is acceptable > to alter this in accordance to my folder naming conventions?. > > > Thanks > Vasudev > > On 20 August 2016 at 17:02, Glasser, Matthew <[email protected]> wrote: > >> Without knowing more about your data, I don’t know what changes you need >> to make. I bet you could figure some of them out by doing what I suggest >> and then could ask questions about those you don’t understand. >> >> Peace, >> >> Matt. >> >> From: Dev vasu <[email protected]> >> Date: Saturday, August 20, 2016 at 10:00 AM >> >> To: Matt Glasser <[email protected]> >> Cc: "<[email protected]>" <[email protected]> >> Subject: Re: Images appear to be distorted and cut after Preprocessing >> >> Dear Sir, >> >> Actually , i am not in my research center at the moment, so i cannot send >> you the script to highlight the changes that i have done, if possible >> please let me know the changes that i should make in order to properly run >> the pipeline. >> >> >> Thanks >> Vasudev >> >> On 20 August 2016 at 16:52, Glasser, Matthew <[email protected]> wrote: >> >>> You have written the same thing three times now. How about reading >>> through that script’s comments and asking questions about stuff you don’t >>> understand there, such as all of the settings you need to change to make >>> your data work. >>> >>> Peace, >>> >>> Matt. >>> >>> From: Dev vasu <[email protected]> >>> Date: Saturday, August 20, 2016 at 9:49 AM >>> To: Matt Glasser <[email protected]>, "<[email protected]>" >>> <[email protected]> >>> >>> Subject: Re: Images appear to be distorted and cut after Preprocessing >>> >>> Dear sir, >>> >>> Yes , i have made changes in the code , instead of >>> >>> ${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR2/${Subject}_3T_T1w_MPR2.nii.gz, >>> i have used ${StudyFolder}/${Subject}/T1w/T1w.nii.gz. I did the same >>> while reference the path to T2w image. >>> >>> apart from that i have changed the Path to Study Folder and Subject ID, >>> also set up the path to SetUpHCPPipeline.sh >>> >>> >>> Thanks >>> Vasudev >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 20 August 2016 at 16:31, Glasser, Matthew <[email protected]> wrote: >>> >>>> If you aren’t using data that is exactly the same as the HCP data, you >>>> will likely have to make other changes to the settings. You could read >>>> through the example script and see which places you need to make changes. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: Dev vasu <[email protected]> >>>> Date: Saturday, August 20, 2016 at 9:27 AM >>>> >>>> To: Matt Glasser <[email protected]> >>>> Cc: "<[email protected]>" <[email protected]> >>>> Subject: Re: Images appear to be distorted and cut after Preprocessing >>>> >>>> Dear sir, >>>> >>>> I have made changes to the directory where my subjects are, i have >>>> mentioned the SubjectId and in that there are T1w and T2w images, I have >>>> just referenced to the paths. >>>> >>>> Thanks >>>> Vasudev >>>> >>>> On 20 August 2016 at 16:25, Glasser, Matthew <[email protected]> >>>> wrote: >>>> >>>>> You do have to make changes to the settings so that they are >>>>> appropriate for your study. >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: Dev vasu <[email protected]> >>>>> Date: Saturday, August 20, 2016 at 9:23 AM >>>>> >>>>> To: Matt Glasser <[email protected]> >>>>> Cc: "<[email protected]>" <[email protected]> >>>>> Subject: Re: Images appear to be distorted and cut after Preprocessing >>>>> >>>>> Dear Sir, >>>>> >>>>> I have just altered the path to subject directory and changed the >>>>> Subject ID, apart from that i have not changed much in the code written >>>>> in >>>>> Examples directory. >>>>> >>>>> >>>>> Thanks >>>>> Vasudev >>>>> >>>>> On 20 August 2016 at 16:17, Glasser, Matthew <[email protected]> >>>>> wrote: >>>>> >>>>>> That would suggest something isn’t set up right in the calls to >>>>>> PreFreeSurfer, so you should post them. >>>>>> >>>>>> Peace, >>>>>> >>>>>> Matt. >>>>>> >>>>>> From: Dev vasu <[email protected]> >>>>>> Date: Saturday, August 20, 2016 at 9:16 AM >>>>>> To: Matt Glasser <[email protected]> >>>>>> Cc: "<[email protected]>" <[email protected]> >>>>>> Subject: Re: Images appear to be distorted and cut after >>>>>> Preprocessing >>>>>> >>>>>> Dear Sir, >>>>>> >>>>>> Its happening to every subject . >>>>>> >>>>>> Thanks >>>>>> Vasudev >>>>>> >>>>>> On 20 August 2016 at 00:35, Glasser, Matthew <[email protected]> >>>>>> wrote: >>>>>> >>>>>>> It is only necessary to post to hcp-users. >>>>>>> >>>>>>> Is this happening with every subject or only a few subjects? >>>>>>> >>>>>>> Matt. >>>>>>> >>>>>>> From: <[email protected]> on behalf of Dev vasu < >>>>>>> [email protected]> >>>>>>> Date: Friday, August 19, 2016 at 11:19 AM >>>>>>> To: "<[email protected]>" <[email protected]>, >>>>>>> "[email protected]" <hcp-users-owner@humanconnecto >>>>>>> me.org> >>>>>>> Subject: Images appear to be distorted and cut after Preprocessing >>>>>>> >>>>>>> >>>>>>> Dear Sir / madam, >>>>>>> >>>>>>> After running Prefreesurfer pipeline on 50 Subjects, the T1w and T2w >>>>>>> images appear cut and very distorted , I am attaching the results for >>>>>>> your >>>>>>> verification. >>>>>>> >>>>>>> Please review it and let me know what is the problem . >>>>>>> >>>>>>> Also ,i would like to inform you that my mails are bouncing back, >>>>>>> kindly let me know the issue with my mailing list subscription >>>>>>> >>>>>>> >>>>>>> >>>>>>> Thanks >>>>>>> Vasudev >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> The materials in this message are private and may contain Protected >>>>>>> Healthcare Information or other information of a sensitive nature. If >>>>>>> you >>>>>>> are not the intended recipient, be advised that any unauthorized use, >>>>>>> disclosure, copying or the taking of any action in reliance on the >>>>>>> contents >>>>>>> of this information is strictly prohibited. If you have received this >>>>>>> email >>>>>>> in error, please immediately notify the sender via telephone or return >>>>>>> mail. >>>>>>> >>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> The materials in this message are private and may contain Protected >>>>>> Healthcare Information or other information of a sensitive nature. If you >>>>>> are not the intended recipient, be advised that any unauthorized use, >>>>>> disclosure, copying or the taking of any action in reliance on the >>>>>> contents >>>>>> of this information is strictly prohibited. If you have received this >>>>>> email >>>>>> in error, please immediately notify the sender via telephone or return >>>>>> mail. >>>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> The materials in this message are private and may contain Protected >>>>> Healthcare Information or other information of a sensitive nature. If you >>>>> are not the intended recipient, be advised that any unauthorized use, >>>>> disclosure, copying or the taking of any action in reliance on the >>>>> contents >>>>> of this information is strictly prohibited. If you have received this >>>>> email >>>>> in error, please immediately notify the sender via telephone or return >>>>> mail. >>>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. If you >>>> are not the intended recipient, be advised that any unauthorized use, >>>> disclosure, copying or the taking of any action in reliance on the contents >>>> of this information is strictly prohibited. If you have received this email >>>> in error, please immediately notify the sender via telephone or return >>>> mail. >>>> >>> >>> >>> ------------------------------ >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> >> >> >> ------------------------------ >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
