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 <vasudevamurthy.devulapa...@gmail.com>
wrote:
> Dear Sir,
>
> Can i possibly use rfRMI image in place of T2w image?.
>
> Thanks
> Vasudev
>
> On 31 August 2016 at 15:02, Glasser, Matthew <glass...@wustl.edu> 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 <vasudevamurthy.devulapa...@gmail.com>
>> Date: Wednesday, August 31, 2016 at 7:57 AM
>>
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
>> Subject: Re: 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 <glass...@wustl.edu> wrote:
>>
>>> That T2w image does not cover the whole FOV and is not appropriate for
>>> the HCP Pipelines.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
>>> Date: Wednesday, August 31, 2016 at 6:43 AM
>>>
>>> To: Matt Glasser <glass...@wustl.edu>
>>> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
>>> 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 <glass...@wustl.edu> wrote:
>>>
>>>> It looks like you might have a space in a file name.
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
>>>> Date: Thursday, August 25, 2016 at 12:08 PM
>>>>
>>>> To: Matt Glasser <glass...@wustl.edu>
>>>> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
>>>> 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/Pipeli
>>>> nes-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 <glass...@wustl.edu>
>>>> wrote:
>>>>
>>>>> You need to use 1mm templates instead of 0.7mm templates. Keep the
>>>>> 2mm ones the same.
>>>>>
>>>>> Peace,
>>>>>
>>>>> Matt.
>>>>>
>>>>> From: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
>>>>> Date: Thursday, August 25, 2016 at 12:00 PM
>>>>>
>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
>>>>> 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/Pipeli
>>>>> nes-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
>>>>> ${im1}_roi_linmask -applyxfm "
>>>>>
>>>>>
>>>>>
>>>>> Thanks
>>>>> Vasudev
>>>>>
>>>>>
>>>>> On 25 August 2016 at 18:14, Glasser, Matthew <glass...@wustl.edu>
>>>>> wrote:
>>>>>
>>>>>> You should use the 1mm templates instead if your data are 1mm
>>>>>> isotropic. This might fix the issue…
>>>>>>
>>>>>> Peace,
>>>>>>
>>>>>> Matt.
>>>>>>
>>>>>> From: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
>>>>>> Date: Thursday, August 25, 2016 at 8:53 AM
>>>>>>
>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
>>>>>> Subject: Re: Images appear to be distorted and cut after
>>>>>> Preprocessing
>>>>>>
>>>>>> Dear Sir,
>>>>>>
>>>>>> I have used fslhd, following is the output from the query, do you
>>>>>> think i can still use the default templates mentioned in the pipeline ?
>>>>>>
>>>>>> vasudev@vasudev-OptiPlex-780:~$ fslhd '/media/vasudev/Daten/Struc+fu
>>>>>> nc/Proj4/KON2/T1w/o20121209_203816MR000320MPRAGEisoPAT2PomscharAndreass004a1001.nii.gz'
>>>>>>
>>>>>> filename /media/vasudev/Daten/Struc+fun
>>>>>> c/Proj4/KON2/T1w/o20121209_203816MR000320MPRAGEisoPAT2Pomsch
>>>>>> arAndreass004a1001.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 <glass...@wustl.edu>
>>>>>> 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 <vasudevamurthy.devulapa...@gmail.com>
>>>>>>> Date: Tuesday, August 23, 2016 at 12:39 AM
>>>>>>>
>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org
>>>>>>> >
>>>>>>> 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 <glass...@wustl.edu>
>>>>>>> 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 <vasudevamurthy.devulapa...@gmail.com>
>>>>>>>> Date: Monday, August 22, 2016 at 9:35 AM
>>>>>>>>
>>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>>> Cc: "<hcp-users@humanconnectome.org>" <
>>>>>>>> hcp-users@humanconnectome.org>
>>>>>>>> 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 <vasudevamurthy.devulapally@gm
>>>>>>>> ail.com> 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 <glass...@wustl.edu>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> As long as the script can find the files you can do whatever you
>>>>>>>>>> want regarding input names.
>>>>>>>>>>
>>>>>>>>>> Peace,
>>>>>>>>>>
>>>>>>>>>> Matt.
>>>>>>>>>>
>>>>>>>>>> From: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
>>>>>>>>>> Date: Saturday, August 20, 2016 at 10:07 AM
>>>>>>>>>>
>>>>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>>>>> Cc: "<hcp-users@humanconnectome.org>" <
>>>>>>>>>> hcp-users@humanconnectome.org>
>>>>>>>>>> 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 <glass...@wustl.edu>
>>>>>>>>>> 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 <vasudevamurthy.devulapa...@gmail.com>
>>>>>>>>>>> Date: Saturday, August 20, 2016 at 10:00 AM
>>>>>>>>>>>
>>>>>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>>>>>> Cc: "<hcp-users@humanconnectome.org>" <
>>>>>>>>>>> hcp-users@humanconnectome.org>
>>>>>>>>>>> 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 <glass...@wustl.edu
>>>>>>>>>>> > 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 <vasudevamurthy.devulapa...@gmail.com>
>>>>>>>>>>>> Date: Saturday, August 20, 2016 at 9:49 AM
>>>>>>>>>>>> To: Matt Glasser <glass...@wustl.edu>, "<
>>>>>>>>>>>> hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 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 <
>>>>>>>>>>>> glass...@wustl.edu> 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 <vasudevamurthy.devulapa...@gmail.com>
>>>>>>>>>>>>> Date: Saturday, August 20, 2016 at 9:27 AM
>>>>>>>>>>>>>
>>>>>>>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>>>>>>>> Cc: "<hcp-users@humanconnectome.org>" <
>>>>>>>>>>>>> hcp-users@humanconnectome.org>
>>>>>>>>>>>>> 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 <
>>>>>>>>>>>>> glass...@wustl.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> You do have to make changes to the settings so that they are
>>>>>>>>>>>>>> appropriate for your study.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Peace,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Matt.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> From: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
>>>>>>>>>>>>>> Date: Saturday, August 20, 2016 at 9:23 AM
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>>>>>>>>> Cc: "<hcp-users@humanconnectome.org>" <
>>>>>>>>>>>>>> hcp-users@humanconnectome.org>
>>>>>>>>>>>>>> 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 <
>>>>>>>>>>>>>> glass...@wustl.edu> 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 <vasudevamurthy.devulapa...@gmail.com>
>>>>>>>>>>>>>>> Date: Saturday, August 20, 2016 at 9:16 AM
>>>>>>>>>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>>>>>>>>>> Cc: "<hcp-users@humanconnectome.org>" <
>>>>>>>>>>>>>>> hcp-users@humanconnectome.org>
>>>>>>>>>>>>>>> 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 <
>>>>>>>>>>>>>>> glass...@wustl.edu> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> It is only necessary to post to hcp-users.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Is this happening with every subject or only a few subjects?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Matt.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> From: <mailman-boun...@humanconnectome.org> on behalf of
>>>>>>>>>>>>>>>> Dev vasu <vasudevamurthy.devulapa...@gmail.com>
>>>>>>>>>>>>>>>> Date: Friday, August 19, 2016 at 11:19 AM
>>>>>>>>>>>>>>>> To: "<hcp-users@humanconnectome.org>" <
>>>>>>>>>>>>>>>> hcp-users@humanconnectome.org>, "
>>>>>>>>>>>>>>>> hcp-users-ow...@humanconnectome.org" <
>>>>>>>>>>>>>>>> hcp-users-ow...@humanconnectome.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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>>>>>>>>>>>>>>>> have received this email in error, please immediately notify
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>>>>>>>>>>>> have received this email in error, please immediately notify the
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>>>>>>>>>>> have received this email in error, please immediately notify the
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>>>>>>>>>> If you
>>>>>>>>>> have received this email in error, please immediately notify the
>>>>>>>>>> sender via
>>>>>>>>>> telephone or return mail.
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>>>>>>>> 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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>>>>>>> you
>>>>>>> are not the intended recipient, be advised that any unauthorized use,
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>>>>>>> email
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>>>>>> Healthcare Information or other information of a sensitive nature. If you
>>>>>> are not the intended recipient, be advised that any unauthorized use,
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>>>>>> contents
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>>>>>> email
>>>>>> in error, please immediately notify the sender via telephone or return
>>>>>> mail.
>>>>>>
>>>>>
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>>>>> 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.
>>>>
>>>
>>>
>>> ------------------------------
>>>
>>> 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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