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]> 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]> > Date: Thursday, August 25, 2016 at 12:00 PM > > To: Matt Glasser <[email protected]> > Cc: "<[email protected]>" <[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 > ${im1}_roi_linmask -applyxfm " > > > > Thanks > Vasudev > > > On 25 August 2016 at 18:14, Glasser, Matthew <[email protected]> wrote: > >> You should use the 1mm templates instead if your data are 1mm isotropic. >> This might fix the issue… >> >> Peace, >> >> Matt. >> >> From: Dev vasu <[email protected]> >> Date: Thursday, August 25, 2016 at 8:53 AM >> >> To: Matt Glasser <[email protected]> >> Cc: "<[email protected]>" <[email protected]> >> Subject: Re: Images appear to be distorted and cut after Preprocessing >> >> Dear Sir, >> >> I have used fslhd, following is the output from the query, do you think i >> can still use the default templates mentioned in the pipeline ? >> >> vasudev@vasudev-OptiPlex-780:~$ fslhd '/media/vasudev/Daten/Struc+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 <[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 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> ------------------------------ >>>>>>>>>>>> >>>>>>>>>>>> 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. >>>>>>> >>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> 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. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
