date:20190605

Re: [HCP-Users] Error while running "GenericfMRIVolumeProcessingPipeline.sh"

2019-06-05 Thread Joseph Orr

Yes the updates worked! I was actually about to comment on the github issue
you posted about the similar issue with applywarp when you added the
comment about flirt.
--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A&M Institute for Neuroscience
Texas A&M University
College Station, TX


On Wed, Jun 5, 2019 at 2:02 PM Harms, Michael  wrote:

>
>
> Try the very latest master, which should resolve this issue.  (I was just
> working on this 30 min ago).  Please let us know if it works.
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Associate Professor of Psychiatry
>
> 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: * on behalf of Joseph Orr <
> joseph@tamu.edu>
> *Date: *Wednesday, June 5, 2019 at 1:52 PM
> *To: *Simon Wein 
> *Cc: *HCP Users , Wilhelm Malloni <
> wilhelm.mall...@psychologie.uni-regensburg.de>
> *Subject: *Re: [HCP-Users] Error while running
> "GenericfMRIVolumeProcessingPipeline.sh"
>
>
>
> We ran into the same problem with *flirt*. In FSL 6.0.1, *flirt *can't
> take a 4D file as a reference, but it could in fsl v5. Adding a line before
> 289 to extract the first volume of PhaseTwo_gdc, and modifying flirt
> accordingly fixes the problem:
>
>
>
> ${FSLDIR}/bin/fslroi ${WD}/PhaseTwo_gdc ${WD}/PhaseTwo_gdc_slice -1 -1 -1
> -1 -1 -1 0 1
>
> ${FSLDIR}/bin/flirt -dof 6 -interp spline -in ${WD}/SBRef.nii.gz -ref
> ${WD}/PhaseTwo_gdc_slice -omat ${WD}/SBRef2PhaseTwo_gdc.mat -out
> ${WD}/SBRef2PhaseTwo_gdc
>
> --
>
> Joseph M. Orr, Ph.D.
>
> Assistant Professor
>
> Department of Psychological and Brain Sciences
>
> Texas A&M Institute for Neuroscience
>
> Texas A&M University
>
> College Station, TX
>
>
>
>
>
> On Sat, May 25, 2019 at 8:48 AM Simon Wein <
> simon.w...@psychologie.uni-regensburg.de> wrote:
>
> Thank you very much for your support.
>
> In our pipeline we have set *$GradientDistortionCoeffs = "NONE",* so line
> 189 in
>
>
>
> https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/TopupPreprocessingAll.sh
> 
>
>
>
> was unfortunately skipped. But we could avoid the error by modifying line
> 196 to:
>
>
>
> fslmaths ${WD}/BothPhases.nii.gz -mul 0 -add 1 ${WD}/Mask
>
>
>
>
>
> Mask.nii.gz then has properties:
>
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> *filenameMask.nii.gz size of header348 data_typeFLOAT32
> dim04 dim1104 dim2104 dim372 dim46
> dim51 dim61 dim71 vox_unitsmm time_unitss
> datatype16 nbyper4 bitpix32 pixdim01.00
> pixdim12.00 pixdim22.00 pixdim32.00
> pixdim47.70 pixdim50.00 pixdim60.00
> pixdim70.00 vox_offset352 cal_max0.00
> cal_min0.00 scl_slope1.00 scl_inter0.00
> phase_dim0 freq_dim0 slice_dim0 slice_nameUnknown
> slice_code0 slice_start0 slice_end0 slice_duration0.00
> toffset0.00 intentUnknown intent_code0
> intent_nameintent_p10.00 intent_p20.00 intent_p3
> 0.00 qform_nameScanner Anat qform_code1 qto_xyz:1-1.995593
> 0.092717 0.094922 93.702583 qto_xyz:2-0.105543 -1.976261 -0.288537
> 118.937881 qto_xyz:30.080419 -0.292910 1.976799 -43.901993 qto_xyz:4
> 0.00 0.00 0.00 1.00 qform_xorientRight-to-Left
> qform_yorientAnterior-to-Posterior qform_zorient
> Inferior-to-Superior sform_nameScanner Anat sform_code1
> sto_xyz:1-1.995594 0.092714 0.094922 93.702583 sto_xyz:2-0.105540
> -1.976261 -0.288537 118.937881 sto_xyz:30.080420 -0.292910 1.976799
> -43.901993 sto_xyz:40.00 0.00 0.00 1.00
> sform_xorientRight-to-Left sform_yorientAnterior-to-Posterior
> sform_zorientInferior-to-Superior file_typeNIFTI-1+ file_code1
> descrip6.0.1 aux_file*
>
> The previously mentioned problem with FSL 6.0+ fslmaths could be avoided.
>
> Would you consider this as a good workaround, or would you recommend
> something else?
>
>
>
> But in a later stage, we got another error:
>
>
>
>
>
>
> *Image Exception : #75 :: 3D only method called by higher-dimensional
> volume. 3D only method called by higher-dimensional volume. C

Re: [HCP-Users] Error while running "GenericfMRIVolumeProcessingPipeline.sh"

2019-06-05 Thread Harms, Michael


Try the very latest master, which should resolve this issue.  (I was just 
working on this 30 min ago).  Please let us know if it works.

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
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:  on behalf of Joseph Orr 

Date: Wednesday, June 5, 2019 at 1:52 PM
To: Simon Wein 
Cc: HCP Users , Wilhelm Malloni 

Subject: Re: [HCP-Users] Error while running 
"GenericfMRIVolumeProcessingPipeline.sh"

We ran into the same problem with flirt. In FSL 6.0.1, flirt can't take a 4D 
file as a reference, but it could in fsl v5. Adding a line before 289 to 
extract the first volume of PhaseTwo_gdc, and modifying flirt accordingly fixes 
the problem:

${FSLDIR}/bin/fslroi ${WD}/PhaseTwo_gdc ${WD}/PhaseTwo_gdc_slice -1 -1 -1 -1 -1 
-1 0 1
${FSLDIR}/bin/flirt -dof 6 -interp spline -in ${WD}/SBRef.nii.gz -ref 
${WD}/PhaseTwo_gdc_slice -omat ${WD}/SBRef2PhaseTwo_gdc.mat -out 
${WD}/SBRef2PhaseTwo_gdc
--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A&M Institute for Neuroscience
Texas A&M University
College Station, TX


On Sat, May 25, 2019 at 8:48 AM Simon Wein 
mailto:simon.w...@psychologie.uni-regensburg.de>>
 wrote:
Thank you very much for your support.
In our pipeline we have set $GradientDistortionCoeffs = "NONE", so line 189 in

https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/TopupPreprocessingAll.sh

was unfortunately skipped. But we could avoid the error by modifying line 196 
to:

fslmaths ${WD}/BothPhases.nii.gz -mul 0 -add 1 ${WD}/Mask


Mask.nii.gz then has properties:

filenameMask.nii.gz
size of header348
data_typeFLOAT32
dim04
dim1104
dim2104
dim372
dim46
dim51
dim61
dim71
vox_unitsmm
time_unitss
datatype16
nbyper4
bitpix32
pixdim01.00
pixdim12.00
pixdim22.00
pixdim32.00
pixdim47.70
pixdim50.00
pixdim60.00
pixdim70.00
vox_offset352
cal_max0.00
cal_min0.00
scl_slope1.00
scl_inter0.00
phase_dim0
freq_dim0
slice_dim0
slice_nameUnknown
slice_code0
slice_start0
slice_end0
slice_duration0.00
toffset0.00
intentUnknown
intent_code0
intent_name
intent_p10.00
intent_p20.00
intent_p30.00
qform_nameScanner Anat
qform_code1
qto_xyz:1-1.995593 0.092717 0.094922 93.702583
qto_xyz:2-0.105543 -1.976261 -0.288537 118.937881
qto_xyz:30.080419 -0.292910 1.976799 -43.901993
qto_xyz:40.00 0.00 0.00 1.00
qform_xorientRight-to-Left
qform_yorientAnterior-to-Posterior
qform_zorientInferior-to-Superior
sform_nameScanner Anat
sform_code1
sto_xyz:1-1.995594 0.092714 0.094922 93.702583
sto_xyz:2-0.105540 -1.976261 -0.288537 118.937881
sto_xyz:30.080420 -0.292910 1.976799 -43.901993
sto_xyz:40.00 0.00 0.00 1.00
sform_xorientRight-to-Left
sform_yorientAnterior-to-Posterior
sform_zorientInferior-to-Superior
file_typeNIFTI-1+
file_code1
descrip6.0.1
aux_file
The previously mentioned problem with FSL 6.0+ fslmaths could be avoided.
Would you consider this as a good workaround, or would you recommend something 
else?

But in a later stage, we got another error:

Image Exception : #75 :: 3D only method called by higher-dimensional volume.
3D only method called by higher-dimensional volume.
Could not open matrix file 
/loctmp/CUDA/DATA/VP_101/rfMRI_REST1_PA/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef2PhaseTwo_gdc.mat
Cannot read input-matrix

The file "SBRef2PhaseTwo_gdc.mat" was not created, so the problem might be in 
line 289 in "TopupPreprocessingAll.sh":

${FSLDIR}/bin/flirt -dof 6 -interp spline -in ${WD}/SBRef.nii.gz -ref 
${WD}/PhaseTwo_gdc -omat ${WD}/SBRef2PhaseTwo_gdc.mat -out 
${WD}/SBRef2PhaseTwo_gdc

Properties of SBRef.nii.gz are:

filenameSBRef.nii.gz
size of header348
data_typeUINT16
dim03
dim1104
dim2104
dim372
dim41
dim50
dim60
dim70
vox_unitsmm
time_unitss
datatype512
nbyper2
bitpix16
pixdim01.00
pixdim12.00
pixdim22.00
pixdim32

Re: [HCP-Users] Error while running "GenericfMRIVolumeProcessingPipeline.sh"

2019-06-05 Thread Joseph Orr

We ran into the same problem with *flirt*. In FSL 6.0.1, *flirt *can't take
a 4D file as a reference, but it could in fsl v5. Adding a line before 289
to extract the first volume of PhaseTwo_gdc, and modifying flirt
accordingly fixes the problem:

${FSLDIR}/bin/fslroi ${WD}/PhaseTwo_gdc ${WD}/PhaseTwo_gdc_slice -1 -1 -1
-1 -1 -1 0 1
${FSLDIR}/bin/flirt -dof 6 -interp spline -in ${WD}/SBRef.nii.gz -ref
${WD}/PhaseTwo_gdc_slice -omat ${WD}/SBRef2PhaseTwo_gdc.mat -out
${WD}/SBRef2PhaseTwo_gdc
--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A&M Institute for Neuroscience
Texas A&M University
College Station, TX


On Sat, May 25, 2019 at 8:48 AM Simon Wein <
simon.w...@psychologie.uni-regensburg.de> wrote:

> Thank you very much for your support.
> In our pipeline we have set *$GradientDistortionCoeffs = "NONE",* so line
> 189 in
>
>
> https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/TopupPreprocessingAll.sh
> 
>
> was unfortunately skipped. But we could avoid the error by modifying line
> 196 to:
>
> fslmaths ${WD}/BothPhases.nii.gz -mul 0 -add 1 ${WD}/Mask
>
>
> Mask.nii.gz then has properties:
>
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> *filenameMask.nii.gzsize of header348data_typeFLOAT32dim0
> 4dim1104dim2104dim372dim46dim5
> 1dim61dim71vox_unitsmmtime_unitssdatatype
> 16nbyper4bitpix32pixdim01.00pixdim1
> 2.00pixdim22.00pixdim32.00pixdim4
> 7.70pixdim50.00pixdim60.00pixdim7
> 0.00vox_offset352cal_max0.00cal_min
> 0.00scl_slope1.00scl_inter0.00phase_dim0freq_dim
> 0slice_dim0slice_nameUnknownslice_code0slice_start
> 0slice_end0slice_duration0.00toffset0.00intent
> Unknownintent_code0intent_nameintent_p10.00intent_p2
> 0.00intent_p30.00qform_nameScanner Anatqform_code
> 1qto_xyz:1-1.995593 0.092717 0.094922 93.702583 qto_xyz:2-0.105543
> -1.976261 -0.288537 118.937881 qto_xyz:30.080419 -0.292910 1.976799
> -43.901993 qto_xyz:40.00 0.00 0.00 1.00
> qform_xorientRight-to-Leftqform_yorient
> Anterior-to-Posteriorqform_zorientInferior-to-Superiorsform_name
> Scanner Anatsform_code1sto_xyz:1-1.995594 0.092714 0.094922
> 93.702583 sto_xyz:2-0.105540 -1.976261 -0.288537 118.937881
> sto_xyz:30.080420 -0.292910 1.976799 -43.901993 sto_xyz:40.00
> 0.00 0.00 1.00 sform_xorientRight-to-Leftsform_yorient
> Anterior-to-Posteriorsform_zorientInferior-to-Superiorfile_type
> NIFTI-1+file_code1descrip6.0.1aux_file*
>
> The previously mentioned problem with FSL 6.0+ fslmaths could be avoided.
> Would you consider this as a good workaround, or would you recommend
> something else?
>
> But in a later stage, we got another error:
>
>
>
>
> *Image Exception : #75 :: 3D only method called by higher-dimensional
> volume.3D only method called by higher-dimensional volume.Could not open
> matrix file
> /loctmp/CUDA/DATA/VP_101/rfMRI_REST1_PA/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef2PhaseTwo_gdc.matCannot
> read input-matrix*
>
> The file *"SBRef2PhaseTwo_gdc.mat*" was not created, so the problem might
> be in line 289 in *"TopupPreprocessingAll.sh":*
>
> * ${FSLDIR}/bin/flirt -dof 6 -interp spline -in ${WD}/SBRef.nii.gz -ref
> ${WD}/PhaseTwo_gdc -omat ${WD}/SBRef2PhaseTwo_gdc.mat -out
> ${WD}/SBRef2PhaseTwo_gdc*
>
> Properties of *SBRef.nii.gz* are:
>
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> *filenameSBRef.nii.gzsize of header348data_typeUINT16dim0
> 3dim1104dim2104dim372dim41dim5
> 0dim60dim70vox_unitsmmtime_unitssdatatype
> 512nbyper2bitpix16pixdim01.00pixdim1
> 2.00pixdim22.00pixdim32.00pixdim4
> 0.73pixdim50.00pixdim60.00pixdim7
> 0.00vox_offset352cal_max0.00cal_min
> 0.00scl_slope1.00scl_inter0.00phase_dim2freq_dim
> 1slice_dim3slice_namesequential_increasingslice_code
> 1slice_start0slice_end0slice_duration0.00toffset
> 0.00intentUnknownintent_code0intent_nameintent_p1
> 0.00intent_p20.00int

Re: [HCP-Users] wb_command -cifti-gradient

2019-06-05 Thread Timothy Coalson

"wb_command -gifti-help" is intended to help explain these file formats:

https://www.humanconnectome.org/software/workbench-command/-gifti-help

There are other -*-help options for other formats, and other aspects of
wb_command, like how to read the command usage info:

https://www.humanconnectome.org/software/workbench-command

Tim


On Tue, Jun 4, 2019 at 10:05 PM Glasser, Matthew  wrote:

> You can use the midthickness surfaces .surf.gii in the same folder.
>
>
>
> Matt.
>
>
>
> *From: *秦键 
> *Date: *Tuesday, June 4, 2019 at 10:02 PM
> *To: *"Glasser, Matthew" 
> *Cc: *"hcp-users@humanconnectome.org" 
> *Subject: *Re: [HCP-Users] wb_command -cifti-gradient
>
>
>
> A 32k fs_LR surface file with suffix of 'dscalar.nii', and a
> thickness.32k_fs_LR.dscalar.nii can be an example.
>
>
>
>
>
> [image: Image removed by sender.]
>
> *秦**键*
>
> 邮箱：qinjian...@126.com
>
> 签名由 网易邮箱大师  定制
>
> On 06/05/2019 10:36, Glasser, Matthew  wrote:
>
> What file did you try to run this on?
>
>
> Matt.
>
>
>
> *From: * on behalf of 秦键 <
> qinjian...@126.com>
> *Date: *Tuesday, June 4, 2019 at 9:32 PM
> *To: *"hcp-users@humanconnectome.org" 
> *Subject: *[HCP-Users] wb_command -cifti-gradient
>
>
>
>
>
> Dear professors,
>
> When I used the wb_command -cifti-gradient for fs_LR 32k cifti file, I was
> asked to input the left and right surface files, where can I find the left
> and right surface files and what are the format of them?  Can I have an
> example of the use of the wb_command -cifti-gradient?
>
> Thank you and best wishes!
>
>
>
>
>
>
>
> ___
> 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.
>
>
> --
>
> 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
>

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Re: [HCP-Users] Error while running "GenericfMRIVolumeProcessingPipeline.sh"

Re: [HCP-Users] Error while running "GenericfMRIVolumeProcessingPipeline.sh"

Re: [HCP-Users] Error while running "GenericfMRIVolumeProcessingPipeline.sh"

Re: [HCP-Users] wb_command -cifti-gradient

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