Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

Call for Nominations – OHBM Student and Postdoc Special Interest Group
by Heidi Emmanuel Foo 22 Aug '19

22 Aug '19

External Email - Use Caution Dear All, The OHBM Student and Postdoc Special Interest Group (SIG) is seeking nominations for open seats on the 2019-2020 SIG Committee. The SIG provides a community of shared interests for OHBM trainees. The Committee aims to provide professional, personal and career development for OHBM trainees as well as social and mentoring opportunities at the Annual Meeting. Committee members benefit from being an integral part of the SIG community, directing its activities, and working with the OHBM Executive Office and wider community. We are committed to diversity and equality and are seeking representation from trainees across the world. Eligibility • Nominees must be current students or postdocs. Students are defined as those working full time towards a graduate degree - M.A., M.S., Ph.D. or M.D. degree. Postdocs are individuals who are no more than four years after completing such a degree at the time of the next Annual Meeting. • Nominees must be members of OHBM in good standing at the time of the next Annual Meeting. • Nominees must be attendance at the next two Annual Meetings in Montreal 2020 and Seoul 2021, and be likely to attend the meeting in 2022, and preferably have secured funding to support conference travel. To nominate yourself for election to the SIG Committee please complete this nomination form and attach your CV: https://docs.google.com/forms/d/e/1FAIpQLSeJRKKLi8FmcKdjw3PbT7BLjQyZ3ZmU4yr… no later than September 9th, 2019. Visit our website (https://www.ohbmtrainees.com/terms-of-reference) or email ohbmtrainees(a)gmail.com if you have any questions. Nominations close on the 9th September, 2019. Kind Regards, OHBM Student and Postdoc SIG

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mris_convert segmentation fault on R hemisphere aparc.a2009s only?
by Damion V Demeter 22 Aug '19

22 Aug '19

External Email - Use Caution Hi Bruce, My apologizes, I just saw this reply because I didn't realize I had the list on digest mode. I would very much appreciate your help! How/where should I upload the files? Thank you! Damion Hi Damion if you upload the relevant files so that we can replicate this we will fix it cheers Bruce On Wed, 14 Aug 2019, Damion V Demeter wrote: > >* External Email - Use Caution *> >* I am having an issue processing some of my subjects through the HCP pipeline *>* and have no idea what this error means. If anyone could help out, I'd *>* appreciate it! Here is all the info: *> >* 1. Some (not all) of my subjects are getting a segmentation fault error *>* during the post-freesurfer step of the HCP pipeline. Previous subjects were *>* fully processed fine without error (over 100 of them) and are from the same *>* group (all scanner and acquisition settings identical). Here is the *>* segmentation fault error line: *> >* FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 294: 46979 Segmentation *>* fault mris_convert --annot *>* "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot *>* "$FreeSurferFolder"/surf/"$hemisphere"h.white"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native. *>* label.gii *> >* 2. I have narrowed down this error further and have found that it only *>* happens on the right hemisphere aparc.a2009s file. I have manually run the *>* command above for the left and right hemisphere files separately as a test, *>* and the L hemisphere files complete without fail. The R hemisphere, however, *>* always gets this segmentation fault. *> >* This only occurs on certain subjects, but all the files this command is *>* using look good and error free. All previous steps appeared to finish *>* without fail and all expected files were written and can be opened (I'm 99% *>* sure...I might have missed something). I am at a complete loss at how to *>* troubleshoot this further or fix this error. Does anyone have any ideas or *>* solutions? *> >* Thank you! *> > ----- Damion Demeter, MA Doctoral Student UT Austin | Cognitive Neuroscience DCN Lab <https://labs.la.utexas.edu/church-lang/>

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FreeSurfer development version masks
by Hurtado, Aura Maria 22 Aug '19

22 Aug '19

Hello, I am trying to freeze the development freesurfer version for today and I am denied access to copy the following files: /usr/local/freesurfer/dev.backup/average/mult-comp-cor/fsaverage/rh/cortex/mask.mgh /usr/local/freesurfer/dev.backup/average/mult-comp-cor/fsaverage/lh/cortex/mask.mgh /usr/local/freesurfer/dev.backup/subjects/fsaverage6 /usr/local/freesurfer/dev.backup/subjects/fsaverage/scripts/fix-surf7.log /usr/local/freesurfer/dev.backup/subjects/fsaverage3 /usr/local/freesurfer/dev.backup/subjects/fsaverage_sym/scripts/fix-surf7.log /usr/local/freesurfer/dev.backup/subjects/fsaverage4 Are they instrumental? Are they the same as stable6? How can I have access to these? (I am in the Martinos cluster) Thank you, Aura M.

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ERROR reading /<my data path>/fsaverage/label/lh.BA1_exvivo.label
by liuxingze1993 21 Aug '19

21 Aug '19

External Email - Use Caution Hello，Dear FreeSurfer Developers, I’m a doctoral student from Xiangya 2nd Hospital of Central South University, and also a beginner to FreeSurfer. I'm attempting to follow the steps descripted on ‘Practice Working with Data’ (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our own data, but I’ve met the same problem several times when I programing the command ‘recon-all -all -i 61492283 -s Sub219’: (**ps: 61492283 is the T1 file I found after programing the command 'dcmunpack -src . -scanonly.log') SUBJECTS_DIR /media/dell/AA32E/Data_prac/219/20181211/19470000 (**PS: 19470000 is the folder where the T1 located) FREESURFER_HOME /usr/local/freesurfer Loading source label Invalid argument ERROR reading /media/dell/AA32E/Data_prac/219/20181211/19470000/fsaverage/label/lh.BA1_exvivo.label recon-all -s Sub219 exited with ERRORS at <local time here> I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such file here. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu14.04 LTS 3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank u for viewing, and I will be waiting here for your professional advice !

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mris_pmake on the inflated surface
by Lee, Jeungchan 21 Aug '19

21 Aug '19

Hi, I’m trying to calculate Dijkstra distance between startVertex and endVertex on the inflated surface (fsaverage, lh.inflated) using mris_pmake. I see several options: --surface0, --surface1, --curv0, --curv1 I think I can use ‘--surface0 inflated’, but not sure about other options e.g., --surface1, --curv0, and --curv1. I read the instruction (curv0 for curvature, curv1 for height parameter…) but was not able to understand what those mean exactly and what to use. Would you explain what the meaning is and what to use? Here is the command line that I have: Mris_pmake --subject fsaverage --hemi lh --surface0 inflated --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs `more ./input_D.txt` (where input_D.txt says startVertex:8762,endVertex:1, for example) Thanks in advance, jeungchan

2 1

Hippocampal mask from the subfields masks
by Ole Johan Evjenth Sørhaug 21 Aug '19

21 Aug '19

External Email - Use Caution Dear freesurfer experts, I wish to use the subfield segmentations from the 6.0 version of freesurfer to have a segmentation of the whole hippocampus. As far as I have understood, a segmentation of the whole hippocampus is not provided by default by the subfields module. Would the correct way to obtain this be by using the command mri_mergelabels on the subfield segmentations, then use mri_label2vol to create an mgz volume of the whole hippocampus? Regards Ole Johan Evjenth Sørhaug

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Re-running lGI flag
by Avi Gharehgazlou 20 Aug '19

20 Aug '19

External Email - Use Caution Hi, I have a very quick question... I've ran the lGI flag (-localGI) on my participants. However, I've then performed manual edits (i.e. control points, etc) on some participants and re-ran recon-all and lGI flag after my edits.. To be sure, I want to re-run the lGI flag (-localGI) on all my participants again before performing statistical analysis (because I've been working on this data for a while now and want to make sure I have ran the lGI flag on all edited and final cortices before stats and that I haven't missed anyone by accident). I wanted to ask if this would be okay? I mean, would it be okay to run lGI for a brain that I may have already ran the lGI flag on? Or do I have to delete anything before doing so? I would really appreciate your reply, Thank you so much, Avi

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mris_label2annot gives wrong label
by Rachel S 20 Aug '19

20 Aug '19

External Email - Use Caution Hi Freesurfer community, I was trying to use mris_label2annot to generate annotation file, my commands are: mris_label2annot --s p6 --h rh --a t500 --ldir $SUBJECTS_DIR/p6/label/regenerated_rh_500 --nhits nhits.mgh --ctab /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt --l $SUBJECTS_DIR/p6/label/regenerated_rh_500/rh.pericalcarine_7.label --surf pial The output of the command is: Reading ctab /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt Number of ctab entries 1016 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/rachelsun/Software/freesurfer/subjects/fsaverage5/mri cmdline mris_label2annot --s p6 --h rh --a t500 --ldir /home/rachelsun/Software/freesurfer/subjects/p6/label/regenerated_rh_500 --nhits nhits.mgh --ctab /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt --l /home/rachelsun/Software/freesurfer/subjects/p6/label/regenerated_rh_500/rh.pericalcarine_7.label --surf pial sysname Linux hostname rachel-pc machine x86_64 user rachelsun subject p6 hemi rh SUBJECTS_DIR /home/rachelsun/Software/freesurfer/subjects ColorTable /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt AnnotName t500 NHitsFile nhits.mgh nlables 1 LabelThresh 0 0.000000 Loading /home/rachelsun/Software/freesurfer/subjects/p6/surf/rh.pial 1 107939 rh.lateralorbitofrontal_9 Mapping unhit to unknown Found 123130 unhit vertices Writing annot to /home/rachelsun/Software/freesurfer/subjects/p6/label/rh.t500.annot I am sure I have rh.pericalcarine_7 in the folder, but the code always generates rh.lateralorbitofrontal_9 region. And I also attached my colortable file for your reference. Thank you for your help. Best regards, Rachel

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BIDS Steering Group nominations
by Franklin Feingold 19 Aug '19

19 Aug '19

External Email - Use Caution Hi FreeSurfer! We are announcing the nomination period for our fellow colleagues (or self-nomination) to the BIDS Steering Group! The BIDS Steering Group is proposed within our governance document<https://docs.google.com/document/d/1R-J2lL9V_wIkYhye4zH-feyl4P4J8NyO40rIYyY…>. This group is charged with preserving the longevity and sustainability of the BIDS standard. This will be a 5 person group that represents different modalities and perspectives. To nominate please fill out this form<https://forms.gle/scwDrFJHTiddyVMG6>. We will be running the nominations until August 28 at 11:59pm PST. Thank you! Franklin

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mri_robust_template in FMRIprep rotation should not scale error
by Dylan Nielson 19 Aug '19

19 Aug '19

External Email - Use Caution Hi Freesurfer folks, I'm running Freesurfer's longitudinal pipeline as part of FMRIprep and I've got two subjects generating similar errors in the mri_robust_template step, one of which I've copied below. I've defaced these subjects and saved the working directories so I can share them with you on the ftp site if you'd like. Thanks for your help, Dylan Nielson Error for subject 22477: RuntimeError: Command: mri_robust_template --satit --mov /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz --inittp 1 --iscale --template sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_template.nii.gz --subsample 200 --lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta Standard output: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --satit: Will estimate SAT iteratively! --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz as movable/source volume. Total: 4 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --template: Using sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_template.nii.gz as template output volume. --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'... converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'... converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'... converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz'... converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) to TP 1 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) [init] ========================= TP 4 to TP 1 ============================== Register TP 4 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz ) to TP 1 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) to TP 1 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) - Max Resolution used: 2 -- gpS ( 51 , 64 , 64 ) -- gpT ( 51 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 51 , 64 , 64 ) -- gpT ( 51 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 51 , 64 , 64 ) -- gpT ( 51 , 64 , 64 ) - running loop to estimate saturation parameter: * WARNING: TP 2 to 1 did not converge !! * WARNING: TP 3 to 1 did not converge !! * WARNING: TP 4 to 1 did not converge !! Input rotation's max deviation from rotation is: 6.17523e-05 computing mean coord of TP 1 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) mapping back to rot, err = 1.92296e-16 computing mean coord of TP 2 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) mapping back to rot, err = 5.2975e-15 computing mean coord of TP 3 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) mapping back to rot, err = 7.55033e-16 computing mean coord of TP 4 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz ) Standard error:Internal Error for tp 3 -> template Rotation should not scale ( 3.08776e-05 ) Debug Info: A = [ ... 0.9969922338242 -0.0778269037878 0.0033377292333 0.0777901549173 0.9969203604879 0.0099370478686 -0.0041009199390 -0.0096472102695 0.9999450558122 ] R = [ ... 0.9969614041457 -0.0778255626866 0.0033377292333 0.0777890868352 0.9969203142925 0.0099370478686 -0.0041008064181 -0.0096472142869 0.9999450558122 ] S = [ ... 1.0000308195503 -0.0000013334491 -0.0000000000000 -0.0000013334491 1.0000001503863 0.0000000000000 -0.0000000000000 0.0000000000000 1.0000000000000 ] Internal Error: Rotation should not scale. Return code: 248 Error for subject 24028: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 265, in run return super(FSCommandOpenMP, self).run(**inputs) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run return super(FSCommand, self).run(**inputs) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: mri_robust_template --satit --mov /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz --inittp 1 --iscale --template sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_template.nii.gz --subsample 200 --lta /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta Standard output: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --satit: Will estimate SAT iteratively! --mov: Using /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz as movable/source volume. --mov: Using /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz as movable/source volume. Total: 2 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --template: Using sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_template.nii.gz as template output volume. --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz'... converting source '/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz'... converting source '/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz ) to TP 1 ( /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz ) - Max Resolution used: 2 -- gpS ( 43 , 64 , 64 ) -- gpT ( 43 , 64 , 64 ) - running loop to estimate saturation parameter: * WARNING: TP 2 to 1 did not converge !! Input rotation's max deviation from rotation is: 4.27526e-05 computing mean coord of TP 1 ( /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz ) mapping back to rot, err = 0 computing mean coord of TP 2 ( /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz ) Standard error:Internal Error for tp 1 -> template Rotation should not scale ( 2.13756e-05 ) Debug Info: A = [ ... 0.9976866765353 0.0613358758176 0.0285823594087 -0.0624208989520 0.9972963115456 0.0387788304011 -0.0261239538328 -0.0404768298397 0.9988387368875 ] R = [ ... 0.9977078546957 0.0613362673314 0.0285814448261 -0.0624218986995 0.9972961437200 0.0387802563678 -0.0261255285353 -0.0404754744389 0.9988389223132 ] S = [ ... 0.9999787668370 -0.0000003656818 0.0000010063421 -0.0000003656818 1.0000001982183 -0.0000013585088 0.0000010063421 -0.0000013585088 0.9999997856304 ] Internal Error: Rotation should not scale. Return code: 248

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