Dear Sir, Can i possibly use rfRMI image in place of T2w image?.
Thanks Vasudev On 31 August 2016 at 15:02, Glasser, Matthew <[email protected]> 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 <[email protected]> > Date: Wednesday, August 31, 2016 at 7:57 AM > > To: Matt Glasser <[email protected]> > Cc: "<[email protected]>" <[email protected]> > 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 <[email protected]> wrote: > >> That T2w image does not cover the whole FOV and is not appropriate for >> the HCP Pipelines. >> >> Peace, >> >> Matt. >> >> From: Dev vasu <[email protected]> >> Date: Wednesday, August 31, 2016 at 6:43 AM >> >> To: Matt Glasser <[email protected]> >> Cc: "<[email protected]>" <[email protected]> >> 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 <[email protected]> wrote: >> >>> It looks like you might have a space in a file name. >>> >>> Peace, >>> >>> Matt. >>> >>> From: Dev vasu <[email protected]> >>> Date: Thursday, August 25, 2016 at 12:08 PM >>> >>> To: Matt Glasser <[email protected]> >>> Cc: "<[email protected]>" <[email protected]> >>> 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 <[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/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 >>>> ${im1}_roi_linmask -applyxfm " >>>> >>>> >>>> >>>> Thanks >>>> Vasudev >>>> >>>> >>>> On 25 August 2016 at 18:14, Glasser, Matthew <[email protected]> >>>> wrote: >>>> >>>>> You should use the 1mm templates instead if your data are 1mm >>>>> isotropic. This might fix the issue… >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: Dev vasu <[email protected]> >>>>> Date: Thursday, August 25, 2016 at 8:53 AM >>>>> >>>>> To: Matt Glasser <[email protected]> >>>>> Cc: "<[email protected]>" <[email protected]> >>>>> Subject: Re: Images appear to be distorted and cut after Preprocessing >>>>> >>>>> Dear Sir, >>>>> >>>>> I have used fslhd, following is the output from the query, do you >>>>> think i can still use the default templates mentioned in the pipeline ? >>>>> >>>>> vasudev@vasudev-OptiPlex-780:~$ 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]>, " >>>>>>>>>>>>>>> [email protected]" < >>>>>>>>>>>>>>> [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. 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