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 17:41, Dev vasu <vasudevamurthy.devulapa...@gmail.com>
wrote:
> 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.devulapa...@gmail.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
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> The materials in this message are private and may contain
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>>>>>>>>>>>>>>>>> have received this email in error, please immediately notify
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>>>>>>>>>>>>>>>
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>>>>>>>>>>>>>> action in
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>>>>>>>>>>>>>> have received this email in error, please immediately notify the
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>>>>>>>>>>>> sensitive
>>>>>>>>>>>> nature. If you are not the intended recipient, be advised that any
>>>>>>>>>>>> unauthorized use, disclosure, copying or the taking of any action
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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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>>>>>>>>> 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.
>>>>>>
>>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> 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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