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
>>>>
>>>>
>>>> ------------------------------
>>>>
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>>>> 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
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>>> 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.
>
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