Welcome! Log In Create A New Profile

AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates

Previous Message Next Message

Message List New Topic Print View

isa

July 05, 2013 11:55AM

Hi Daniel,

This is my command line:

align_epi_anat.py -volreg on -tshift off -epi2anat -epi S002.LingRun1.RTRs.6+orig
-anat S002.anatomical.5+orig -epi_base 8 -child_epi S002.LingRun2.RTRs.3+orig S002.ColorRun2.RTRs.4+orig S002.ColorRun1.RTRs.3+orig -AddEdge

For each EPI, I get the following output:

S002.ColorRun1.RTRs.3_al_mat.aff12.1D
S002.ColorRun1.RTRs.3_al_reg_mat.aff12.1D
S002.ColorRun1.RTRs.3_vr_motion.1D

However, I do not get the _al .BRIK and .HEAD files.

If it helps, I ran the exact same command on another iMAC with Snow Leopard and it works fine- I do not get any errors and have all the output files.

This is part of the output:
#++ align_epi_anat version: 1.44
#++ turning on volume registration
#++ -child_epi or child_dset2 option given
#Script is running (command trimmed):
3dAttribute DELTA ./S002.LingRun1.RTRs.6+orig
#Script is running (command trimmed):
3dAttribute DELTA ./S002.LingRun1.RTRs.6+orig
#Script is running:
3dAttribute DELTA /Volumes/Timbit/Quantifiers/MINC/S002/S002.anatomical.5+orig
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_S002.LingRun1.RTRs.6*
#Script is running:
\rm -f ./__tt_S002.anatomical.5*
#Script is running (command trimmed):
3dcopy ./S002.anatomical.5+orig ./__tt_S002.anatomical.5
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Jul 2 2013) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_S002.anatomical.5+orig -prefix ./__tt_S002.anatomical.5_ns
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 84, avoid_vent -1
#Script is running (command trimmed):
3dinfo ./__tt_S002.anatomical.5_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /Volumes/Timbit/Quantifiers/MINC/S002/__tt_S002.anatomical.5_ns+orig is not oblique
#Script is running (command trimmed):
3dinfo ./S002.LingRun1.RTRs.6+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /Volumes/Timbit/Quantifiers/MINC/S002/S002.LingRun1.RTRs.6+orig is not oblique
#++ Volume registration for epi data
#Script is running (command trimmed):
3dvolreg -1Dfile ./S002.LingRun1.RTRs.6_vr_motion.1D -1Dmatrix_save ./__tt_S002.LingRun1.RTRs.6_vr_mat.aff12.1D -prefix ./__tt_S002.LingRun1.RTRs.6_vr -base 8 -cubic ./S002.LingRun1.RTRs.6+orig
++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Jul 2 2013) [64-bit]
++ Authored by: RW Cox
++ Max displacement in automask = 1.40 (mm) at sub-brick 399
** Warning: overwriting file ./S002.LingRun1.RTRs.6_vr_motion.1D
#++ Creating representative epi sub-brick
#Script is running (command trimmed):
3dbucket -prefix ./__tt_S002.LingRun1.RTRs.6_vr_ts ./__tt_S002.LingRun1.RTRs.6_vr+orig'[8]'
++ 3dbucket: AFNI version=AFNI_2011_12_21_1014 (Jul 2 2013) [64-bit]
#++ resampling epi to match anat data
#Script is running (command trimmed):
3dresample -master ./__tt_S002.anatomical.5_ns+orig -prefix ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs -inset ./__tt_S002.LingRun1.RTRs.6_vr_ts+orig'' -rmode Cu
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs+orig -prefix ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns+orig
#++ Applying threshold of 648.000000 on /Volumes/Timbit/Quantifiers/MINC/S002/__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns_wt -a ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns+orig -expr 'min(1,(a/648.000000))'
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Jul 2 2013) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns_wt+orig.BRIK
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix ./__tt_S002.anatomical.5_ns_al_wtal -weight ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns_wt+orig -source ./__tt_S002.anatomical.5_ns+orig -prefix ./__tt_S002.anatomical.5_al -base ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns+orig -nocmass -1Dmatrix_save ./S002.anatomical.5_al_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

dyld: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

#++ Aligning /Volumes/Timbit/Quantifiers/MINC/S002/S002.LingRun1.RTRs.6+orig to anat
#++ Inverting anat to epi matrix
#Script is running (command trimmed):
cat_matvec -ONELINE ./S002.anatomical.5_al_mat.aff12.1D -I > ./S002.LingRun1.RTRs.6_al_mat.aff12.1D
** FATAL ERROR: Can't read file './S002.anatomical.5_al_mat.aff12.1D'
** Program compile date = Jul 2 2013
#++ Concatenating volreg and epi to anat transformations
#Script is running (command trimmed):
cat_matvec -ONELINE ./S002.anatomical.5_al_mat.aff12.1D -I ./__tt_S002.LingRun1.RTRs.6_vr_mat.aff12.1D > ./S002.LingRun1.RTRs.6_al_reg_mat.aff12.1D
** FATAL ERROR: Can't read file './S002.anatomical.5_al_mat.aff12.1D'
** Program compile date = Jul 2 2013
#++ Applying transformation of epi to anat
#Script is running (command trimmed):
3dAllineate -base ./S002.anatomical.5+orig -1Dmatrix_apply ./S002.LingRun1.RTRs.6_al_reg_mat.aff12.1D -prefix ./S002.LingRun1.RTRs.6_al -input ./S002.LingRun1.RTRs.6+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

dyld: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

#Script is running:
cd ./; \rm -f AddEdge/*
#++ Applying transformation for epi to anat for @AddEdge
#Script is running (command trimmed):
3dAllineate -base ./S002.anatomical.5+orig -1Dmatrix_apply './S002.LingRun1.RTRs.6_al_reg_mat.aff12.1D{8}' -prefix ./__tt_S002.LingRun1.RTRs.6_addedge -input ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns+orig -master BASE
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

dyld: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

#Script is running:
mkdir ./AddEdge
mkdir: ./AddEdge: File exists
#Script is running (command trimmed):
3dcopy -overwrite ./__tt_S002.anatomical.5_ns+orig ./AddEdge/S002.anatomical.5_ns
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Jul 2 2013) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite ./__tt_S002.LingRun1.RTRs.6_vr_ts_rs_ns+orig ./AddEdge/S002.LingRun1.RTRs.6_ns
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Jul 2 2013) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite ./__tt_S002.LingRun1.RTRs.6_addedge+orig ./AddEdge/S002.LingRun1.RTRs.6_al
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Jul 2 2013) [64-bit]
*+ WARNING: missing view dataset: ./__tt_S002.LingRun1.RTRs.6_addedge+orig - SKIPPING
** FATAL ERROR: no datasets found!
** Program compile date = Jul 2 2013
#Script is running (command trimmed):
cd ./AddEdge; @AddEdge -no_deoblique S002.anatomical.5_ns+orig S002.LingRun1.RTRs.6_ns+orig S002.LingRun1.RTRs.6_al+orig; cd -
*** Can't open dataset S002.LingRun1.RTRs.6_al+orig
d1: Subscript out of range.
d1: Subscript out of range.
d1: Subscript out of range.
if: Expression Syntax.
/Volumes/Timbit/Quantifiers/MINC/S002
#++ Creating final output: epi data aligned to anat
# copy is not necessary
#++ Saving history
#Script is running (command trimmed):
3dNotes -h "align_epi_anat.py -volreg on -tshift off -epi2anat -epi \
S002.LingRun1.RTRs.6+orig -anat S002.anatomical.5+orig -epi_base 8 \
-child_epi S002.LingRun2.RTRs.3+orig S002.ColorRun2.RTRs.4+orig \
S002.ColorRun1.RTRs.3+orig -AddEdge" \
./S002.LingRun1.RTRs.6_al+orig

Error: Cannot open dataset
#++ Parent /Volumes/Timbit/Quantifiers/MINC/S002/S002.LingRun1.RTRs.6+orig: Child: /Volumes/Timbit/Quantifiers/MINC/S002/S002.LingRun2.RTRs.3+orig
#++ Volume registration for epi data
#Script is running (command trimmed):
3dvolreg -1Dfile ./S002.LingRun2.RTRs.3_vr_motion.1D -1Dmatrix_save ./__tt_S002.LingRun2.RTRs.3_vr_mat.aff12.1D -prefix ./__tt_S002.LingRun2.RTRs.3_vr -base ./S002.LingRun1.RTRs.6+orig.'[8]' -cubic ./S002.LingRun2.RTRs.3+orig
++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Jul 2 2013) [64-bit]
++ Authored by: RW Cox
++ Max displacement in automask = 7.45 (mm) at sub-brick 261
** Warning: overwriting file ./S002.LingRun2.RTRs.3_vr_motion.1D
#++ Aligning /Volumes/Timbit/Quantifiers/MINC/S002/S002.LingRun2.RTRs.3+orig to anat
#++ Inverting anat to epi matrix
#Script is running (command trimmed):
cat_matvec -ONELINE ./S002.anatomical.5_al_mat.aff12.1D -I > ./S002.LingRun2.RTRs.3_al_mat.aff12.1D
** FATAL ERROR: Can't read file './S002.anatomical.5_al_mat.aff12.1D'
** Program compile date = Jul 2 2013
#++ Concatenating volreg and epi to anat transformations
#Script is running (command trimmed):
cat_matvec -ONELINE ./S002.anatomical.5_al_mat.aff12.1D -I ./__tt_S002.LingRun2.RTRs.3_vr_mat.aff12.1D > ./S002.LingRun2.RTRs.3_al_reg_mat.aff12.1D
** FATAL ERROR: Can't read file './S002.anatomical.5_al_mat.aff12.1D'
** Program compile date = Jul 2 2013
#++ Applying transformation of epi to anat
#Script is running (command trimmed):
3dAllineate -base ./S002.anatomical.5+orig -1Dmatrix_apply ./S002.LingRun2.RTRs.3_al_reg_mat.aff12.1D -prefix ./S002.LingRun2.RTRs.3_al -input ./S002.LingRun2.RTRs.3+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

dyld: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_S002.LingRun2.RTRs.3*
#++ Parent /Volumes/Timbit/Quantifiers/MINC/S002/S002.LingRun1.RTRs.6+orig: Child: /Volumes/Timbit/Quantifiers/MINC/S002/S002.ColorRun2.RTRs.4+orig
#++ Volume registration for epi data
#Script is running (command trimmed):
3dvolreg -1Dfile ./S002.ColorRun2.RTRs.4_vr_motion.1D -1Dmatrix_save ./__tt_S002.ColorRun2.RTRs.4_vr_mat.aff12.1D -prefix ./__tt_S002.ColorRun2.RTRs.4_vr -base ./S002.LingRun1.RTRs.6+orig.'[8]' -cubic ./S002.ColorRun2.RTRs.4+orig
++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Jul 2 2013) [64-bit]
++ Authored by: RW Cox
++ Max displacement in automask = 2.17 (mm) at sub-brick 0
** Warning: overwriting file ./S002.ColorRun2.RTRs.4_vr_motion.1D
#++ Aligning /Volumes/Timbit/Quantifiers/MINC/S002/S002.ColorRun2.RTRs.4+orig to anat
#++ Inverting anat to epi matrix
#Script is running (command trimmed):
cat_matvec -ONELINE ./S002.anatomical.5_al_mat.aff12.1D -I > ./S002.ColorRun2.RTRs.4_al_mat.aff12.1D
** FATAL ERROR: Can't read file './S002.anatomical.5_al_mat.aff12.1D'
** Program compile date = Jul 2 2013
#++ Concatenating volreg and epi to anat transformations
#Script is running (command trimmed):
cat_matvec -ONELINE ./S002.anatomical.5_al_mat.aff12.1D -I ./__tt_S002.ColorRun2.RTRs.4_vr_mat.aff12.1D > ./S002.ColorRun2.RTRs.4_al_reg_mat.aff12.1D
** FATAL ERROR: Can't read file './S002.anatomical.5_al_mat.aff12.1D'
** Program compile date = Jul 2 2013
#++ Applying transformation of epi to anat
#Script is running (command trimmed):
3dAllineate -base ./S002.anatomical.5+orig -1Dmatrix_apply ./S002.ColorRun2.RTRs.4_al_reg_mat.aff12.1D -prefix ./S002.ColorRun2.RTRs.4_al -input ./S002.ColorRun2.RTRs.4+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

dyld: Symbol not found: ___emutls_get_address
Referenced from: /Users/Izzo/abin/libgomp.1.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib

Reply Quote

RSS

Subject	Author	Posted
Error Symbol not found	isa	July 05, 2013 08:11AM
Re: Error Symbol not found	Daniel Glen	July 05, 2013 11:42AM
Re: Error Symbol not found	isa	July 05, 2013 11:55AM
Re: Error Symbol not found	rick reynolds	July 05, 2013 12:10PM
Re: Error Symbol not found	isa	July 05, 2013 12:16PM
Re: Error Symbol not found	Daniel Glen	July 05, 2013 12:26PM
Re: Error Symbol not found	isa	July 05, 2013 12:32PM
Re: Error Symbol not found	rick reynolds	July 05, 2013 08:10PM
Re: Error Symbol not found	Peter Molfese	July 05, 2013 02:08PM
Re: Error Symbol not found	Isa	July 06, 2013 04:40PM
Re: Error Symbol not found	Peter Molfese	July 06, 2013 09:08PM
Re: Error Symbol not found	isa	July 10, 2013 12:52PM
Re: Error Symbol not found	Peter Molfese	July 10, 2013 01:19PM
Re: Error Symbol not found	isa	July 10, 2013 01:59PM
Re: Error Symbol not found	Peter Molfese	July 10, 2013 02:02PM
Re: Error Symbol not found	Isa	July 10, 2013 02:09PM
Re: Error Symbol not found	Peter Molfese	July 10, 2013 02:29PM
Re: Error Symbol not found	Isa	July 10, 2013 02:40PM
Re: Error Symbol not found	Peter Molfese	July 10, 2013 02:53PM
Re: Error Symbol not found	Isa	July 10, 2013 02:59PM
Re: Error Symbol not found	rick reynolds	July 10, 2013 03:31PM
Re: Error Symbol not found	Isa	August 15, 2013 11:15AM