Okay, I got it. The fslhd message was packed and added to the attachment.
But I couldn't see any problem with the header...
Sincerely,
Qunjun
------------------ Original ------------------
From: "Glasser, Matthew"<glass...@wustl.edu>;
Date: Sat, Apr 6, 2019 12:13 PM
To: "Qunjun Liang"<liangqun...@foxmail.com>;
Cc: "hcp-users@humanconnectome.org"<hcp-users@humanconnectome.org>;
Subject: Re: [HCP-Users] An error about subcortical
processinginHCPfMRI-surface pipeline
The files in the error message.
Matt.
From: Qunjun Liang <liangqun...@foxmail.com>
Date: Friday, April 5, 2019 at 11:10 PM
To: Matt Glasser <glass...@wustl.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] An error about subcortical processing
inHCPfMRI-surface pipeline
Hi Matt,
Yes, we don't have an SBRef image. Because at the beginning of this
experiment, the sequence was set referring to the UK Biobank Project. BTW, the
scanner is Siemens 3T trio.
Sorry I don't know clearly about what files you mean... But I searched the
MNINonLinear/ directory and found an file named {task name}_SBRef.nii.gz, so I
used fslhd with this file. The result showed:
#-----------------------
filename
/media/LQJ/Social_Navigation/Social_nifti/201806138_hrw/MNINonLinear/Results/FunTask_AP/FunTask_AP_SBRef.nii.gz
size of header 348
data_type FLOAT32
dim0 3
dim1 91
dim2 108
dim3 91
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 -1.000000
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.200000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.000000
cal_min 0.000000
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
toffset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name MNI_152
qform_code 4
qto_xyz:1 -2.000000 0.000000 -0.000000 90.000000
qto_xyz:2 0.000000 2.000000 -0.000000 -126.000000
qto_xyz:3 0.000000 0.000000 2.000000 -72.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name MNI_152
sform_code 4
sto_xyz:1 -2.000000 0.000000 0.000000 90.000000
sto_xyz:2 0.000000 2.000000 0.000000 -126.000000
sto_xyz:3 0.000000 0.000000 2.000000 -72.000000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL5.0
aux_file
#-------------------
If this file is the file you have mention about or I got an wrong one?
Sincerely,
Qunjun
------------------ Original ------------------
From: "Glasser, Matthew"<glass...@wustl.edu>;
Date: Sat, Apr 6, 2019 11:32 AM
To: "Qunjun Liang"<liangqun...@foxmail.com>;
Cc: "hcp-users@humanconnectome.org"<hcp-users@humanconnectome.org>;
Subject: Re: [HCP-Users] An error about subcortical processing
inHCPfMRI-surface pipeline
Do you not have an SBRef image? I wonder if that feature is not working.
You could paste in fslhd from those two files.
Matt.
From: Qunjun Liang <liangqun...@foxmail.com>
Date: Friday, April 5, 2019 at 10:23 PM
To: Matt Glasser <glass...@wustl.edu>
Subject: Re: [HCP-Users] An error about subcortical processing in
HCPfMRI-surface pipeline
Hi Matt,
Thank you for the prompt reply.
I have packed the batch script I used to call PreFreeSufer, PostFreeSufer,
fMRIVolume and fMRISurface, as well as the log file (.o and .e) after running
the pipelines. The zip file is placed in the attachment.
Sincerely,
Qunjun
------------------ Original ------------------
From: "Glasser, Matthew"<glass...@wustl.edu>;
Date: Sat, Apr 6, 2019 10:39 AM
To: "Qunjun
Liang"<liangqun...@foxmail.com>;"hcp-users@humanconnectome.org"<hcp-users@humanconnectome.org>;
Subject: Re: [HCP-Users] An error about subcortical processing in
HCPfMRI-surface pipeline
Please post how you called PreFreeSurfer, PostFreeSurfer, fMRIVolume, and
fMRISurface.
Matt.
From: <hcp-users-boun...@humanconnectome.org> on behalf of Qunjun Liang
<liangqun...@foxmail.com>
Date: Friday, April 5, 2019 at 9:37 PM
To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: [HCP-Users] An error about subcortical processing in HCP fMRI-surface
pipeline
Dear HCP experts,
An error was occurred when I used fMRI surface generation pipeline:
#----------------------------------
While running:
wb_command -cifti-create-dense-timeseries /{PATH to
subject}/MNINonLinear/Results/{task name}/{task
name}_temp_subject.dtseries.nii -volume /{PATH to
subject}/MNINonLinear/Results/{task name}/{task name}.nii.gz
/{PATH to subject}/MNINonLinear/ROIs/ROIs.2.nii.gz
ERROR: label volume has a different volume space than data volume
#----------------------------------
I used GenericfMRISurfaceProcessingPipelineBatch.sh in Example/ directory to
call the pipeline. The parameters (LowResMesh, FinalfMRIResolution and
GrayordinatesResolution) were set in accord with that inPostFreesurferPipeline
and fMRIVolume pipeline.
Given than my fMRI data were acquired by multiband sequence, so I wonder if
the pipeline was expected to do some extra modifications to fit multiband image?
Environment:
1. Ubuntu 14.04 LTS
2. HCP pipeline 4.0.0
3. Workbench 1.3.2
4. FreeSurfer 6.0
5. FSL 5.0.9
Sincerely,
------------------
Qunjun Liang, Ph.D.
School of psychology
South China Normal University
Zhongshan Avenue West 55, Tianhe District
Guangzhou 510631
P. R. China
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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.
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<<attachment: TwoFile_log.zip>>
