Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
External Email - Use Caution
Thanks
I found a new bug,
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz error: No such file or directory error: MRIvoxelToTalairachVoxel: unsupported slice direction 2^@
Knut Jørgen Bjuland
On 21/07/2020 16:27, Douglas N. Greve wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I could not reproduce that bug, but I did find another one. I created a new version longmc in the same location. I used it yesterday and it ran all the way through, so please git it a try
On 7/22/2020 2:28 PM, Knut J Bjuland wrote:
External Email - Use Caution
Thanks
I found a new bug,
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz error: No such file or directory error: MRIvoxelToTalairachVoxel: unsupported slice direction 2^@
Knut Jørgen Bjuland
On 21/07/2020 16:27, Douglas N. Greve wrote:
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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Knut J Bjuland