NeuroStars News

ICA AROMA agg vs non-agg

David Kennedy — Mon, 11 Mar 2019 8:01:08 GMT

I just want to clarify something. If we’re using the aggressive denoising strategy on the _desc-preproc_bold.nii.gz data, do we also need to include the motion parameters (trans_x trans_y trans_z rot_x rot_y rot_z) in our nuisance regression, or will they already be regressed out by the ICA-AROMA confounds?

I realize that we would want to include these motion parameters in a nuisance regression if we were just using the _desc-preproc_bold.nii.gz data without ICA-AROMA denoising; however, does it make sense to include them with _desc-preproc_bold.nii.gz + aggressive ICA-AROMA confounds, (or even for analyzing the non-aggressive smoothAROMAnonaggr_bold.nii.gz data?).

Thanks for the clarification.

Dmriprep: an fmriprep for diffusion?

David Kennedy — Mon, 11 Mar 2019 7:16:24 GMT

I’m also working on a pipeline for diffusion image processing https://github.com/pennbbl/qsiprep and across-software reconstruction. The preprocessing part is mostly done and the reconstruction part is coming along.

BIDS - b0 correction for DWI

David Kennedy — Mon, 11 Mar 2019 7:10:57 GMT

Dear all,

We acquired a b0 with a reverse phase encoding direction to be used to correct DWI (topup). I would like to know where to put such images in the BIDS format. Should it go to the dwi folder or fmap folder ?

Thank you in advance

Arnaud

GSoC Project Idea 7: Implementing automatic white matter parcellation in Nighres

David Kennedy — Mon, 11 Mar 2019 6:57:22 GMT

Hello @piloubazin. I’m interested in working on the topic ‘’ as a part of GSoC 2019. I’m currently pursuing a Master’s degree in Computer Science and have worked extensively on MR images and machine learning. In order to proceed working on this topic, I’ve started going through the paper mentioned above. Regarding the same, I would like to know whether there are any already preprocessed images available that I can use? If not then I would proceed with the preprocessing steps mentioned in the paper.

GSoC Project Idea 14: Producing publication-ready brain network analysis results and visualisations from the command line

David Kennedy — Mon, 11 Mar 2019 6:09:30 GMT

Hi @KirstieJane . I’m interested to work on this topic as part of the GSoC 2019. I’ve worked on nilearn, matplotlib and networkx. Currently, I’m working on structural connectivity analysis of normal and diseased brains using complex networks and machine learning. In order to start with this topic, I was thinking of using scona and networkx to generate a connectivity matrix. Could you please let me know whether this would be a good way to get started on this topic? If this is not a good idea then could you please suggest some tasks for the same?

Video Data of Subjects in BIDS

David Kennedy — Mon, 11 Mar 2019 4:16:08 GMT

So, to be clear, we have video data of every run for each of our subjects. There is a part of the standard, at least as originally published in Nature, that seems to suggest that it is permissible to place non-BIDS-compliant data in the standard directories wherever common sense would suggest it would go, and hope a standard will come out some day. Is that correct? "For example one may want to include eye tracking data in a vendor specific format that is not covered by this standard. The most sensible place to put it is next to the continuous recording file with the same naming scheme but different extensions. "

Freesurfer error FOV > 256

David Kennedy — Mon, 11 Mar 2019 4:11:09 GMT

Hi, Chris,

I also encountered similar problem with my own data when using recon function (with --fs-no-reconall, I could finish the preprocessing)

Here is the log from recon-all.log:

Mon Mar 11 00:13:28 UTC 2019

/out/out/freesurfer/sub-001

/opt/freesurfer/bin/recon-all

-autorecon1 -i /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz -noskullstrip -cw256 -hires -openmp 7 -subjid sub-001 -sd /out/out/freesurfer -expert /work/fmriprep_wf/single_subject_001_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts

subjid sub-001

setenv SUBJECTS_DIR /out/out/freesurfer

FREESURFER_HOME /opt/freesurfer

Actual FREESURFER_HOME /opt/freesurfer

build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

Linux 3e5932778b80 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

cputime unlimited

filesize unlimited

datasize unlimited

stacksize 8192 kbytes

coredumpsize unlimited

memoryuse unlimited

vmemoryuse unlimited

descriptors 1048576

memorylocked 16384 kbytes

maxproc unlimited

maxlocks unlimited

maxsignal 63302

maxmessage 819200

maxnice 0

maxrtprio 0

maxrttime unlimited
          total        used        free      shared  buff/cache   available
Mem: 16284864 4278568 2888448 294604 9117848 11211380

Swap: 7812092 456192 7355900

########################################

program versions used

$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $

$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $

mri_convert.bin -all-info

ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

FLIRT version 5.5

$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $

mri_convert.bin --version

stable6

ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

Program nu_correct, built from:

Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34

ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400

#######################################

GCADIR /opt/freesurfer/average

GCA RB_all_2016-05-10.vc700.gca

GCASkull RB_all_withskull_2016-05-10.vc700.gca

AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif

GCSDIR /opt/freesurfer/average

GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs

#######################################

-cw256 option is now persistent (remove with -clean-cw256)

/out/out/freesurfer/sub-001

mri_convert /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz /out/out/freesurfer/sub-001/mri/orig/001.mgz

mri_convert.bin /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz /out/out/freesurfer/sub-001/mri/orig/001.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz…

TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (1, 1.94477e-16, -1.10357e-16)

j_ras = (-2e-16, 0.998622, -0.0524728)

k_ras = (1e-16, 0.0524728, 0.998622)

writing to /out/out/freesurfer/sub-001/mri/orig/001.mgz…

#--------------------------------------------

#@# MotionCor Mon Mar 11 00:13:41 UTC 2019

Found 1 runs

/out/out/freesurfer/sub-001/mri/orig/001.mgz

Checking for (invalid) multi-frame inputs…

WARNING: only one run found. This is OK, but motion

correction cannot be performed on one run, so I’ll

copy the run to rawavg and continue.

cp /out/out/freesurfer/sub-001/mri/orig/001.mgz /out/out/freesurfer/sub-001/mri/rawavg.mgz

/out/out/freesurfer/sub-001

mri_convert /out/out/freesurfer/sub-001/mri/rawavg.mgz /out/out/freesurfer/sub-001/mri/orig.mgz --conform_min

mri_convert.bin /out/out/freesurfer/sub-001/mri/rawavg.mgz /out/out/freesurfer/sub-001/mri/orig.mgz --conform_min

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /out/out/freesurfer/sub-001/mri/rawavg.mgz…

TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (1, 1.94477e-16, -1.10357e-16)

j_ras = (-2e-16, 0.998622, -0.0524728)

k_ras = (1e-16, 0.0524728, 0.998622)

changing data type from float to uchar (noscale = 0)…

MRIchangeType: Building histogram

Reslicing using trilinear interpolation

writing to /out/out/freesurfer/sub-001/mri/orig.mgz…

ERROR! FOV=259.201 > 256

Include the flag -cw256 with recon-all!

Inspect orig.mgz to ensure the head is fully visible.

Linux 3e5932778b80 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-001 exited with ERRORS at Mon Mar 11 00:13:54 UTC 2019

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Siemens "Invert RO/PE polarity" detected by dcm2nii?

David Kennedy — Mon, 11 Mar 2019 4:05:33 GMT

Don’t know the details about how dcm2niix accesses the information, but we use the “Invert RO/PE Polarity”-option in the CMRR sequences for our spin echo fieldmaps (Siemens Prisma). And dcm2niix detects this, that is, PhaseEncodingDirection comes out correctly in the associated .json.

Siemens "Invert RO/PE polarity" detected by dcm2nii?

David Kennedy — Mon, 11 Mar 2019 2:27:33 GMT

Many thanks for looking into the documentation and code base, @rwblair. I am reassured that this is not something so obvious that I should have known about it already, and I will keep an eye out for it in our sequences going forward.

GSoC Project Idea 6.2: Improve accessibility and interactivity for datasets in CATMAID

David Kennedy — Mon, 11 Mar 2019 1:50:13 GMT

I might be able to help…how can I begin? I’ve the skillset which is required for this project