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 <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-us...@humanconnectome.or
>>>>>> g>" <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-owner@humanconnecto
>>>>>>>>>> me.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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>>>>>>>>>> If you
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>>>>>>>>>> sender via
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
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>>>>>>>>
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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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>>>> in error, please immediately notify the sender via telephone or return
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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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>> in error, please immediately notify the sender via telephone or return mail.
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>
>
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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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