Dear Anastasia and Team FreeSurfer, First of all thanks so much for developing TRACULA. I think it has a lot of potential! Here is my question: I'm trying to modify "dmrirc_single_subject" file in order to reflect our local sequence and wondered how you are dealing with DTI repeat sequences for the same subject. We acquire 5 B0s and 30 directional scans twice in a row. So our *Diffusion bvalue Table would look like this: ================================================================== * 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 Now I wonder how I would modify the below default settings from the tutorial data to reflect this: ===================================================================== set subjlist = (Diff001)
set runlist = (1)
# Input diffusion DICOMs (file names relative to dcmroot)
set dcmroot = /usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/
set dcmlist = (Diff001/orig/6-1.dcm)
=====================================================================
Oh also, I noticed that in the wiki you have the following settings: =======================================================================
set trainfile = $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt
=============================================================================================== In the latest version of the freesurfer distribution I counted 33 subjects for the training algorithm and therefore use:
"subj,train,difftutorial33.txt" pointing to
/usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033
Does that make sense?
Thanks so much for your help!
Ansgar
Hi Ansgar,
If you have your own bvals and bvecs, you should add the following extra lines to your dmrirc file.
set bvalfile = /path/to/bvals.txt set bvecfile = /path/to/bvecs.txt set nb0 = *No. of low-b images* (In your case you can set nb0 to 5 and tracula will use the first 5 images to get an average lowb image.)
set dcmroot = /path/to/diffusion_data set dcmlist = Diffusion file (relative to dcmroot) //you can specify any image format if you have given th bvals,bvecs info from the paragraph above.
The training dataset that is distributed as a part of freesurfer consists of 33 subjects. For the purposes of the tutorial we used the first 10 subjects for demonstration and hence used the remaining 23 as training subjects.
Hope that helps,
Please let us know if you have any questions, Priti
Dear Anastasia and Team FreeSurfer, First of all thanks so much for developing TRACULA. I think it has a lot of potential! Here is my question: I'm trying to modify "dmrirc_single_subject" file in order to reflect our local sequence and wondered how you are dealing with DTI repeat sequences for the same subject. We acquire 5 B0s and 30 directional scans twice in a row. So our *Diffusion bvalue Table would look like this: ==================================================================
- 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000
1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 Now I wonder how I would modify the below default settings from the tutorial data to reflect this: ===================================================================== set subjlist = (Diff001)
set runlist = (1)
# Input diffusion DICOMs (file names relative to dcmroot)
set dcmroot = /usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/
set dcmlist = (Diff001/orig/6-1.dcm)
=====================================================================
Oh also, I noticed that in the wiki you have the following settings:
set trainfile = $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt
=============================================================================================== In the latest version of the freesurfer distribution I counted 33 subjects for the training algorithm and therefore use:
"subj,train,difftutorial33.txt" pointing to
/usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033
Does that make sense?
Thanks so much for your help!
Ansgar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Priti, Thanks so much for your prompt reply! I have specified all our specs like you suggested below. However, I'm a bit confused as I thought this shouldn't be necessary as we feed TRACULA with original GE DICOM files. Doesn't TRACULA read this info from the DICOM headers? Also, it looks like TRACULA assumes that there is only one folder (sequence) per subject. However, as we repeat ours we have 2 per subject meaning I'd like to point to 2 different folders with the 1st image of each defining the sequence like set dcmlist = 014/MRI/AxDTI1/IM-0013-0001.dcm & set dcmlist = 014/MRI/AxDTI2/IM-0014-0001.dcm
Additionally, I got some errors running trac-preproc with just one series (I include my dmrirc at the end of this message). Any clue where I screw up here?
Thanks so much!
Ansgar
New invocation of trac-preproc
ajfurst VALinux1 Linux VALinux1 2.6.35.14-95.fc14.x86_64 #1 SMP Tue Aug 16 21:01:58 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024
total used free shared buffers cached Mem: 8062732 3565084 4497648 0 197864 2413064 -/+ buffers/cache: 954156 7108576 Swap: 10158076 2288 10155788
#------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Sep 20 17:10:45 PDT 2011 mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm... Starting DICOMRead2() dcmfile = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm dcmdir = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1 Ref Series No = 13 Found 2032 files, checking for dicoms Found 2030 dicom files in series. First Sorting Computing Slice Direction Vs: 0.051 -0.354 2.4743 Vs: 0.0203999 -0.141599 0.989714 Second Sorting Counting frames nframes = 35 nslices = 58 ndcmfiles = 2030 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=6600.00, TE=84.20, TI=0.00, flip angle=90.00 i_ras = (-0.999791, -0.00289925, -0.0202339) j_ras = (0, -0.989897, 0.141789) k_ras = (-0.0203999, 0.141599, 0.989714) writing to /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz... mri_probedicom --i /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dcminfo.dat
cp /home/ajfurst/Data/WRIISC/scripts/30+5gradtable.txt /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs cp /home/ajfurst/Data/WRIISC/scripts/bvalfile_1sess.txt /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals flip4fsl /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2.19727 fslswapdim /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz x -y z /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: found /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvecs /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvals /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvals eddy_correct /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz 0 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0000 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0001 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0002 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0003 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0004 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0005 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0006 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0007 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0008 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0009 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0010 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0011 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0012 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0013 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0014 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0015 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0016 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0017 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0018 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0019 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0020 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0021 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0022 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0023 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0024 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0025 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0026 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0027 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0028 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0029 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0030 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0031 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0032 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0033 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0034 mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs.norot xfmrot /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.ecclog /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs.norot /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs fslroi /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz 0 5 fslmaths /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz -Tmean /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz bet /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain_mask.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/diff #------------------------------------- #@# Inter-subject registration Tue Sep 20 17:42:31 PDT 2011 flirt -in /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain_mni.nii.gz -omat /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/xfms/diff2mni.mat -cost mutualinfo convert_xfm -omat /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/xfms/mni2diff.mat -inverse /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Tue Sep 20 17:44:14 PDT 2011 #------------------------------------- #@# Tensor fit Tue Sep 20 17:44:14 PDT 2011 dtifit -k /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz -m /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/diff/lowb_brain_mask.nii.gz -r /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs -b /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvals -o /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dtifit 0 256 0 256 0 58 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed #------------------------------------- #@# Priors Tue Sep 20 17:44:44 PDT 2011 /usr/local/freesurfer/bin/dmri_train --outdir /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.014.9330.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/mni/lowb_brain_mask.flt.nii.gz --fa /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug ERROR: fio_pushd: /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/mni ERROR: must specify brain mask volume for output subject Linux VALinux1 2.6.35.14-95.fc14.x86_64 #1 SMP Tue Aug 16 21:01:58 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Sep 20 17:44:44 PDT 2011 ==============================================================================================
# Run command file generated automatically by trac-all # setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /home/ajfurst/Data/WRIISC set dtroot = (/home/ajfurst/Data/WRIISC/TRACULA) set subj = (014) # # Processing steps to be performed # set docorr = (1) set dointra = (1) set dointer = (1) set domasks = (1) set dotensor = (1) set dopriors = (1) # # Options for image corrections and tensor fit # set dcmroot = (/home/ajfurst/Data/WRIISC) set dcmfile = (014/MRI/AxDTI1/IM-0013-0001.dcm) set bvecfile = (/home/ajfurst/Data/WRIISC/scripts/30+5gradtable.txt) set bvalfile = (/home/ajfurst/Data/WRIISC/scripts/bvalfile_1sess.txt) set nb0 = (5) set dob0 = (0) set b0mfile = () set b0pfile = () set echospacing = () set doeddy = (1) set dorotbvecs = (1) set thrbet = (0.3) # # Options for registrations # set doregflt = (1) set doregbbr = (1) set doregmni = (1) set doregcvs = (0) set mnitemp = (/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz) set cvstempdir = (/usr/local/freesurfer/subjects) set cvstemp = (cvs_avg35) # # Options for path reconstructions # set usemaskanat = (1) set pathlist = (lh.cst_AS rh.cst_AS lh.ilf_AS rh.ilf_AS lh.unc_AS rh.unc_AS fmajor_PP fminor_PP lh.atr_PP rh.atr_PP lh.cab_PP rh.cab_PP lh.ccg_PP rh.ccg_PP lh.slfp_PP rh.slfp_PP lh.slft_PP rh.slft_PP) set ncptlist = (5) set trainsubjlist = (/usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033) set ntrainlist = (33) set avgname = (avg) set reinit = (0) set usetrunc = (0) set doprior = (0) set dosegprior = (1) set dopathsubdirs = (0) set fmin = (0.05) set nburnin = (200) set nsample = (5000) set nupdate = (0) set nkeep = (5) set doinitprop = (0) set trcdir = (/usr/local/freesurfer/bin)
On Fri, Sep 16, 2011 at 8:29 AM, Priti Srinivasan < rspriti@nmr.mgh.harvard.edu> wrote:
Hi Ansgar,
If you have your own bvals and bvecs, you should add the following extra lines to your dmrirc file.
set bvalfile = /path/to/bvals.txt set bvecfile = /path/to/bvecs.txt set nb0 = *No. of low-b images* (In your case you can set nb0 to 5 and tracula will use the first 5 images to get an average lowb image.)
set dcmroot = /path/to/diffusion_data set dcmlist = Diffusion file (relative to dcmroot) //you can specify any image format if you have given th bvals,bvecs info from the paragraph above.
The training dataset that is distributed as a part of freesurfer consists of 33 subjects. For the purposes of the tutorial we used the first 10 subjects for demonstration and hence used the remaining 23 as training subjects.
Hope that helps,
Please let us know if you have any questions, Priti
Dear Anastasia and Team FreeSurfer, First of all thanks so much for developing TRACULA. I think it has a lot of potential! Here is my question: I'm trying to modify "dmrirc_single_subject" file in order to reflect our local sequence and wondered how you are dealing with DTI repeat sequences for the same subject. We acquire 5 B0s and 30 directional scans twice in a row. So our *Diffusion bvalue Table would look like this: ==================================================================
- 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000
1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 Now I wonder how I would modify the below default settings from the tutorial data to reflect this: ===================================================================== set subjlist = (Diff001)
set runlist = (1)
# Input diffusion DICOMs (file names relative to dcmroot)
set dcmroot = /usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/
set dcmlist = (Diff001/orig/6-1.dcm)
=====================================================================
Oh also, I noticed that in the wiki you have the following settings:
set trainfile = $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt
===============================================================================================
In the latest version of the freesurfer distribution I counted 33 subjects for the training algorithm and therefore use:
"subj,train,difftutorial33.txt" pointing to
/usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033
Does that make sense?
Thanks so much for your help!
Ansgar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Ansgar - Currently there's no way to specify multiple scans for the same subject as dicom files, sorry. You can concatenate the DWIs from the 2 scans in one nifti file, and also concatenate the bvecs/bvals from the two scans, and pass the concatenation to dmrirc.
As for your error, it looks like maybe the freesurfer recon wasn't found, so it skipped some steps (diffusion-to-anatomical registration and mask creation). Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist?
a.y
On Thu, 22 Sep 2011, Ansgar Furst wrote:
Hi Priti, Thanks so much for your prompt reply! I have specified all our specs like you suggested below. However, I'm a bit confused as I thought this shouldn't be necessary as we feed TRACULA with original GE DICOM files. Doesn't TRACULA read this info from the DICOM headers? Also, it looks like TRACULA assumes that there is only one folder (sequence) per subject. However, as we repeat ours we have 2 per subject meaning I'd like to point to 2 different folders with the 1st image of each defining the sequence like set dcmlist = 014/MRI/AxDTI1/IM-0013-0001.dcm & set dcmlist = 014/MRI/AxDTI2/IM-0014-0001.dcm
Additionally, I got some errors running trac-preproc with just one series (I include my dmrirc at the end of this message). Any clue where I screw up here?
Thanks so much!
Ansgar
New invocation of trac-preproc
ajfurst VALinux1 Linux VALinux1 2.6.35.14-95.fc14.x86_64 #1 SMP Tue Aug 16 21:01:58 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024
total used free shared buffers cached Mem: 8062732 3565084 4497648 0 197864 2413064 -/+ buffers/cache: 954156 7108576 Swap: 10158076 2288 10155788
#------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Sep 20 17:10:45 PDT 2011 mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm... Starting DICOMRead2() dcmfile = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm dcmdir = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1 Ref Series No = 13 Found 2032 files, checking for dicoms Found 2030 dicom files in series. First Sorting Computing Slice Direction Vs: 0.051 -0.354 2.4743 Vs: 0.0203999 -0.141599 0.989714 Second Sorting Counting frames nframes = 35 nslices = 58 ndcmfiles = 2030 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=6600.00, TE=84.20, TI=0.00, flip angle=90.00 i_ras = (-0.999791, -0.00289925, -0.0202339) j_ras = (0, -0.989897, 0.141789) k_ras = (-0.0203999, 0.141599, 0.989714) writing to /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz... mri_probedicom --i /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dcminfo.dat
cp /home/ajfurst/Data/WRIISC/scripts/30+5gradtable.txt /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs cp /home/ajfurst/Data/WRIISC/scripts/bvalfile_1sess.txt /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals flip4fsl /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2.19727 fslswapdim /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz x -y z /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz INFO: found /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvecs /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvals /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvals eddy_correct /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz 0 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0000 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0001 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0002 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0003 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0004 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0005 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0006 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0007 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0008 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0009 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0010 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0011 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0012 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0013 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0014 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0015 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0016 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0017 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0018 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0019 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0020 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0021 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0022 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0023 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0024 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0025 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0026 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0027 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0028 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0029 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0030 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0031 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0032 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0033 processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0034 mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs.norot xfmrot /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.ecclog /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs.norot /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs fslroi /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz 0 5 fslmaths /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz -Tmean /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz bet /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain_mask.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/diff #------------------------------------- #@# Inter-subject registration Tue Sep 20 17:42:31 PDT 2011 flirt -in /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain_mni.nii.gz -omat /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/xfms/diff2mni.mat -cost mutualinfo convert_xfm -omat /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/xfms/mni2diff.mat -inverse /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Tue Sep 20 17:44:14 PDT 2011 #------------------------------------- #@# Tensor fit Tue Sep 20 17:44:14 PDT 2011 dtifit -k /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz -m /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/diff/lowb_brain_mask.nii.gz -r /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs -b /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvals -o /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dtifit 0 256 0 256 0 58 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed #------------------------------------- #@# Priors Tue Sep 20 17:44:44 PDT 2011 /usr/local/freesurfer/bin/dmri_train --outdir /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.014.9330.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask/home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/mni/lowb_brain_mask.flt.nii.gz --fa /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug ERROR: fio_pushd: /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/mni ERROR: must specify brain mask volume for output subject Linux VALinux1 2.6.35.14-95.fc14.x86_64 #1 SMP Tue Aug 16 21:01:58 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Sep 20 17:44:44 PDT 2011
===========================================================================
# Run command file generated automatically by trac-all # setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /home/ajfurst/Data/WRIISC set dtroot = (/home/ajfurst/Data/WRIISC/TRACULA) set subj = (014) # # Processing steps to be performed # set docorr = (1) set dointra = (1) set dointer = (1) set domasks = (1) set dotensor = (1) set dopriors = (1) # # Options for image corrections and tensor fit # set dcmroot = (/home/ajfurst/Data/WRIISC) set dcmfile = (014/MRI/AxDTI1/IM-0013-0001.dcm) set bvecfile = (/home/ajfurst/Data/WRIISC/scripts/30+5gradtable.txt) set bvalfile = (/home/ajfurst/Data/WRIISC/scripts/bvalfile_1sess.txt) set nb0 = (5) set dob0 = (0) set b0mfile = () set b0pfile = () set echospacing = () set doeddy = (1) set dorotbvecs = (1) set thrbet = (0.3) # # Options for registrations # set doregflt = (1) set doregbbr = (1) set doregmni = (1) set doregcvs = (0) set mnitemp = (/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz) set cvstempdir = (/usr/local/freesurfer/subjects) set cvstemp = (cvs_avg35) # # Options for path reconstructions # set usemaskanat = (1) set pathlist = (lh.cst_AS rh.cst_AS lh.ilf_AS rh.ilf_AS lh.unc_AS rh.unc_AS fmajor_PP fminor_PP lh.atr_PP rh.atr_PP lh.cab_PP rh.cab_PP lh.ccg_PP rh.ccg_PP lh.slfp_PP rh.slfp_PP lh.slft_PP rh.slft_PP) set ncptlist = (5) set trainsubjlist = (/usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033) set ntrainlist = (33) set avgname = (avg) set reinit = (0) set usetrunc = (0) set doprior = (0) set dosegprior = (1) set dopathsubdirs = (0) set fmin = (0.05) set nburnin = (200) set nsample = (5000) set nupdate = (0) set nkeep = (5) set doinitprop = (0) set trcdir = (/usr/local/freesurfer/bin)
On Fri, Sep 16, 2011 at 8:29 AM, Priti Srinivasan rspriti@nmr.mgh.harvard.edu wrote: Hi Ansgar,
If you have your own bvals and bvecs, you should add the following extra lines to your dmrirc file. set bvalfile = /path/to/bvals.txt set bvecfile = /path/to/bvecs.txt set nb0 = *No. of low-b images* (In your case you can set nb0 to 5 and tracula will use the first 5 images to get an average lowb image.) set dcmroot = /path/to/diffusion_data set dcmlist = Diffusion file (relative to dcmroot) //you can specify any image format if you have given th bvals,bvecs info from the paragraph above. The training dataset that is distributed as a part of freesurfer consists of 33 subjects. For the purposes of the tutorial we used the first 10 subjects for demonstration and hence used the remaining 23 as training subjects. Hope that helps, Please let us know if you have any questions, PritiDear Anastasia and Team FreeSurfer, First of all thanks so much for developing TRACULA. I think it has a
lot
of potential! Here is my question: I'm trying to modify "dmrirc_single_subject"
file in
order to reflect our local sequence and wondered how you are dealing
with
DTI repeat sequences for the same subject. We acquire 5 B0s and 30 directional scans twice in a row. So our *Diffusion bvalue Table would look like this: ==================================================================
- 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000
1000
1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
1000
1000 1000 1000 1000 1000 1000 1000 1000 1000 0 0 0 0 0 1000
1000
1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
1000
1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
1000
1000 1000 1000 Now I wonder how I would modify the below default settings from the tutorial data to reflect this:
=====================================================================
set subjlist = (Diff001)
set runlist = (1)
# Input diffusion DICOMs (file names relative to dcmroot)
set dcmroot =
/usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/
set dcmlist = (Diff001/orig/6-1.dcm)
=====================================================================
Oh also, I noticed that in the wiki you have the following settings:
=======================================================================
set trainfile = $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt
===========================================================================
====================
In the latest version of the freesurfer distribution I counted 33 subjects for the training algorithm and therefore use:
"subj,train,difftutorial33.txt" pointing to
/usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033
Does that make sense?
Thanks so much for your help!
Ansgar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Anastasia, Thanks so much for your message. You were right about the recon directory, the contents had been accidentally moved elsewhere (sorry!) and once I moved them back and reran the script everything worked like a charm without any errors. However, it looks like I'm now stuck at the next processing stage (fsl's bedpostX). I pasted the output with the error message below. FYI: I'm unfortunately forced to run the bedpostX on a single Linux box (64-bit dual core with 8GB of RAM) which I hope is OK? Thanks so much for all your help,
Ansgar
================================================== trac-all -bedp -c scripts/dmrirc_single_subject_1only INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA Actual FREESURFER_HOME /usr/local/freesurfer ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /home/ajfurst/Data/WRIISC/TRACULA/015/dmri subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 9 slices processed 10 slices processed 11 slices processed 11 slices processed 12 slices processed 12 slices processed 13 slices processed 14 slices processed 14 slices processed 14 slices processed 15 slices processed 15 slices processed 16 slices processed 16 slices processed 16 slices processed 17 slices processed 17 slices processed 17 slices processed 18 slices processed 18 slices processed 18 slices processed 18 slices processed 19 slices processed 19 slices processed 19 slices processed 19 slices processed 20 slices processed 20 slices processed 20 slices processed 20 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 22 slices processed 22 slices processed 22 slices processed 22 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 40 slices processed 40 slices processed 40 slices processed 40 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 42 slices processed 42 slices processed 42 slices processed 42 slices processed 43 slices processed 43 slices processed 43 slices processed 43 slices processed 44 slices processed 44 slices processed 44 slices processed 44 slices processed 45 slices processed 45 slices processed 45 slices processed 46 slices processed 46 slices processed 46 slices processed 46 slices processed 47 slices processed 47 slices processed 47 slices processed 48 slices processed 48 slices processed 49 slices processed 49 slices processed 49 slices processed 50 slices processed 50 slices processed 51 slices processed 51 slices processed 52 slices processed 53 slices processed Queuing post processing stage 58 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /usr/local/freesurfer/bin/bedpostx_seychelles: line 281: kill: (12792) - No such process ===================================================
On Thu, Sep 22, 2011 at 5:17 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Ansgar - Currently there's no way to specify multiple scans for the same subject as dicom files, sorry. You can concatenate the DWIs from the 2 scans in one nifti file, and also concatenate the bvecs/bvals from the two scans, and pass the concatenation to dmrirc.
As for your error, it looks like maybe the freesurfer recon wasn't found, so it skipped some steps (diffusion-to-anatomical registration and mask creation). Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist?
a.y
Hi Ansgar - Most likely everything is fine. Sometimes the script that's built into bedpost to monitor its progress gives this error but in fact everything has ran fine. You should check that all the outputs are there in the dmri.bedpostX directory. See for list of bedpost output files: http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html
a.y
On Wed, 28 Sep 2011, Ansgar Furst wrote:
Hi Anastasia, Thanks so much for your message. You were right about the recon directory, the contents had been accidentally moved elsewhere (sorry!) and once I moved them back and reran the script everything worked like a charm without any errors. However, it looks like I'm now stuck at the next processing stage (fsl's bedpostX). I pasted the output with the error message below. FYI: I'm unfortunately forced to run the bedpostX on a single Linux box (64-bit dual core with 8GB of RAM) which I hope is OK? Thanks so much for all your help,
Ansgar
================================================== trac-all -bedp -c scripts/dmrirc_single_subject_1only INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA Actual FREESURFER_HOME /usr/local/freesurfer ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /home/ajfurst/Data/WRIISC/TRACULA/015/dmri subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 9 slices processed 10 slices processed 11 slices processed 11 slices processed 12 slices processed 12 slices processed 13 slices processed 14 slices processed 14 slices processed 14 slices processed 15 slices processed 15 slices processed 16 slices processed 16 slices processed 16 slices processed 17 slices processed 17 slices processed 17 slices processed 18 slices processed 18 slices processed 18 slices processed 18 slices processed 19 slices processed 19 slices processed 19 slices processed 19 slices processed 20 slices processed 20 slices processed 20 slices processed 20 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 22 slices processed 22 slices processed 22 slices processed 22 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 40 slices processed 40 slices processed 40 slices processed 40 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 42 slices processed 42 slices processed 42 slices processed 42 slices processed 43 slices processed 43 slices processed 43 slices processed 43 slices processed 44 slices processed 44 slices processed 44 slices processed 44 slices processed 45 slices processed 45 slices processed 45 slices processed 46 slices processed 46 slices processed 46 slices processed 46 slices processed 47 slices processed 47 slices processed 47 slices processed 48 slices processed 48 slices processed 49 slices processed 49 slices processed 49 slices processed 50 slices processed 50 slices processed 51 slices processed 51 slices processed 52 slices processed 53 slices processed Queuing post processing stage 58 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /usr/local/freesurfer/bin/bedpostx_seychelles: line 281: kill: (12792) - No such process ===================================================
On Thu, Sep 22, 2011 at 5:17 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ansgar - Currently there's no way to specify multiple scans for the same subject as dicom files, sorry. You can concatenate the DWIs from the 2 scans in one nifti file, and also concatenate the bvecs/bvals from the two scans, and pass the concatenation to dmrirc. As for your error, it looks like maybe the freesurfer recon wasn't found, so it skipped some steps (diffusion-to-anatomical registration and mask creation). Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? a.y
Dear Anastasia, Re-running bedpostX just did it and I didn't encounter the problem on any subjects after that. Everything is running great now. I just had 2 more follow-up questions: what's the best way to concatenate the 2 repeat DICOM DWI series into 1 NIFTI file (you mentioned that below)? How do I extract average FA values constrained by the extracted fiber tracts? Thanks so much for all your help, Ansgar
On Wed, Sep 28, 2011 at 5:07 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Ansgar - Most likely everything is fine. Sometimes the script that's built into bedpost to monitor its progress gives this error but in fact everything has ran fine. You should check that all the outputs are there in the dmri.bedpostX directory. See for list of bedpost output files: http://www.fmrib.ox.ac.uk/fsl/**fdt/fdt_bedpostx.htmlhttp://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html
a.y
On Wed, 28 Sep 2011, Ansgar Furst wrote:
Hi Anastasia,
Thanks so much for your message. You were right about the recon directory, the contents had been accidentally moved elsewhere (sorry!) and once I moved them back and reran the script everything worked like a charm without any errors. However, it looks like I'm now stuck at the next processing stage (fsl's bedpostX). I pasted the output with the error message below. FYI: I'm unfortunately forced to run the bedpostX on a single Linux box (64-bit dual core with 8GB of RAM) which I hope is OK? Thanks so much for all your help,
Ansgar
==============================**==================== trac-all -bedp -c scripts/dmrirc_single_subject_**1only INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC INFO: Diffusion root is /home/ajfurst/Data/WRIISC/**TRACULA Actual FREESURFER_HOME /usr/local/freesurfer ln -sf /home/ajfurst/Data/WRIISC/**TRACULA/015/dlabel/diff/anat_** brain_mask.bbr.nii.gz /home/ajfurst/Data/WRIISC/**TRACULA/015/dmri/nodif_brain_**mask.nii.gz ln -sf /home/ajfurst/Data/WRIISC/**TRACULA/015/dmri/dwi.nii.gz /home/ajfurst/Data/WRIISC/**TRACULA/015/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /home/ajfurst/Data/WRIISC/**TRACULA/015/dmri subjectdir is /home/ajfurst/Data/WRIISC/**TRACULA/015/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 9 slices processed 10 slices processed 11 slices processed 11 slices processed 12 slices processed 12 slices processed 13 slices processed 14 slices processed 14 slices processed 14 slices processed 15 slices processed 15 slices processed 16 slices processed 16 slices processed 16 slices processed 17 slices processed 17 slices processed 17 slices processed 18 slices processed 18 slices processed 18 slices processed 18 slices processed 19 slices processed 19 slices processed 19 slices processed 19 slices processed 20 slices processed 20 slices processed 20 slices processed 20 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 22 slices processed 22 slices processed 22 slices processed 22 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 40 slices processed 40 slices processed 40 slices processed 40 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 42 slices processed 42 slices processed 42 slices processed 42 slices processed 43 slices processed 43 slices processed 43 slices processed 43 slices processed 44 slices processed 44 slices processed 44 slices processed 44 slices processed 45 slices processed 45 slices processed 45 slices processed 46 slices processed 46 slices processed 46 slices processed 46 slices processed 47 slices processed 47 slices processed 47 slices processed 48 slices processed 48 slices processed 49 slices processed 49 slices processed 49 slices processed 50 slices processed 50 slices processed 51 slices processed 51 slices processed 52 slices processed 53 slices processed Queuing post processing stage 58 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /usr/local/freesurfer/bin/**bedpostx_seychelles: line 281: kill: (12792)
- No such
process ==============================**=====================
On Thu, Sep 22, 2011 at 5:17 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ansgar - Currently there's no way to specify multiple scans for the same subject as dicom files, sorry. You can concatenate the DWIs from the 2 scans in one nifti file, and also concatenate the bvecs/bvals from the two scans, and pass the concatenation to dmrirc. As for your error, it looks like maybe the freesurfer recon wasn't found, so it skipped some steps (diffusion-to-anatomical registration and mask creation). Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? a.yThe 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/**compliancelinehttp://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.
Hi Ansgar - If the 2 series are in register with each other, you can just concatenate them with mri_concat. You'd also have to concatenate the respective bvals and bvecs in the same order.
For average FA, look in the pathstats.overall.txt file of each reconstructed pathway. For more on this see the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
Hope this helps, a.y
On Fri, 28 Oct 2011, Ansgar Furst wrote:
Dear Anastasia, Re-running bedpostX just did it and I didn't encounter the problem on any subjects after that. Everything is running great now. I just had 2 more follow-up questions: what's the best way to concatenate the 2 repeat DICOM DWI series into 1 NIFTI file (you mentioned that below)? How do I extract average FA values constrained by the extracted fiber tracts? Thanks so much for all your help, Ansgar
On Wed, Sep 28, 2011 at 5:07 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ansgar - Most likely everything is fine. Sometimes the script that's built into bedpost to monitor its progress gives this error but in fact everything has ran fine. You should check that all the outputs are there in the dmri.bedpostX directory. See for list of bedpost output files: http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html a.yOn Wed, 28 Sep 2011, Ansgar Furst wrote:
Hi Anastasia, Thanks so much for your message. You were right about the recon directory, the contents had been accidentally moved elsewhere (sorry!) and once I moved them back and reran the script everything worked like a charm without any errors. However, it looks like I'm now stuck at the next processing stage (fsl's bedpostX). I pasted the output with the error message below. FYI: I'm unfortunately forced to run the bedpostX on a single Linux box (64-bit dual core with 8GB of RAM) which I hope is OK? Thanks so much for all your help, Ansgar ================================================== trac-all -bedp -c scripts/dmrirc_single_subject_1only INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA Actual FREESURFER_HOME /usr/local/freesurfer ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /home/ajfurst/Data/WRIISC/TRACULA/015/dmri subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 9 slices processed 10 slices processed 11 slices processed 11 slices processed 12 slices processed 12 slices processed 13 slices processed 14 slices processed 14 slices processed 14 slices processed 15 slices processed 15 slices processed 16 slices processed 16 slices processed 16 slices processed 17 slices processed 17 slices processed 17 slices processed 18 slices processed 18 slices processed 18 slices processed 18 slices processed 19 slices processed 19 slices processed 19 slices processed 19 slices processed 20 slices processed 20 slices processed 20 slices processed 20 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 22 slices processed 22 slices processed 22 slices processed 22 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 40 slices processed 40 slices processed 40 slices processed 40 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 42 slices processed 42 slices processed 42 slices processed 42 slices processed 43 slices processed 43 slices processed 43 slices processed 43 slices processed 44 slices processed 44 slices processed 44 slices processed 44 slices processed 45 slices processed 45 slices processed 45 slices processed 46 slices processed 46 slices processed 46 slices processed 46 slices processed 47 slices processed 47 slices processed 47 slices processed 48 slices processed 48 slices processed 49 slices processed 49 slices processed 49 slices processed 50 slices processed 50 slices processed 51 slices processed 51 slices processed 52 slices processed 53 slices processed Queuing post processing stage 58 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /usr/local/freesurfer/bin/bedpostx_seychelles: line 281: kill: (12792) - No such process =================================================== On Thu, Sep 22, 2011 at 5:17 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Ansgar - Currently there's no way to specify multiple scans for the same subject as dicom files, sorry. You can concatenate the DWIs from the 2 scans in one nifti file, and also concatenate the bvecs/bvals from the two scans, and pass the concatenation to dmrirc. As for your error, it looks like maybe the freesurfer recon wasn't found, so it skipped some steps (diffusion-to-anatomical registration and mask creation). Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? a.yThe 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
-
Anastasia Yendiki -
Ansgar Furst -
Priti Srinivasan