Hi Tim,

Thank you for your detailed replay, I have fixed the errors read:
mghRead(/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file
mghRead(/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file
mghRead(/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file
/home/yoson/Applications/HCP_Pipelines/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh:
 line 63: /100307/T1w/100307/mri/c_ras.mat: No such file or directory

As you suppose, the reason for having these errors is the wrong path directing 
to  brain.finalsurfs.mgz, so after checking the script I use to invoke 
PostFreeSurferPipeline.sh, I find out that I set the the value 
/Users/YOSON/Projects/HcpPipelinesExampleDataGDC to a wrong variable name 
SStudyFolder where I duplicate the capital S.However, successive errors appear 
even after I set the right path.

In case errors would have occurred in the first two part, I deleted all 
generated files and re-runed pre-freesurfer and freesurfer process. After that, 
I found that the FreeSurferPipeline.sh.e
23511 and PreFreeSurferPipeline.sh.e13527 were blank, while there were errors 
in PostFreeSurferPipeline.sh.e23895. 
The errors read:
mghRead(/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/100307/mri/brain.finalsurfs.mgz,
 -1): could not open file
mghRead(/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/100307/mri/brain.finalsurfs.mgz,
 -1): could not open file
mghRead(/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/100307/mri/brain.finalsurfs.mgz,
 -1): could not open file
Cannot open volume 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/wmparc_1mm for 
reading!

I checked the data repository, and could not find 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/100307/mri/brain.finalsurfs.mgz
 and /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/wmparc_1mm.


Here is the info of PreFreeSurferPipeline.sh.o13527:
Fri Oct 14 15:28:05 CST 2016 - PreFreeSurferPipeline.sh - Platform Information 
Follows: 
Linux yoson-Precision-Tower-3620 4.4.0-42-generic #62-Ubuntu SMP Fri Oct 7 
23:11:45 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Fri Oct 14 15:28:05 CST 2016 - PreFreeSurferPipeline.sh - Parsing Command Line 
Options
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Finished Parsing 
Command Line Options
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - StudyFolder: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Subject: 100307
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wInputImages: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/unprocessed/3T/T1w_MPR1/100307_3T_T1w_MPR1.nii.gz@
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wInputImages: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/unprocessed/3T/T2w_SPC1/100307_3T_T2w_SPC1.nii.gz@
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wTemplate: 
/home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_0.7mm.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wTemplateBrain: 
/home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wTemplate2mm: 
/home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_2mm.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wTemplate: 
/home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T2_0.7mm.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wTemplateBrain: 
/home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wTemplate2mm: 
/home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T2_2mm.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - TemplateMask: 
/home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Template2mmMask: 
/home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - BrainSize: 150
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - FNIRTConfig: 
/home/yoson/Applications/HCP_Pipelines/global/config/T1_2_MNI152_2mm.cnf
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - MagnitudeInputName: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/unprocessed/3T/T1w_MPR1/100307_3T_FieldMap_Magnitude.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - PhaseInputName: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/unprocessed/3T/T1w_MPR1/100307_3T_FieldMap_Phase.nii.gz
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - GEB0InputName: NONE
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - TE: 2.46
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - 
SpinEchoPhaseEncodeNegative: NONE
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - 
SpinEchoPhaseEncodePositive: NONE
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - DwellTime: NONE
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - SEUnwarpDir: NONE
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wSampleSpacing: 
0.0000074
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wSampleSpacing: 
0.0000021
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - UnwarpDir: z
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - 
GradientDistortionCoeffs: NONE
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - AvgrdcSTRING: 
SiemensFieldMap
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - TopupConfig: NONE
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - 
BiasFieldSmoothingSigma: 
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - UseJacobian: true
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - FSLDIR: 
/usr/share/fsl/5.0
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - HCPPIPEDIR: 
/home/yoson/Applications/HCP_Pipelines
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - HCPPIPEDIR_Global: 
/home/yoson/Applications/HCP_Pipelines/global/scripts
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - HCPPIPEDIR_PreFS: 
/home/yoson/Applications/HCP_Pipelines/PreFreeSurfer/scripts
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wFolder: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wFolder: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - AtlasSpaceFolder: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/MNINonLinear
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/xfms/
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/xfms/
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/MNINonLinear/xfms/
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - POSIXLY_CORRECT=
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Processing Modality:  
T1w
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - NOT PERFORMING 
GRADIENT DISTORTION CORRECTION
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Not Averaging T1w 
Images
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - ONLY ONE AVERAGE 
FOUND: COPYING
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Aligning T1w image to 
0.7mm MNI T1wTemplate to create native volume space
Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/ACPCAlignment
 
 START: ACPCAlignment
Final FOV is: 
0.000000 256.000000 0.000000 320.000000 58.000000 214.000000 

 END: ACPCAlignment
Fri Oct 14 15:31:39 CST 2016 - PreFreeSurferPipeline.sh - Performing Brain 
Extraction using FNIRT-based Masking
Fri Oct 14 15:31:39 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/BrainExtraction_FNIRTbased
 
 START: BrainExtraction_FNIRT
 
 END: BrainExtraction_FNIRT
Fri Oct 14 15:39:20 CST 2016 - PreFreeSurferPipeline.sh - Processing Modality:  
T2w
Fri Oct 14 15:39:20 CST 2016 - PreFreeSurferPipeline.sh - NOT PERFORMING 
GRADIENT DISTORTION CORRECTION
Fri Oct 14 15:39:21 CST 2016 - PreFreeSurferPipeline.sh - Not Averaging T2w 
Images
Fri Oct 14 15:39:21 CST 2016 - PreFreeSurferPipeline.sh - ONLY ONE AVERAGE 
FOUND: COPYING
Fri Oct 14 15:39:21 CST 2016 - PreFreeSurferPipeline.sh - Aligning T2w image to 
0.7mm MNI T2wTemplate to create native volume space
Fri Oct 14 15:39:21 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/ACPCAlignment
 
 START: ACPCAlignment
Final FOV is: 
0.000000 256.000000 0.000000 320.000000 60.000000 214.000000 

 
 END: ACPCAlignment
Fri Oct 14 15:42:32 CST 2016 - PreFreeSurferPipeline.sh - Performing Brain 
Extraction using FNIRT-based Masking
Fri Oct 14 15:42:32 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/BrainExtraction_FNIRTbased
 
 START: BrainExtraction_FNIRT
 
 END: BrainExtraction_FNIRT
Fri Oct 14 15:50:12 CST 2016 - PreFreeSurferPipeline.sh - Performing 
SiemensFieldMap Readout Distortion Correction
Fri Oct 14 15:50:12 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/T2wToT1wDistortionCorrectAndReg
 
 START: T2WToT1wDistortionCorrectAndReg.sh
 START: Field Map Preprocessing and Gradient Unwarping
Loading volumes
Phase loaded
Magnitude loaded
Mask loaded
Rewrapping phase range to [-pi,pi]
Number of phase splits = 8
Calculating starting matrices (6143 by 6143)
Finished connection_matrices
18546 constraints left
8771 constraints left
6835 constraints left
5338 constraints left
3472 constraints left
1841 constraints left
192 constraints left
Did while loop 6142 times
Done. Created 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/FieldMap
 for use with FEAT.
DONE: fsl_prepare_fieldmap.sh
 
 END: Field Map Preprocessing and Gradient Unwarping
Running FAST segmentation
FLIRT pre-alignment
Running BBR
0.348442 0.999983 -0.005782 0.001238 0.000000 0.005833 0.998931 -0.045856 
0.000000 -0.000971 0.045863 0.998947 0.000000 -1.228439 -3.729267 6.633881 
1.000000 
 
 END: T2WToT1wDistortionCorrectAndReg.sh
Fri Oct 14 16:10:31 CST 2016 - PreFreeSurferPipeline.sh - Performing Bias Field 
Correction
Fri Oct 14 16:10:31 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/BiasFieldCorrection_sqrtT1wXT1w
 
 START: BiasFieldCorrection
0.240737
0.975605
.8552365
 
 END: BiasFieldCorrection
Fri Oct 14 16:12:55 CST 2016 - PreFreeSurferPipeline.sh - Performing Atlas 
Registration to MNI152 (FLIRT and FNIRT)
 
 START: AtlasRegistration to MNI152
 
 END: AtlasRegistration to MNI152
Fri Oct 14 16:23:58 CST 2016 - PreFreeSurferPipeline.sh - Completed

And the info of FreeSurferPipeline.sh.o23511:
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - Parsing Command Line 
Options
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - Finished Parsing Command 
Line Options
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - SubjectID: 100307
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - SubjectDIR: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - T1wImage: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/T1w_acpc_dc_restore.nii.gz
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - T1wImageBrain: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/T1w_acpc_dc_restore_brain.nii.gz
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - T2wImage: 
/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/T2w_acpc_dc_restore.nii.gz
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - recon_all_seed: 
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - seed_cmd_appendix: 
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - HCPPIPEDIR: 
/home/yoson/Applications/HCP_Pipelines
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - HCPPIPEDIR_FS: 
/home/yoson/Applications/HCP_Pipelines/FreeSurfer/scripts
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - which flirt: 
/usr/share/fsl/5.0/bin/flirt
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - flirt -version: FLIRT 
version 6.0
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - which applywarp: 
/usr/share/fsl/5.0/bin/applywarp
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - which fslstats: 
/usr/share/fsl/5.0/bin/fslstats
Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - which fslmaths: 
/usr/share/fsl/5.0/bin/fslmaths
Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - which recon-all: 
/home/yoson/Applications/freesurfer/bin/recon-all
Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - recon-all --version: 
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - which mri_convert: 
/home/yoson/Applications/freesurfer/bin/mri_convert
Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - which mri_em_register: 
/home/yoson/Applications/freesurfer/bin/mri_em_register
Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - mri_em_register 
--version: 

 ======= NUMBER OF OPENMP THREADS = 4 ======= 
stable5
Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - which mri_watershed: 
/home/yoson/Applications/freesurfer/bin/mri_watershed
Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - mri_watershed --version: 
stable5
Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - Make Spline Interpolated 
Downsample to 1mm
Fri Oct 14 18:02:40 CST 2016 - FreeSurferPipeline.sh - Initial Recon-all Steps
ERROR: You are trying to re-run an existing subject with (possibly)
 new input data (-i). If this is truly new input data, you should delete
 the subject folder and re-run, or specify a different subject name.
 If you are just continuing an analysis of an existing subject, then 
 omit all -i flags.

I really appreciate your help.

Best,
YC Yao



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