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 <glass...@wustl.edu> 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 <vasudevamurthy.devulapa...@gmail.com>
> Date: Saturday, August 20, 2016 at 10:00 AM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
> 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 <glass...@wustl.edu> 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 <vasudevamurthy.devulapa...@gmail.com>
>> Date: Saturday, August 20, 2016 at 9:49 AM
>> To: Matt Glasser <glass...@wustl.edu>, "<hcp-users@humanconnectome.org>"
>> <hcp-users@humanconnectome.org>
>>
>> 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 <glass...@wustl.edu> 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 <vasudevamurthy.devulapa...@gmail.com>
>>> Date: Saturday, August 20, 2016 at 9:27 AM
>>>
>>> To: Matt Glasser <glass...@wustl.edu>
>>> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
>>> 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 <glass...@wustl.edu> wrote:
>>>
>>>> You do have to make changes to the settings so that they are
>>>> appropriate for your study.
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
>>>> Date: Saturday, August 20, 2016 at 9:23 AM
>>>>
>>>> To: Matt Glasser <glass...@wustl.edu>
>>>> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
>>>> 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 <glass...@wustl.edu>
>>>> 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 <vasudevamurthy.devulapa...@gmail.com>
>>>>> Date: Saturday, August 20, 2016 at 9:16 AM
>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
>>>>> 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 <glass...@wustl.edu>
>>>>> wrote:
>>>>>
>>>>>> It is only necessary to post to hcp-users.
>>>>>>
>>>>>> Is this happening with every subject or only a few subjects?
>>>>>>
>>>>>> Matt.
>>>>>>
>>>>>> From: <mailman-boun...@humanconnectome.org> on behalf of Dev vasu <
>>>>>> vasudevamurthy.devulapa...@gmail.com>
>>>>>> Date: Friday, August 19, 2016 at 11:19 AM
>>>>>> To: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>,
>>>>>> "hcp-users-ow...@humanconnectome.org" <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
>>>>>>
>>>>>>
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>>>>>> contents
>>>>>> of this information is strictly prohibited. If you have received this
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>>>>>> in error, please immediately notify the sender via telephone or return
>>>>>> mail.
>>>>>>
>>>>>
>>>>>
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>>>>>
>>>>
>>>>
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>>>>
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>> 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,
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>
>
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> 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.
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