Re: [HCP-Users] Images appear to be distorted and cut after Preprocessing

[Harms, Michael]

Hi, I think you need to met with someone at your scanner that knows how to change the FOV of your T2w scan.   The NIFTI file you sent had dimensions of 384 x 384 x 60 with 0.6 mm voxels, which is a FOV of just 36 mm in the 3rd dimension, which isn’t nearly enough for full brain coverage. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu <vasudevamurthy.devulapa...@gmail.com> Date: Wednesday, August 31, 2016 at 7:57 AM To: "Glasser, Matthew" <glass...@wustl.edu> Cc: "<hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] 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.devulapally@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.devulapally@gmail.com> Date: Thursday, August 25, 2016 at 12:08 PM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@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/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 <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.devulapally@gmail.com> Date: Thursday, August 25, 2016 at 12:00 PM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@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/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 ${im1}_roi_linmask -applyxfm "   Thanks Vasudev On 25 August 2016 at 18:14, Glasser, Matthew <glass...@wustl.edu> wrote: You should use the 1mm templates instead if your data are 1mm isotropic.  This might fix the issue… Peace, Matt. From: Dev vasu <vasudevamurthy.devulapally@gmail.com> Date: Thursday, August 25, 2016 at 8:53 AM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@humanconnectome.org>" <hcp-users@humanconnectome.org> Subject: Re: Images appear to be distorted and cut after Preprocessing Dear Sir, I have used fslhd, following is the output from the query, do you think i can still use the default templates mentioned in the pipeline ? vasudev@vasudev-OptiPlex-780:~$ fslhd '/media/vasudev/Daten/Struc+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.devulapally@gmail.com> Date: Tuesday, August 23, 2016 at 12:39 AM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@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.devulapally@gmail.com> Date: Monday, August 22, 2016 at 9:35 AM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@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@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.devulapally@gmail.com> Date: Saturday, August 20, 2016 at 10:07 AM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@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.devulapally@gmail.com> Date: Saturday, August 20, 2016 at 10:00 AM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@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.devulapally@gmail.com> Date: Saturday, August 20, 2016 at 9:49 AM To: Matt Glasser <glass...@wustl.edu>, "<hcp-us...@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.devulapally@gmail.com> Date: Saturday, August 20, 2016 at 9:27 AM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@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.devulapally@gmail.com> Date: Saturday, August 20, 2016 at 9:23 AM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@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.devulapally@gmail.com> Date: Saturday, August 20, 2016 at 9:16 AM To: Matt Glasser <glass...@wustl.edu> Cc: "<hcp-us...@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-bounces@humanconnectome.org> on behalf of Dev vasu <vasudevamurthy.devulapally@gmail.com> Date: Friday, August 19, 2016 at 11:19 AM To: "<hcp-us...@humanconnectome.org>" <hcp-users@humanconnectome.org>, "hcp-users-owner@humanconnectome.org" <hcp-users-owner@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 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. 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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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users