It doesn’t matter exactly what you call your inputs, just don’t call them the
same thing as a pipeline intermediate. One thing that I often do is to make a
${StudyFolder}/${Subject}/RawData folder and then put files in that.
You can use fslhd to find out the voxel resolution of your images.
Peace,
Matt.
From: Dev vasu
<[email protected]<mailto:[email protected]>>
Date: Tuesday, August 23, 2016 at 12:39 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,
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]<mailto:[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]<mailto:[email protected]>>
Date: Monday, August 22, 2016 at 9:35 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 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]<mailto:[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]<mailto:[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]<mailto:[email protected]>>
Date: Saturday, August 20, 2016 at 10:07 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 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]<mailto:[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]<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
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immediately notify the sender via telephone or return mail.
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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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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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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
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