permutations turned off

[lconcha]

Thank you for the fantastic work on BROCCOLI. I am still new at this toolbox and migrating from fsl's Feat.

I am able to run FirstLevelAnalysis but I cannot get the permutations to work. Every time I use the -permute switch I get the error thatpermutation testing is currently turned off. If I do not use the -pemute switch the command runs and dhe resulting copes and betas look fine. Perhaps I am not using the correct syntax or completely misunderstanding the use of -permute in the scope of First level analyses.

Thanks in advance for your help.

FYI, my command is:

FirstLevelAnalysis /misc/mansfield/lconcha/TMP/circe/forBroccoli/frs404.nii.gz \
/misc/mansfield/lconcha/TMP/circe/forBroccoli/brs404.nii.gz \
/home/inb/lconcha/fmrilab_software/fsl_5.0.6/data/standard/MNI152_T1_2mm_brain.nii.gz \
outbase_regressors.txt \
outbase_contrasts.txt \
-smoothing 5 \
-saveall \
-output outbase_brocproc \
-verbose \
-savedesignmatrix \
-saveoriginaldesignmatrix \
-regressmotion \
-permute \
-permutations 1000 \
-inferencemode 1 \
-cdt 2.3

Permutation testing is currently turned off!

Cheers,

Luis

Device info  
---------------------------------------------
Platform number: 0
---------------------------------------------
Platform vendor: NVIDIA Corporation
Platform name: NVIDIA CUDA
Platform extentions: cl_khr_byte_addressable_store cl_khr_icd cl_khr_gl_sharing cl_nv_compiler_options cl_nv_device_attribute_query cl_nv_pragma_unroll 
Platform profile: FULL_PROFILE
---------------------------------------------

---------------------------------------------
Device number: 0
---------------------------------------------
Device vendor: NVIDIA Corporation
Device name: Quadro K2000
Hardware version: OpenCL 1.1 CUDA
Software version: 304.135
OpenCL C version: OpenCL C 1.1 
Device extensions: cl_khr_byte_addressable_store cl_khr_icd cl_khr_gl_sharing cl_nv_compiler_options cl_nv_device_attribute_query cl_nv_pragma_unroll  cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_khr_fp64 
Global memory size in MB: 2047
Size of largest memory object in MB: 511
Global memory cache size in KB: 32
Local memory size in KB: 48
Constant memory size in KB: 64
Parallel compute units: 2
Clock frequency in MHz: 954
Max number of threads per block: 1024
Max number of threads in each dimension: 1024 1024 64

[wanderine]

Yes permutation testing for first level analysis is currently disabled (I need to need to do some more testing), but you can use it for group analyses with the function "RandomiseGroupLevel".

2017-11-03 2:15 GMT+01:00 Luis Concha notifications@github.com:

Thank you for the fantastic work on BROCCOLI. I am still new at this toolbox and migrating from fsl's Feat.

I am able to run FirstLevelAnalysis but I cannot get the permutations to work. Every time I use the -permute switch I get the error thatpermutation testing is currently turned off. If I do not use the -pemute switch the command runs and dhe resulting copes and betas look fine. Perhaps I am not using the correct syntax or completely misunderstanding the use of -permute in the scope of First level analyses.

Thanks in advance for your help.

FYI, my command is:

FirstLevelAnalysis /misc/mansfield/lconcha/TMP/circe/forBroccoli/frs404.nii.gz \ /misc/mansfield/lconcha/TMP/circe/forBroccoli/brs404.nii.gz \ /home/inb/lconcha/fmrilab_software/fsl_5.0.6/data/standard/MNI152_T1_2mm_brain.nii.gz \ outbase_regressors.txt \ outbase_contrasts.txt \ -smoothing 5 \ -saveall \ -output outbase_brocproc \ -verbose \ -savedesignmatrix \ -saveoriginaldesignmatrix \ -regressmotion \ -permute \ -permutations 1000 \ -inferencemode 1 \ -cdt 2.3

Permutation testing is currently turned off!

Cheers,

Luis

Device info

Platform number: 0

Platform vendor: NVIDIA Corporation Platform name: NVIDIA CUDA Platform extentions: cl_khr_byte_addressable_store cl_khr_icd cl_khr_gl_sharing cl_nv_compiler_options cl_nv_device_attribute_query cl_nv_pragma_unroll Platform profile: FULL_PROFILE

---

Device number: 0

Device vendor: NVIDIA Corporation Device name: Quadro K2000 Hardware version: OpenCL 1.1 CUDA Software version: 304.135 OpenCL C version: OpenCL C 1.1 Device extensions: cl_khr_byte_addressable_store cl_khr_icd cl_khr_gl_sharing cl_nv_compiler_options cl_nv_device_attribute_query cl_nv_pragma_unroll cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_khr_fp64 Global memory size in MB: 2047 Size of largest memory object in MB: 511 Global memory cache size in KB: 32 Local memory size in KB: 48 Constant memory size in KB: 64 Parallel compute units: 2 Clock frequency in MHz: 954 Max number of threads per block: 1024 Max number of threads in each dimension: 1024 1024 64

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/wanderine/BROCCOLI/issues/41, or mute the thread https://github.com/notifications/unsubscribe-auth/AEGryL5OD_dbUzx03xVO5MvMxEolyx6Cks5symlLgaJpZM4QQjTc .

-- Anders Eklund, PhD