[eji]

Dear all, I am using BrainSuite for EPI correction and am receiving an error related to gunzip in matlab. Does anyone have experience with this / know what could be going wrong? Thank you. I’m pasting my command and the error below.

for subj in SPN01_CMH_0135_01 SPN01_CMH_0136_01; do cd $subj/mri; ~/newdata/downloads/BrainSuite19b/bdp/bdp.sh T1.bfc.nii.gz –nii $dtipath/$subj/data.nii.gz –bvec $dtipath/$subj/bvec.bvec –bval $dtipath/$subj/bval.bval –output-subdir bdp; cd $SUBJECTS_DIR/; done

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gunzip>gunzipwrite (line 239)
Unexpected end of input stream when attempting to GUNZIP the file “/tmp/tpcdba91ff_0c66_4ae7_b49d_648ad34b6adf/data.nii”.

Error in gunzip>gunzipEntries (line 155)

Error in gunzip (line 91)

Error in load_untouch_nii_gz (line 71)

Error in check_nifti_file (line 40)

Error in bdp_setup (line 894)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:gunzip:javaCopyStreamError

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gzip>gzipwrite (line 112)
Java exception occurred:
java.io.IOException: Disk quota exceeded
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:326)
at java.util.zip.GZIPOutputStream.finish(GZIPOutputStream.java:168)
at java.util.zip.DeflaterOutputStream.close(DeflaterOutputStream.java:238)

Error in gzip (line 52)

Error in save_untouch_nii_gz (line 80)

Error in reorient_nifti_sform>save_nii_with_qform (line 222)

Error in reorient_nifti_sform (line 54)

Error in bdp_setup (line 849)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:Java:GenericException

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gunzip>gunzipwrite (line 239)
Unexpected end of input stream when attempting to GUNZIP the file “/tmp/tpf2e8f73a_ef6d_48de_9d0f_83ce96670d8d/data.nii”.

Error in gunzip>gunzipEntries (line 155)

Error in gunzip (line 91)

Error in load_untouch_nii_gz (line 71)

Error in check_nifti_file (line 40)

Error in bdp_setup (line 894)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:gunzip:javaCopyStreamError

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gunzip>gunzipwrite (line 239)
Unexpected end of input stream when attempting to GUNZIP the file “/tmp/tp20f42e81_6d83_403c_a5b3_67460ea17af0/data.nii”.

Error in gunzip>gunzipEntries (line 155)

Error in gunzip (line 91)

Error in load_untouch_nii_gz (line 71)

Error in check_nifti_file (line 40)

Error in bdp_setup (line 894)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:gunzip:javaCopyStreamError

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gunzip>gunzipwrite (line 239)
Unexpected end of input stream when attempting to GUNZIP the file “/tmp/tp796fe916_5de9_433c_ab61_cad86d0268fb/data.nii”.

Error in gunzip>gunzipEntries (line 155)

Error in gunzip (line 91)

Error in load_untouch_nii_gz (line 71)

Error in check_nifti_file (line 40)

Error in bdp_setup (line 894)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:gunzip:javaCopyStreamError

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…

Output sub-directory already exists:
/mnt/newdata/projects/spins/freesurfer/SPN01_MRC_0015_01/mri/bdp
The files in the output folder can be overwritten.
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gunzip>gunzipwrite (line 239)
Unexpected end of input stream when attempting to GUNZIP the file “/tmp/tp9c9f3e2d_1c7b_435f_aaa0_c2982ea396bb/data.nii”.

Error in gunzip>gunzipEntries (line 155)

Error in gunzip (line 91)

Error in load_untouch_nii_gz (line 71)

Error in check_nifti_file (line 40)

Error in bdp_setup (line 894)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:gunzip:javaCopyStreamError

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…

Output sub-directory already exists:
/mnt/newdata/projects/spins/freesurfer/SPN01_MRC_0021_01/mri/bdp
The files in the output folder can be overwritten.
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gunzip>gunzipwrite (line 239)
Unexpected end of input stream when attempting to GUNZIP the file “/tmp/tpa04553ed_25f4_41b8_b8e7_5c17cb653637/data.nii”.

Error in gunzip>gunzipEntries (line 155)

Error in gunzip (line 91)

Error in load_untouch_nii_gz (line 71)

Error in check_nifti_file (line 40)

Error in bdp_setup (line 894)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:gunzip:javaCopyStreamError

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gzip>gzipwrite (line 114)
Could not open file “/tmp/tp62c87322_2487_495a_a3fc_f9b2e0e6ed1f/066911a1413c4c4.nii.gz” for writing.

Error in gzip (line 52)

Error in save_untouch_nii_gz (line 80)

Error in reorient_nifti_sform>save_nii_with_qform (line 222)

Error in reorient_nifti_sform (line 54)

Error in bdp_setup (line 849)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:gzip:javaOutputOpenError

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gunzip>gunzipwrite (line 239)
Unexpected end of input stream when attempting to GUNZIP the file “/tmp/tp21d28ce6_c2d1_46be_90d8_9da960152fc9/data.nii”.

Error in gunzip>gunzipEntries (line 155)

Error in gunzip (line 91)

Error in load_untouch_nii_gz (line 71)

Error in check_nifti_file (line 40)

Error in bdp_setup (line 894)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:gunzip:javaCopyStreamError

Located Matlab installation with runtime directory.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

BDP Version: 19b (build #0077), released 2019-12-31

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…

Output sub-directory already exists:
/mnt/newdata/projects/spins/freesurfer/SPN01_MRC_0034_01/mri/bdp
The files in the output folder can be overwritten.
Did not detect –FRT/–FRACT/–tensor/–3dshore/–gqi/–erfo. Using default
setting of estimating tensors.

Checking input files…
Error using gunzip>gunzipwrite (line 239)
Unexpected end of input stream when attempting to GUNZIP the file “/tmp/tp1eee7ef4_a6db_4fd9_a5fb_44f9d15322c5/data.nii”.

Error in gunzip>gunzipEntries (line 155)

Error in gunzip (line 91)

Error in load_untouch_nii_gz (line 71)

Error in check_nifti_file (line 40)

Error in bdp_setup (line 894)

Error in BrainSuite_Diffusion_pipeline (line 13)

MATLAB:gunzip:javaCopyStreamError

[vito]

Did you deal with this problem somehow?
I have a similar one, with each choice of each of the three options of the atlas.

Error using gunzip>gunzipwrite (line 239)
Unexpected end of input stream when attempting to GUNZIP the file “C:\Users\VIto\AppData\Local\Temp\tp1bb67d40_d03c_42c0_8fb6_51c11a4df4ee\ernie_T1.surfreg.map.nii”.

Error in gunzip>gunzipEntries (line 155)

Error in gunzip (line 91)

Error in load_untouch_nii_gz (line 71)

Error in check_nifti_file (line 59)

Error in load_nii_BIG_Lab (line 45)
Error in load_nii_z (line 38)

Error in extend_deformation_laplacian_hippo (line 129)

Error in svreg_volreg (line 224)

MATLAB:gunzip:javaCopyStreamError

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