Dear Sir,
Could you please let me know what should i replace in the place of
${StudyFolder}/${Subject}/T1w/T1w.nii.gz and
${StudyFolder}/${Subject}/T2w/T2w.nii.gz,
also the raw data that i have got doesn't mention the voxel resolution, how
could i evaluate voxel resolution in this case ?.
Thanks
Vasudev
On 23 August 2016 at 01:38, Glasser, Matthew <[email protected]> wrote:
> I wouldn’t use the names ${StudyFolder}/${Subject}/T1w/T1w.nii.gz and
> ${StudyFolder}/${Subject}/T2w/T2w.nii.gz as these are actually
> intermediate outputs of the pipeline. Also, I would check to make sure the
> templates you are using match the input data in terms of the voxel
> resolution.
>
> Peace,
>
> Matt.
>
> From: Dev vasu <[email protected]>
> Date: Monday, August 22, 2016 at 9:35 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 am attaching the script , you can see the changes that i have made in
> it. Kindly let me know where i was wrong.
>
>
> Thanks
> Vasudev
>
>
>
> On 20 August 2016 at 17:11, Dev vasu <[email protected]
> > wrote:
>
>> 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]>, "hcp-users-owner@humanconnecto
>>>>>>>>> me.org" <[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
>>>>>>>>>
>>>>>>>>>
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>>>>>>>>> If you
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>>>>>>>>
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>>>>>
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>>
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