---action=src

Barbara Kreilkamp

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Oct 5, 2021, 8:33:41 AM10/5/21

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Dear Frank,

I am running the src step but am having problems with it, see below. Can you make out why it won't work?

Thank you,

Kind wishes,

Barbara

singularity exec /usr/users/kreilkamp/dsistudio_latest.sif dsi_studio --action=src --source=C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii --bval=C_AHKP99A_DTI.bvals --bvec=C_AHKP99A_DTI_eddy_eddy_rotated_bvecs --output=C_AHKP99A.src.gz

WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (83) bind mounts
ERROR: ld.so: object 'libdlfaker.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libvglfaker.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
DSI Studio Nov 3 2020, Fang-Cheng Yeh
source=C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii
action=src
output=C_AHKP99A.src.gz
image=C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii
loading
invalid file format
Warning: --bval is not used. Please check command line syntax.
Warning: --bvec is not used. Please check command line syntax.

Frank Yeh

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Oct 5, 2021, 9:58:13 AM10/5/21

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Sorry about the error.

Could you update your DSI Studio ( dsistudio_latest.sif ) and try again?

The new version will tell more detail about the error.

Best,

Frank

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Barbara Kreilkamp

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Oct 6, 2021, 7:26:36 AM10/6/21

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Dear Frank,

Thank you for your reply.

Do you mean the download from http://dsi-studio.labsolver.org/dsi-studio-download ? It seems like there is no associated file to download from that site.

Kind wishes,

Barbara

Frank Yeh

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Oct 6, 2021, 10:07:06 AM10/6/21

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You can remove the sif file and run

singularity pull docker://dsistudio/dsistudio:latest

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Barbara Kreilkamp

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Oct 7, 2021, 7:18:06 AM10/7/21

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Thank you Frank. It seems I have a library issue now instead:

Any insights would be appreciated, thanks! Barbara

singularity exec /usr/users/kreilkamp/dsistudio_latest.sif dsi_studio --action=src --source=C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii.gz --bval=/usr/users/nmri/projects/kreilkamp/GoeEpiLongterm_anon/dsistudio_singularity_output/C.AHKP99A/C_AHKP99A_DTI_bvals --bvec=/usr/users/nmri/projects/kreilkamp/GoeEpiLongterm_anon/dsistudio_singularity_output/C.AHKP99A/C_AHKP99A_DTI_eddy_eddy_rotated_bvecs --output=C_AHKP99A.src.gz

ERROR: ld.so: object 'libdlfaker.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libvglfaker.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.

/opt/dsi-studio/dsi_studio: error while loading shared libraries: libQt5Core.so.5: cannot open shared object file: No such file or directory

Frank Yeh

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Oct 7, 2021, 2:40:15 PM10/7/21

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What is your operating system?

Is it Ubuntu or CentOS?

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Frank Yeh

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Oct 7, 2021, 3:29:56 PM10/7/21

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If possible, you may upload the nii.gz/bval/bvec using the link provided on the DSI Studio website, and I can help to check the data.

Sorry for all the issues.

Frank

Barbara Kreilkamp

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Oct 8, 2021, 4:17:49 AM10/8/21

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Thank you Frank,

I have uploaded the data.

Kind wishes,

Barbara

Barbara Kreilkamp

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Oct 8, 2021, 4:19:55 AM10/8/21

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My operating system is CentOs as far as I can see:

uname -r

3.10.0-1160.24.1.el7.x86_64
bash-4.2$ cat /etc/os-release
NAME="Scientific Linux"
VERSION="7.9 (Nitrogen)"
ID="scientific"
ID_LIKE="rhel centos fedora"
VERSION_ID="7.9"
PRETTY_NAME="Scientific Linux 7.9 (Nitrogen)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:scientificlinux:scientificlinux:7.9:GA"
HOME_URL="http://www.scientificlinux.org//"
BUG_REPORT_URL="mailto:scientific-...@listserv.fnal.gov"

REDHAT_BUGZILLA_PRODUCT="Scientific Linux 7"
REDHAT_BUGZILLA_PRODUCT_VERSION=7.9
REDHAT_SUPPORT_PRODUCT="Scientific Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.9"

Frank Yeh

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Oct 8, 2021, 3:48:22 PM10/8/21

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Could you run singularity pull again and see if it works?

Here's the result I got from testing the data you sent me: The SRC file can be generated.

]$ singularity exec /ocean/projects/cis200024p/frankyeh/dsistudio_latest.sif dsi_studio --action=src --source=C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii.gz --bval=C_AHKP99A_DTI_bvals --bvec=C_AHKP99A_DTI_eddy_eddy_rotated_bvecs

DSI Studio Oct 7 2021 Fang-Cheng Yeh
source=C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii.gz
action=src
loading nifti
bval=C_AHKP99A_DTI_bvals
flip_by=1
bvec=C_AHKP99A_DTI_eddy_eddy_rotated_bvecs
output src to C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii.gz.src.gz
sort_b_table=0
up_sampling=0
Save Files

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Barbara Kreilkamp

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Oct 11, 2021, 6:07:45 AM10/11/21

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It seems that it is not fixed on my end:

singularity exec /usr/users/kreilkamp/dsistudio_latest.sif dsi_studio --action=src --source=/usr/users/nmri/projects/kreilkamp/GoeEpiLongterm_anon/dsistudio_singularity_output/C.AHKP99A/C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii.gz --bval=/usr/users/nmri/projects/kreilkamp/GoeEpiLongterm_anon/dsistudio_singularity_output/C.AHKP99A/C_AHKP99A_DTI_bvals --bvec=/usr/users/nmri/projects/kreilkamp/GoeEpiLongterm_anon/dsistudio_singularity_output/C.AHKP99A/C_AHKP99A_DTI_eddy_eddy_rotated_bvecs --output=C_AHKP99A.src.gz

ERROR: ld.so: object 'libdlfaker.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libvglfaker.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.

DSI Studio Oct 8 2021 Fang-Cheng Yeh
source=/usr/users/nmri/projects/kreilkamp/GoeEpiLongterm_anon/dsistudio_singularity_output/C.AHKP99A/C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii.gz
action=src
loading nifti
ERROR loading dwi file:Cannot read the file. No reading privilege or the file does not exist.

Warning: --bval is not used. Please check command line syntax.
Warning: --bvec is not used. Please check command line syntax.

Warning: --output is not used. Please check command line syntax.

Do you have another clue?

Thank you,

Kind wishes,
Barbara

Frank Yeh

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Oct 11, 2021, 9:32:25 AM10/11/21

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" No reading privilege or the file does not exist."

Please check reading privileges and the file path.
When you "ls /usr/users/nmri/projects/kreilkamp/GoeEpiLongterm_anon/dsistudio_singularity_output/C.AHKP99A/C_AHKP99A_DTI_B0_mean_brain_output_dwi_epicorr.nii.gz
"
the system should show the file.

Frank

On Mon, Oct 11, 2021 at 6:08 AM 'Barbara Kreilkamp' via DSI Studio

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