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I re-ran bedpostx after binarizing the nodif_brain_mask.nii.gz. I've attached some screenshots of what the volumes look like (the "dti_" is not on the nifti volume). The commands.txt file is correctly populated with 80 calls to bedpostx_single_slice.sh, but it seems only some of the slices are reconstructed into the post-processed volumes. data.nii.gz - 112 x 112 x 80 nodif_brain_mask.nii.gz - 112 x 112 x 80 dyads1_dispersion.nii.gz : 112 x 112 x 48 dyads1.nii.gz : 112 x 112 x 48 dyads2_dispersion.nii.gz : 112 x 112 x 57 dyads2.nii.gz : 112 x 112 x 57 mean_dsamples.nii.gz : 112 x 112 x 66 mean_f1samples.nii.gz : 112 x 112 x 55 mean_f2samples.nii.gz : 112 x 112 x 63 mean_ph1samples.nii.gz : 112 x 112 x 52 mean_ph2samples.nii.gz : 112 x 112 x 61 mean_S0samples.nii.gz : 112 x 112 x 67 mean_th1samples.nii.gz : 112 x 112 x 48 mean_th2samples.nii.gz : 112 x 112 x 57 merged_f1samples.nii.gz : 112 x 112 x 55 merged_f2samples.nii.gz : 112 x 112 x 63 merged_ph1samples.nii.gz : 112 x 112 x 52 merged_ph2samples.nii.gz : 112 x 112 x 61 merged_th1samples.nii.gz : 112 x 112 x 48 merged_th2samples.nii.gz : 112 x 112 x 57 -- Keith Yoder PhD Candidate, Integrative Neuroscience Social Cognitive Neuroscience Laboratory The University of Chicago 5846 S. University Avenue, Kelly 312 Chicago, IL 60637 Phone: 574-215-9678 [log in to unmask] On Thu, Jul 26, 2012 at 5:52 PM, Stamatios Sotiropoulos <[log in to unmask] > wrote: > Keith, could you please rerun bedpostx with a binary mask? > > Cheers > Stam > > > > On 26 Jul 2012, at 23:12, Keith Yoder wrote: > > Thanks for the quick response. I'm CC'ing the FSL list because it looks > like bedpostx is not executing properly. > > The nodif_brain_mask looks good (I've attached a representative > screenshot). > > However, the bedpostx output is not the right size and does not seem to be > reconstructing the whole brain. The input image (data.nii.gz) is 112 x 112 > x 80, but the merged images are not. For instance, merged_f1samples.nii.gz > is only 112 x 112 x 48. When viewing the volumes, most of the inferior > slices are simply not there. The attached f1_missing_slices.png shows one > of these images. > > Also strange, the bedpostX directory still has the diff_slices folder, but > the folder only has data_slice_0016 through data_slice_0028. > > -Keith > -- > Keith Yoder > PhD Candidate, Integrative Neuroscience > Social Cognitive Neuroscience Laboratory > The University of Chicago > 5846 S. University Avenue, Kelly 312 > Chicago, IL 60637 > Phone: 574-215-9678 > [log in to unmask] > > > > On Thu, Jul 26, 2012 at 3:53 PM, Anastasia Yendiki < > [log in to unmask]> wrote: > >> >> Hi Keith - This seems to be a different problem here, since all the >> bedpostx outputs are there and are loaded in without a problem. The error >> occurs after that. What's the size of your images? Does the mask file look >> normal? >> >> Thanks, >> a.y >> >> >> On Thu, 26 Jul 2012, Keith Yoder wrote: >> >> Hi, >>> >>> Was there any resolution to this issue? I'm having a similar problem >>> running trac-all on a Linux cluster. >>> >>> I think bedpostx works if I call it directly from the command line >>> twice. >>> The first time, bedpostx_postproc.sh doesn't seem to work and the >>> *samples.nii.gz files are only created if I rerun bedpostx. However, >>> trac-all...-path fails. I've attached the trac-all-path output and >>> pasted >>> the relevant section below: >>> >>> Creating output directory/mnt/ide0/home/**kjyoder/research/conduct_** >>> disorder/fs/1001/dpath/lh.cst_**AS_av >>> g33_mni_flt >>> Loading DWIs from >>> /mnt/ide0/home/kjyoder/**research/conduct_disorder/fs/** >>> 1001/dmri/dwi.nii.gz >>> Loading mask from/mnt/ide0/home/kjyoder/**research/conduct_disorder/fs/* >>> *1001/dlabel/diff/aparc+ >>> aseg_mask.flt.nii.gz >>> Loading BEDPOST parameter samples from >>> /mnt/ide0/home/kjyoder/**research/conduct_disorder/fs/** >>> 1001/dmri.bedpostX >>> Loading segmentation map from/mnt/ide0/home/kjyoder/** >>> research/conduct_disorder/fs/**1001/dlabel/mni/aparc+a >>> seg.nii.gz >>> Loading b-values from >>> /mnt/ide0/home/kjyoder/**research/conduct_disorder/fs/**1001/dmri/bvals >>> Loading gradients from >>> /mnt/ide0/home/kjyoder/**research/conduct_disorder/fs/**1001/dmri/bvecs >>> Segmentation fault (core dumped) >>> >>> Here are the contents of the subjects bedpostX directory: >>> >>> bvals >>> bvecs >>> commands.txt >>> diff_slices >>> dyads1_dispersion.nii.gz >>> dyads1.nii.gz >>> dyads2_dispersion.nii.gz >>> dyads2.nii.gz >>> logs >>> mean_dsamples.nii.gz >>> mean_f1samples.nii.gz >>> mean_f2samples.nii.gz >>> mean_ph1samples.nii.gz >>> mean_ph2samples.nii.gz >>> mean_S0samples.nii.gz >>> mean_th1samples.nii.gz >>> mean_th2samples.nii.gz >>> merged_f1samples.nii.gz >>> merged_f2samples.nii.gz >>> merged_ph1samples.nii.gz >>> merged_ph2samples.nii.gz >>> merged_th1samples.nii.gz >>> merged_th2samples.nii.gz >>> monitor >>> nodif_brain_mask.nii.gz >>> xfms >>> >>> Also, I'm attaching the bvals, bvecs, dmrirc.local, trac-all.error, and >>> trac-all.log for the subject. Let me know if there is any other >>> information >>> you need. >>> >>> Thanks in advance, >>> Keith >>> -- >>> Keith YoderPhD Candidate, Integrative Neuroscience >>> >>> Social Cognitive Neuroscience Laboratory >>> The University of Chicago >>> 5846 S. University Avenue, Kelly 312 >>> Chicago, IL 60637 >>> Phone: 574-215-9678 >>> [log in to unmask] >>> >>> >>> >>> >>> On Fri, Oct 7, 2011 at 10:04 AM, Anastasia Yendiki >>> <[log in to unmask]> wrote: >>> >>> Hi Judit, >>> >>> 1. If you can run bedpostx directly then you should do: >>> bedpostx /usr/local/freesurfer/**subjects/C001/dmri >>> >>> Note that this dmri directory and the one you tried to run >>> bedpostx_single_slice.sh on are different, so I'm not sure which >>> location is the right one where your data is, but in any case >>> you don't need to run bedpostx_single_slice.sh. >>> >>> 2. The error seems to occur either when it's reading the bvecs >>> file, or right after that when it's accessing the bedpostx >>> outputs. So I'd try to look those for that subject and see if >>> everything is ok. >>> >>> Hope this helps, >>> a.y >>> >>> On Fri, 7 Oct 2011, Judit Haasz wrote: >>> >>> >>> Hi, >>> >>> I ran into 2 problems related to tracula. >>> >>> 1. trac-all -bedp command exits with following >>> message. >>> >>> WARN: Running FSL's bedbost locally - this might >>> take a while >>> >> > WARN: It is recommended to run this step on a >>> cluster >>> >> > bedpostx_seychelles >>> /usr/local/freesurfer/**subjects/C001/dmri >>> >> > subjectdir is >>> /usr/local/freesurfer/**subjects/C001/dmri >>> >> > Making bedpostx directory structure >>> >> > Queuing preprocessing stages >>> >> > [: 223: NONE: unexpected operator >>> >> > [: 314: NONE: unexpected operator >>> >> > [: 327: xbedpostx_pre: unexpected operator >>> >> > [: 486: x: unexpected operator >>> >> > [: 486: -le: argument expected >>> >> > Queuing parallel processing stage >>> >> > [: 223: NONE: unexpected operator >>> >> > [: 327: xbedpostx: unexpected operator >>> >> > [: 486: x53: unexpected operator >>> >> > 0 slices processed >>> >> > Queuing post processing stage >>> >> > [: 223: NONE: unexpected operator >>> >> > [: 314: NONE: unexpected operator >>> >> > [: 327: xbedpostx_post: unexpected operator >>> >> > [: 486: x: unexpected operator >>> >> > [: 486: -le: argument expected >>> >> > >>> >>> This problem has been posted in May and June. >>> bedpostx from command line >>> runs perfectly and that is how I have been running >>> it so far. One of u >>> suggested to try the following: >>> >>> /usr/local/fsl/bin/bedpostx_**single_slice.sh/disks/open/** >>> judit/subjects/diffu<http://bedpostx_single_slice.sh/disks/open/judit/subjects/diffu> >>> sion_tutorial/dtisubjects2005/**subj_523/dmri >>> 2 1 1000 1250 25 1 0 >>> >>> then I got: >>> >>> ** ERROR (nifti_image_read): failed to find header >>> filefor'/disks/open/judit/**subjects/diffusion_tutorial/** >>> dtisubjects2005/subj_523/ >>> dmr >>> i/data_slice_0000' >>> **ERROR:nifti_image_open(/**disks/open/judit/subjects/** >>> diffusion_tutorial/dtisub >>> jects2 >>> 005/subj_523/dmri/data_slice_**0000): bad header info >>> ERROR: failed to openfile/disks/open/judit/** >>> subjects/diffusion_tutorial/**dtisubjects2005/subj_523/ >>> dmri >>> /data_slice_0000 >>> ERROR: Could not openimage/disks/open/judit/** >>> subjects/diffusion_tutorial/**dtisubjects2005/subj_523 >>> /dmri >>> /data_slice_0000 >>> Image Exception : #22 :: Failed to >>> readvolume/disks/open/judit/**subjects/diffusion_tutorial/** >>> dtisubjects2005/subj_52 >>> 3/dmri >>> /data_slice_0000 >>> >>> An exception has been thrown >>> Failed to readvolume/disks/open/judit/** >>> subjects/diffusion_tutorial/**dtisubjects2005/subj_52 >>> 3/dmri >>> /data_slice_0000Trace: read_volume4DROI. >>> >>> Done >>> >>> Can u suggest a reason behind all this? This happens >>> on Linux machine >>> (2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM >>> Version: Java >>> 1.6.0_17-b04 with Sun Microsystems Inc. Java >>> HotSpot(TM) 64-Bit Server VM >>> mixed mode). >>> On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz >>> 6-core Intel Xeon >>> processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp >>> runs well. >>> >>> My other question is: >>> trac-all -path exists with error (in case of a >>> single subject): >>> >>> Loading DWIsfrom/disks/open/judit/** >>> subjects/diffusion_tutorial/**dtisubjects2005/subj_501/ >>> dmri >>> /dwi.nii.gz >>> Loading maskfrom/disks/open/judit/** >>> subjects/diffusion_tutorial/**dtisubjects2005/subj_501/ >>> dlab >>> el/diff/aparc+aseg_mask.bbr.**nii.gz >>> Loading BEDPOST parameter samplesfrom/disks/open/judit/** >>> subjects/diffusion_tutorial/**dtisubjects2005/subj_501/ >>> dmri >>> .bedpostX >>> Loading segmentation mapfrom/disks/open/judit/** >>> subjects/diffusion_tutorial/**dtisubjects2005/subj_501/ >>> dlab >>> el/mni/aparc+aseg.nii.gz >>> Loading b-valuesfrom/disks/open/judit/** >>> subjects/diffusion_tutorial/**dtisubjects2005/subj_501/ >>> dmri >>> /bvals >>> Loading gradientsfrom/disks/open/**judit/subjects/diffusion_ >>> **tutorial/dtisubjects2005/subj_**501/ >>> dmri >>> /bvecs >>> Segmentation fault >>> Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar >>> 18 18:42:20 UTC 2011 >>> x86_64 GNU/Linux >>> >>> trac-paths exited with ERRORS at Fri Oct 7 10:21:20 >>> CEST 2011 >>> >>> thanks for help. >>> Judit >>> >>> >>> >>> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> [log in to unmask] >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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 mailing list >> [log in to unmask] >> 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. >> >> > <nodif_brain_mask.png><f1_missing_slices.png> > > >