Hi,
The problem with this is that the image does not have full brain coverage. A
large part of the brain is not in the image. This is the problem and it is not
possible to make parts of the brain that were not scanned appear in the image
through any post-processing. So there is nothing that can be done after the
scan is taken to improve the amount of brain coverage, which is what counts.
All the best,
Mark
From: <[email protected]> on behalf of Dev vasu
<[email protected]>
Date: Wednesday, 31 August 2016 at 13:57
To: "Glasser, Matthew" <[email protected]>
Cc: "<[email protected]>" <[email protected]>
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 persists even with this, I am annexing another T2w image for
your reference.
Thanks
Vasudev
On 31 August 2016 at 14:14, Glasser, Matthew
<[email protected]<mailto:[email protected]>> wrote:
That T2w image does not cover the whole FOV and is not appropriate for the HCP
Pipelines.
Peace,
Matt.
From: Dev vasu
<[email protected]<mailto:[email protected]>>
Date: Wednesday, August 31, 2016 at 6:43 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,
The problem still persists , i am still incurring images where registration is
improper,Gradient distortion correction fails, I am sending you the script and
T1w and T2w images of one particular subject, also the images that i have got
after running the pipeline
Thanks
Vasudev
On 25 August 2016 at 19:14, Glasser, Matthew
<[email protected]<mailto:[email protected]>> wrote:
It looks like you might have a space in a file name.
Peace,
Matt.
From: Dev vasu
<[email protected]<mailto:[email protected]>>
Date: Thursday, August 25, 2016 at 12:08 PM
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,
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/MNI152_
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/vasudev/Documents/Pipelines-3.14.1/PreFreeSurfer/scripts/AnatomicalAverage.sh:
line 134: 14043 Aborted "
Thanks
Vasudev
On 25 August 2016 at 19:01, Glasser, Matthew
<[email protected]<mailto:[email protected]>> wrote:
You need to use 1mm templates instead of 0.7mm templates. Keep the 2mm ones
the same.
Peace,
Matt.
From: Dev vasu
<[email protected]<mailto:[email protected]>>
Date: Thursday, August 25, 2016 at 12:00 PM
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,
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'
/home/vasudev/Documents/Pipelines-3.14.1/PreFreeSurfer/scripts/AnatomicalAverage.sh:
line 134: 9995 Aborted (core dumped) $FSLDIR/bin/flirt -init
${im1}_std2roi.mat -in "$StandardMask" -ref ${im1}_roi -out ${im1}_roi_linmask
-applyxfm "
Thanks
Vasudev
On 25 August 2016 at 18:14, Glasser, Matthew
<[email protected]<mailto:[email protected]>> wrote:
You should use the 1mm templates instead if your data are 1mm isotropic. This
might fix the issue…
Peace,
Matt.
From: Dev vasu
<[email protected]<mailto:[email protected]>>
Date: Thursday, August 25, 2016 at 8:53 AM
To: Matt Glasser <[email protected]<mailto:[email protected]>>
Cc: "<[email protected]<mailto:[email protected]>>"
<[email protected]<mailto:[email protected]>>
Subject: Re: Images appear to be distorted and cut after Preprocessing
Dear Sir,
I have used fslhd, following is the output from the query, do you think i can
still use the default templates mentioned in the pipeline ?
vasudev@vasudev-OptiPlex-780:~$ fslhd
'/media/vasudev/Daten/Struc+func/Proj4/KON2/T1w/o20121209_203816MR000320MPRAGEisoPAT2PomscharAndreass004a1001.nii.gz'
filename
/media/vasudev/Daten/Struc+func/Proj4/KON2/T1w/o20121209_203816MR000320MPRAGEisoPAT2PomscharAndreass004a1001.nii.gz
sizeof_hdr 348
data_type INT16
dim0 3
dim1 160
dim2 256
dim3 256
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 2.100000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 75601.468750
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 1.000000 0.000000 0.000000 -79.500000
qto_xyz:2 0.000000 1.000000 0.000000 -127.000000
qto_xyz:3 0.000000 0.000000 1.000000 -123.973358
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 1.000000 0.000000 0.000000 -79.500000
sto_xyz:2 0.000000 1.000000 0.000000 -127.000000
sto_xyz:3 0.000000 0.000000 1.000000 -123.973358
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Left-to-Right
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
Thanks
Vasudev
On 23 August 2016 at 14:28, Glasser, Matthew
<[email protected]<mailto:[email protected]>> wrote:
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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