It is only necessary to post to hcp-users.
Is this happening with every subject or only a few subjects?
Matt.
From:
mailto:mailman-boun...@humanconnectome.org>>
on behalf of Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Friday, August 19, 2016 at 11:19 AM
To: "mailto:hcp-users@
Dear Sir,
Its happening to every subject .
Thanks
Vasudev
On 20 August 2016 at 00:35, Glasser, Matthew wrote:
> It is only necessary to post to hcp-users.
>
> Is this happening with every subject or only a few subjects?
>
> Matt.
>
> From: on behalf of Dev vasu <
> vasudevamurthy.devulapa...@
That would suggest something isn't set up right in the calls to PreFreeSurfer,
so you should post them.
Peace,
Matt.
From: Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Saturday, August 20, 2016 at 9:16 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "mailto:hcp-users@humanc
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 wrote:
> That would suggest something isn’t set up right in t
You do have to make changes to the settings so that they are appropriate for
your study.
Peace,
Matt.
From: Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Saturday, August 20, 2016 at 9:23 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "mailto:hcp-users@humanconnectome.org>>
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 wrote:
> You do have to make changes to the settings s
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
mailto:vasudevamurthy.devulapa...@gmail.com>>
Da
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 Stu
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
mailto:vasudevamurthy.devulapa...@
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,
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
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Sat
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?.
Thank
As long as the script can find the files you can do whatever you want regarding
input names.
Peace,
Matt.
From: Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Saturday, August 20, 2016 at 10:07 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "mailto:hcp-users@humanconnectome.
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 wrote:
> As long as the script can find the files you can do whatever you want
> regarding input names.
>
> Peace,
>
> Matt.
>
> From: Dev vasu
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,
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 ?.
Thank
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.
Pe
Dear Sir,
I have used fslhd, following is the output from the query, do you think i
can still use the default templates mentioned in the pipeline ?
vasudev@vasudev-OptiPlex-780:~$ fslhd
'/media/vasudev/Daten/Struc+func/Proj4/KON2/T1w/o20121209_203816MR000320MPRAGEisoPAT2PomscharAndreass004a1001.n
You should use the 1mm templates instead if your data are 1mm isotropic. This
might fix the issue…
Peace,
Matt.
From: Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Thursday, August 25, 2016 at 8:53 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "mailto:hcp-users@humanconne
Dear Sir,
When i use 1mm templates instead of 2mm as mentioned in
PreFreeSurferPipeline.sh , I am incurring following error
" ERROR: Could not open image
/home/vasudev/Documents/Pipelines-3.14.1/global/templates/MNI152_
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/h
You need to use 1mm templates instead of 0.7mm templates. Keep the 2mm ones
the same.
Peace,
Matt.
From: Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Thursday, August 25, 2016 at 12:00 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "mailto:hcp-users@humanconnectome.org>>"
Dear Sir,
Same error persists even after changing the templates
" About to use fsl_sub to queue or run
/home/vasudev/Documents/Pipelines-3.14.1/PreFreeSurfer/PreFreeSurferPipeline.sh
Image Exception : #22 :: ERROR: Could not open image
/home/vasudev/Documents/Pipelines-3.14.1/global/templates/MNI
It looks like you might have a space in a file name.
Peace,
Matt.
From: Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Thursday, August 25, 2016 at 12:08 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "mailto:hcp-users@humanconnectome.org>>"
mailto:hcp-users@humanconnectome.
That T2w image does not cover the whole FOV and is not appropriate for the HCP
Pipelines.
Peace,
Matt.
From: Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Wednesday, August 31, 2016 at 6:43 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "mailto:hcp-users@humanconnectome.org
That image has an even smaller FOV. You need whole brain coverage in your
images. You set that on the scanner.
Peace,
Matt.
From: Dev vasu
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Wednesday, August 31, 2016 at 7:57 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "mailto:hcp-use
Dear Sir,
Can i possibly use rfRMI image in place of T2w image?.
Thanks
Vasudev
On 31 August 2016 at 15:02, Glasser, Matthew wrote:
> That image has an even smaller FOV. You need whole brain coverage in your
> images. You set that on the scanner.
>
> Peace,
>
> Matt.
>
> From: Dev vasu
> Dat
Dear Sir,
How could i possibly measure FOV of an image, and what specific
requirements pertaining to FOV for HCP pipelines ?.
Thanks
Vasudev
On 31 August 2016 at 15:06, Dev vasu
wrote:
> Dear Sir,
>
> Can i possibly use rfRMI image in place of T2w image?.
>
> Thanks
> Vasudev
>
> On 31 August
Dear Sir,
The field of view for my image is 256 mm and an isotropic spatial
resolution of 1.0x1.0x1.0 mm3, when i consider the imaging requirements (
http://www.humanconnectome.org/documentation/Q1/imaging-protocols.html ),
the specifications match well .
Thanks
Vasudev
On 31 August 2016 at 1
can be done after the
scan is taken to improve the amount of brain coverage, which is what counts.
All the best,
Mark
From: on behalf of Dev vasu
Date: Wednesday, 31 August 2016 at 13:57
To: "Glasser, Matthew"
Cc: ""
Subject: Re: [HCP-Users] Images appear
ot;<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Images appear to be distorted and cut after Preprocessing
Dear Sir,
Is there any way to change FOV ,We have even acquired another sequence of T2w, but the problem persis
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