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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 10:00 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 9:49 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 9:27 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 9:23 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 9:16 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> on behalf of Dev vasu <[email protected]<mailto:[email protected]>> Date: Friday, August 19, 2016 at 11:19 AM To: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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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