Yep, I just found that error yesterday. I put a new longmc script in
that same location with another fix -- but I have not fully tested it yet:)
On 7/21/2020 1:12 AM, Knut J Bjuland wrote:
External Email - Use Caution
Thanks it worked for subjects with more than one timepoint but when I
ran on subjects with one timepoint I get this error? I can upload this
subjects.
mri_robust_template --mov
/cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz
/cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz --ixforms
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/001.lta
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/002.lta
--average 1 --noit --template
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/rawavg.mgz
--iscalein
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/001-iscale.txt
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/002-iscale.txt
7.1.0
--mov: Using /cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz as
movable/source volume.
--mov: Using /cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz as
movable/source volume.
Total: 2 input volumes
--ixforms: Will use init XFORMS.
--average: Using method 1 for template computation.
--noit: Will output only first template (no iterations)!
--template: Using
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/rawavg.mgz
as template output volume.
--iscalein: Will use init intensity scales
reading source '/cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz'...
converting source
'/cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz'...
converting source
'/cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz' to bspline ...
MRItoBSpline degree 3
error: No such file or directory
error:
ltaReadFile(/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/001.lta):
can't open file^@
Segmentation fault (core dumped)
ERROR:
@#@FSTIME 2020:07:20:23:24:12 longmc N 5 e 17.11 S 0.79 U 1.54 P 13%
M 73600 F 111 R 30867 W 0 c 319 w 50082 I 48874 O 142592 L 42.23 41.81
41.92
@#@FSLOADPOST 2020:07:20:23:24:29 longmc N 5 42.24 41.84 41.92
Linux c5-57 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32 UTC
2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s KG01_Run1.long.KG01_Run1_base exited with ERRORS at Mon
20 Jul 23:24:29 CEST 2020
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
#New# invocation of recon-all
On 17/07/2020 16:28, Douglas N. Greve wrote:
I think you might have found a bug when a cross subject has more than
one input. Can you download
https://gate.nmr.mgh.harvard.edu/safelinks/greve/longmc
Copy it to $FREESURFER/bin (make a copy of the one that is there)
Then re-run?
thanks
On 7/16/2020 11:57 AM, Knut J Bjuland wrote:
External Email - Use Caution
Thanks
Sure,
Here is the log file.
Knut Jørgen
On 16/07/2020 16:12, Douglas N. Greve wrote:
Can you send the log file?
On 7/15/2020 1:51 PM, Knut J Bjuland wrote:
External Email - Use Caution
Dear freesurfer experts
I was able to run the same subects on the longitudinal stream
using FS 6 , but when I use FS7.1 I got this error
RROR: Number of filenames for --iscalein should agree with number
of init LTAs (--ixforms)!
ERROR:
@#@FSTIME 2020:07:15:18:43:31 longmc N 5 e 1.75 S 0.47 U 0.15 P
35% M 2444 F 88 R 26962 W 0 c 321 w 33906 I 19328 O 14 L 31.52
31.63 31.62
@#@FSLOADPOST 2020:07:15:18:43:33 longmc N 5 31.55 31.64 31.63
Linux c5-31 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 007_Run1.long.007_Run1_base exited with ERRORS at Wed
Jul 15 18:43:33 CEST 2020
Knut Jørgen Bjuland
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