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
${im1}_roi_linmask -applyxfm "
Thanks
Vasudev
On 25 August 2016 at 18:14, Glasser, Matthew <[email protected]> wrote:
> You should use the 1mm templates instead if your data are 1mm isotropic.
> This might fix the issue…
>
> Peace,
>
> Matt.
>
> From: Dev vasu <[email protected]>
> Date: Thursday, August 25, 2016 at 8:53 AM
>
> To: Matt Glasser <[email protected]>
> Cc: "<[email protected]>" <[email protected]>
> Subject: Re: Images appear to be distorted and cut after Preprocessing
>
> Dear Sir,
>
> I have used fslhd, following is the output from the query, do you think i
> can still use the default templates mentioned in the pipeline ?
>
> vasudev@vasudev-OptiPlex-780:~$ 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]> 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]>
>> Date: Tuesday, August 23, 2016 at 12:39 AM
>>
>> To: Matt Glasser <[email protected]>
>> Cc: "<[email protected]>" <[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]> 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]>
>>> Date: Monday, August 22, 2016 at 9:35 AM
>>>
>>> To: Matt Glasser <[email protected]>
>>> Cc: "<[email protected]>" <[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 <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 <[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]>
>>>>> Date: Saturday, August 20, 2016 at 10:07 AM
>>>>>
>>>>> To: Matt Glasser <[email protected]>
>>>>> Cc: "<[email protected]>" <[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]>
>>>>> 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]>
>>>>>> Date: Saturday, August 20, 2016 at 10:00 AM
>>>>>>
>>>>>> To: Matt Glasser <[email protected]>
>>>>>> Cc: "<[email protected]>" <[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]>
>>>>>> 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]>
>>>>>>> Date: Saturday, August 20, 2016 at 9:49 AM
>>>>>>> To: Matt Glasser <[email protected]>, "<
>>>>>>> [email protected]>" <[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]>
>>>>>>> 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]>
>>>>>>>> Date: Saturday, August 20, 2016 at 9:27 AM
>>>>>>>>
>>>>>>>> To: Matt Glasser <[email protected]>
>>>>>>>> Cc: "<[email protected]>" <
>>>>>>>> [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]>
>>>>>>>> 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]>
>>>>>>>>> Date: Saturday, August 20, 2016 at 9:23 AM
>>>>>>>>>
>>>>>>>>> To: Matt Glasser <[email protected]>
>>>>>>>>> Cc: "<[email protected]>" <
>>>>>>>>> [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]>
>>>>>>>>> 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]>
>>>>>>>>>> Date: Saturday, August 20, 2016 at 9:16 AM
>>>>>>>>>> To: Matt Glasser <[email protected]>
>>>>>>>>>> Cc: "<[email protected]>" <
>>>>>>>>>> [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]>
>>>>>>>>>> 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]> on behalf of Dev
>>>>>>>>>>> vasu <[email protected]>
>>>>>>>>>>> Date: Friday, August 19, 2016 at 11:19 AM
>>>>>>>>>>> To: "<[email protected]>" <
>>>>>>>>>>> [email protected]>, "hcp-users-owner@humanconnecto
>>>>>>>>>>> me.org" <[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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>>>>>>>>>>> prohibited. If you
>>>>>>>>>>> have received this email in error, please immediately notify the
>>>>>>>>>>> sender via
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>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ------------------------------
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>>>>>>>>>> have received this email in error, please immediately notify the
>>>>>>>>>> sender via
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>>>>>>>>>
>>>>>>>>>
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>>>>>>>>> have received this email in error, please immediately notify the
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>>>>>>>> The materials in this message are private and may contain Protected
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>>>>>>>> are not the intended recipient, be advised that any unauthorized use,
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>>>>>>> are not the intended recipient, be advised that any unauthorized use,
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>>>>>> are not the intended recipient, be advised that any unauthorized use,
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>>>>>> contents
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>>>>> are not the intended recipient, be advised that any unauthorized use,
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>>>>> contents
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>>>>> in error, please immediately notify the sender via telephone or return
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>> disclosure, copying or the taking of any action in reliance on the contents
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