Hi Bruce,
Were you able to take a look at the error we discussed previously?
We are very concerned about this problem, because our study depends on the preprocessing of these images. The previous e-mail with logs from the error is copied below. Any help would be very much appreciated.
Thanks in advance and kind regards, Anna Garcia
The recon-all.log file from the tailaraich processes on reads as follows:
#@# Talairach Tue Sep 22 13:07:35 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri
talairach --i orig.mgz --xfm transforms/talairach.auto.xfm
/psiquiatria/home/anna/subjects/prova/mri /psiquiatria/software/freesurfer/bin/talairach --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux Tue Sep 22 13:07:36 CEST 2015 tmpdir is transforms/tmp.talairach.22322 /psiquiatria/home/anna/subjects/prova/mri mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc input_transform(): error reading transform elem [1,1] input_transform: error reading transform. error loading transform from /psiquiatria/home/anna/subjects/prova/mri/transforms/talairach.xfm $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.40604e-09, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (-6.90488e-09, 1, 4.65661e-10) writing to transforms/tmp.talairach.22322/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /psiquiatria/software/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.22322/src.mnc transforms/talairach.auto.xfm
Tue Sep 22 13:08:01 CEST 2015 talairach done
INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Tue Sep 22 13:08:02 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ltMNIreadEx: could not read row 1 from transforms/talairach.xfm (Linear_Transform = ) ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s prova exited with ERRORS at Tue Sep 22 13:08:04 CEST 2015
For more details, see the log file /psiquiatria/home/anna/subjects/prova/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Also, a recon-all.error file was created, and says the following:
SUBJECT prova DATE Mon Sep 28 18:56:32 CEST 2015 USER anna HOST blade07 PROCESSOR x86_64 OS Linux Linux blade07 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ /psiquiatria/software/freesurfer/bin/recon-all PWD /psiquiatria/home/anna/subjects/prova/mri CMD mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
(The same exact recon-all.error file appears when using the -notal-check flag)
Kind regards, Anna Garcia
On Wed, Oct 28, 2015 at 2:36 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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Today's Topics:
- mri_parse_sdcmdir splitting a single series into two? (Oliver Hinds)
- Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study (Don Hagler)
- Re: FreeSurfer pve correction tool (Mohamed Ali Bahri)
- Re: A mixed effect model approach in within subject dataset {Disarmed} (Martin Reuter)
- Re: FreeSurfer pve correction tool (Douglas N Greve)
- Understanding the brainstem AtlasMesh file structure format (Jonathan Plasencia)
- Re: comparison of 4 groups: mri_glmfit or Qdec? (Sandy Schramm)
- Re: Talairach_afd error (Bruce Fischl) (Bruce Fischl)
- error finding Matlab (Jason Haberman)
Message: 1 Date: Tue, 27 Oct 2015 15:14:25 -0400 (EDT) From: Oliver Hinds ohinds@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_parse_sdcmdir splitting a single series into two? To: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1510271455210.6558@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset=US-ASCII
Hi,
I'm running into an issue where the slices from one DICOM series are being parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate series.
A few example lines from a scan.out:
6 AR_t.s40.c0 ok 64 64 41 1 <long file name> 7 AR_t.s40.c0 ok 64 64 23 1 <different long file name>
The scan AR_t.s40.c0 was run as a single series on the scanner, with 64 slices. Inspection of the dicom header shows that the series UID is the same for the DICOM files in each, except there is an extra string '.0.0.0' at the end of series UID in the DICOMS that are parsed into the second series.
Has anyone else experienced this behavior? If so, is there a workaround?
Thanks, Oliver
Message: 2 Date: Tue, 27 Oct 2015 13:41:36 -0700 From: Don Hagler dhaglerjr@hotmail.com Subject: [Freesurfer] Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study To: freesurfer@nmr.mgh.harvard.edu Message-ID: BLU436-SMTP65024FB31221FBD3A8E848A6220@phx.gbl Content-Type: text/plain; charset="us-ascii"
Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study
University of California, San Diego
Several funded postdoctoral positions are available in image analysis method development, including automated cortical- and subcortical segmentation, advanced diffusion tractography, and fMRI mapping and time series analysis. We are looking to build a team to help build the next generation of analysis pipelines and visualization tools for a newly funded study to follow 10,000 children with longitudinal structural and functional imaging across 19 sites across the US. The study will use a cross-platform Harmonized Human Connectome Protocol, optimized for quantitative accuracy and consistency of imaging biomarkers across scanners and time. To learn more about the ABCD study, please see http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-land... < http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-land...
.
Requirements: Applicants should have research experience in any of the above fields, with a Ph.D. or equivalent degree. They should be comfortable working in a distributed team environment, and should have a track record of quality scientific publications. Candidates are expected to be experienced in programming with Matlab, Python, and/or <> C/C++. Experience with FreeSurfer, FSL, and the Human Connectome analysis pipelines is strongly preferred.
To formally apply, submit a current CV, a personal statement describing your research experience and interests, and contact information for 2-3 references to abcd@ucsd.edu mailto:abcd@ucsd.edu. Or feel free to email Dr. Donald Hagler (dhagler@ucsd.edu mailto:dhagler@ucsd.edu) or Anders M. Dale (amdale@ucsd.edu mailto:amdale@ucsd.edu) for more information.
The University of California, San Diego is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy.
Hi Anna,
I'm going to be looking into this for you and trying to help troubleshoot. I'm not sure if you saw Bruce's reply, since this thread is a little split up, but it said:
"Hi Anna
this error is puzzling:
mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc input_transform(): error reading transform elem [1,1] input_transform: error reading transform. error loading transform from /psiquiatria/home/anna/subjects/prova/mri/transforms/talairach.xfm
are you sure you have write access and the disk isn't full? That .xfm file is a very small text file. You should be able to cat it and take a look, but something basic must be wrong if it is not being written. Can you check a bit further up in the log and see what it says when it is writing this file?
cheers Bruce "
Could you check these things for me and let me know?
Thank you, Ani
On 11/27/2015 04:36 AM, Anna I. Garcia Diaz wrote:
Hi Bruce,
Were you able to take a look at the error we discussed previously?
We are very concerned about this problem, because our study depends on the preprocessing of these images. The previous e-mail with logs from the error is copied below. Any help would be very much appreciated.
Thanks in advance and kind regards, Anna Garcia
The recon-all.log file from the tailaraich processes on reads as follows:
#@# Talairach Tue Sep 22 13:07:35 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri
talairach --i orig.mgz --xfm transforms/talairach.auto.xfm
/psiquiatria/home/anna/subjects/prova/mri /psiquiatria/software/freesurfer/bin/talairach --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux Tue Sep 22 13:07:36 CEST 2015 tmpdir is transforms/tmp.talairach.22322 /psiquiatria/home/anna/subjects/prova/mri mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc input_transform(): error reading transform elem [1,1] input_transform: error reading transform. error loading transform from /psiquiatria/home/anna/subjects/prova/mri/transforms/talairach.xfm $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.40604e-09, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (-6.90488e-09, 1, 4.65661e-10) writing to transforms/tmp.talairach.22322/src.mnc...
mritotal -verbose -debug -clobber -modeldir /psiquiatria/software/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.22322/src.mnc transforms/talairach.auto.xfm Tue Sep 22 13:08:01 CEST 2015 talairach done
INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Tue Sep 22 13:08:02 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ltMNIreadEx: could not read row 1 from transforms/talairach.xfm (Linear_Transform = ) ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s prova exited with ERRORS at Tue Sep 22 13:08:04 CEST 2015
For more details, see the log file /psiquiatria/home/anna/subjects/prova/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Also, a recon-all.error file was created, and says the following:
SUBJECT prova DATE Mon Sep 28 18:56:32 CEST 2015 USER anna HOST blade07 PROCESSOR x86_64 OS Linux Linux blade07 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ /psiquiatria/software/freesurfer/bin/recon-all PWD /psiquiatria/home/anna/subjects/prova/mri CMD mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
(The same exact recon-all.error file appears when using the -notal-check flag)
Kind regards, Anna Garcia
On Wed, Oct 28, 2015 at 2:36 PM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. mri_parse_sdcmdir splitting a single series into two? (Oliver Hinds) 2. Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study (Don Hagler) 3. Re: FreeSurfer pve correction tool (Mohamed Ali Bahri) 4. Re: A mixed effect model approach in within subject dataset {Disarmed} (Martin Reuter) 5. Re: FreeSurfer pve correction tool (Douglas N Greve) 6. Understanding the brainstem AtlasMesh file structure format (Jonathan Plasencia) 7. Re: comparison of 4 groups: mri_glmfit or Qdec? (Sandy Schramm) 8. Re: Talairach_afd error (Bruce Fischl) (Bruce Fischl) 9. error finding Matlab (Jason Haberman) ---------------------------------------------------------------------- Message: 1 Date: Tue, 27 Oct 2015 15:14:25 -0400 (EDT) From: Oliver Hinds <ohinds@nmr.mgh.harvard.edu <mailto:ohinds@nmr.mgh.harvard.edu>> Subject: [Freesurfer] mri_parse_sdcmdir splitting a single series into two? To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1510271455210.6558@gate.nmr.mgh.harvard.edu <mailto:alpine.LRH.2.20.1510271455210.6558@gate.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=US-ASCII Hi, I'm running into an issue where the slices from one DICOM series are being parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate series. A few example lines from a scan.out: 6 AR_t.s40.c0 ok 64 64 41 1 <long file name> 7 AR_t.s40.c0 ok 64 64 23 1 <different long file name> The scan AR_t.s40.c0 was run as a single series on the scanner, with 64 slices. Inspection of the dicom header shows that the series UID is the same for the DICOM files in each, except there is an extra string '.0.0.0' at the end of series UID in the DICOMS that are parsed into the second series. Has anyone else experienced this behavior? If so, is there a workaround? Thanks, Oliver ------------------------------ Message: 2 Date: Tue, 27 Oct 2015 13:41:36 -0700 From: Don Hagler <dhaglerjr@hotmail.com <mailto:dhaglerjr@hotmail.com>> Subject: [Freesurfer] Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <BLU436-SMTP65024FB31221FBD3A8E848A6220@phx.gbl> Content-Type: text/plain; charset="us-ascii" Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study University of California, San Diego Several funded postdoctoral positions are available in image analysis method development, including automated cortical- and subcortical segmentation, advanced diffusion tractography, and fMRI mapping and time series analysis. We are looking to build a team to help build the next generation of analysis pipelines and visualization tools for a newly funded study to follow 10,000 children with longitudinal structural and functional imaging across 19 sites across the US. The study will use a cross-platform Harmonized Human Connectome Protocol, optimized for quantitative accuracy and consistency of imaging biomarkers across scanners and time. To learn more about the ABCD study, please see http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-landmark-study-substance-use-adolescent-brain-development <http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-landmark-study-substance-use-adolescent-brain-development>. Requirements: Applicants should have research experience in any of the above fields, with a Ph.D. or equivalent degree. They should be comfortable working in a distributed team environment, and should have a track record of quality scientific publications. Candidates are expected to be experienced in programming with Matlab, Python, and/or <> C/C++. Experience with FreeSurfer, FSL, and the Human Connectome analysis pipelines is strongly preferred. To formally apply, submit a current CV, a personal statement describing your research experience and interests, and contact information for 2-3 references to abcd@ucsd.edu <mailto:abcd@ucsd.edu> <mailto:abcd@ucsd.edu <mailto:abcd@ucsd.edu>>. Or feel free to email Dr. Donald Hagler (dhagler@ucsd.edu <mailto:dhagler@ucsd.edu> <mailto:dhagler@ucsd.edu <mailto:dhagler@ucsd.edu>>) or Anders M. Dale (amdale@ucsd.edu <mailto:amdale@ucsd.edu> <mailto:amdale@ucsd.edu <mailto:amdale@ucsd.edu>>) for more information. The University of California, San Diego is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy.
freesurfer@nmr.mgh.harvard.edu
-
Ani Varjabedian -
Anna I. Garcia Diaz