It looks like you might have a space in a file name. Peace,
Matt. From: Dev vasu <[email protected]<mailto:[email protected]>> Date: Thursday, August 25, 2016 at 12:08 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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/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]<mailto:[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]<mailto:[email protected]>> Date: Thursday, August 25, 2016 at 12:00 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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 ${im1}_roi_linmask -applyxfm " Thanks Vasudev On 25 August 2016 at 18:14, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: You should use the 1mm templates instead if your data are 1mm isotropic. This might fix the issue… Peace, Matt. From: Dev vasu <[email protected]<mailto:[email protected]>> Date: Thursday, August 25, 2016 at 8:53 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]>> Subject: Re: Images appear to be distorted and cut after Preprocessing Dear Sir, I have used fslhd, following is the output from the query, do you think i can still use the default templates mentioned in the pipeline ? vasudev@vasudev-OptiPlex-780:~$ 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]<mailto:[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]<mailto:[email protected]>> Date: Tuesday, August 23, 2016 at 12:39 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Monday, August 22, 2016 at 9:35 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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 <[email protected]<mailto:[email protected]>> 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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 10:07 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 10:00 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 9:49 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 9:27 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 9:23 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, August 20, 2016 at 9:16 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> on behalf of Dev vasu <[email protected]<mailto:[email protected]>> Date: Friday, August 19, 2016 at 11:19 AM To: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[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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