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. 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