Hi Anastasia: I fixed that problem - thank you. However, I have another question. i am trying extract trac data but when I set environment, I get an error message:
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : setenv SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons FreeSurfer_Data: Undefined variable. How do I solve this? Thanks again, Alan On Wed, Aug 14, 2013 at 11:06 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Alan - I'm not sure where the output from the one subject ends the the > other starts. For future reference, it's best to attach the entire > trac-all.log files instead of copying and pasting parts of them into your > message. > > I see two error messages here: > 1. "ERROR: must specify as many DWI dicoms as subjects" > This is as it says. Check your configuration file and see if the numbers > of entries in subjlist and dcmlist are the same. > > 2. "ERROR: reading /autofs/space/dali_003/users/** > BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons//118/** > dmri/dwi_frame.nii.gz" > I'm guessing the problem is in the b-value table. How many entries are > there that correspond to low-b images? > > a.y > > > On Tue, 13 Aug 2013, Alan Francis wrote: > > Hi Anastasia: >> >> Thanks to your advice most of the data have been processed using Tracula. >> Two brains gave me error messages that are >> as follows: >> >> >> csh::alanf@cerebro [/autofs/space/dali_003/users/** >> BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons] : trac-all -prep >> -c /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons/dmrirc-**124 >> ERROR: must specify as many DWI dicoms as subjects >> csh::alanf@cerebro [/autofs/space/dali_003/users/** >> BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons] : trac-all -prep >> -c /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons/dmrirc-**118 >> INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/** >> BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons >> INFO: Diffusion root is /autofs/space/dali_003/users/** >> BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons/ >> Actual FREESURFER_HOME /autofs/cluster/freesurfer/** >> centos6_x86_64/stable5_3_0 >> trac-preproc -c >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**scripts/dmrirc.local -log >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**scripts/trac-all.log -cmd >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**scripts/trac-all.cmd >> #-----------------------------**-------- >> /usr/local/freesurfer/stable5_**3_0//bin/trac-preproc >> #-----------------------------**-------- >> #@# Image corrections Mon Aug 12 17:11:05 EDT 2013 >> mri_convert/autofs/space/dali_**003/users/BW_project_DTI/** >> FreeSurfer_5.3_Data/diffusion_**recons//118/Diffusion_Recons/** >> 20090224_14110 >> 2DIFFUSIONHighRess016a001.nii >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig.nii.gz >> mri_convert/autofs/space/dali_**003/users/BW_project_DTI/** >> FreeSurfer_5.3_Data/diffusion_**recons//118/Diffusion_Recons/** >> 20090224_14110 >> 2DIFFUSIONHighRess016a001.nii >> >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig.nii.gz >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from/autofs/space/dali_003/**users/BW_project_DTI/** >> FreeSurfer_5.3_Data/diffusion_**recons//118/Diffusion_Recons/** >> 20090224_14110 >> 2DIFFUSIONHighRess016a001.nii.**.. >> TR=7640.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-0.997762, -0.0667414, -0.00403802) >> j_ras = (-0.0662713, 0.979101, 0.192276) >> k_ras = (0.00887916, -0.192114, 0.981333) >> writing to >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig.nii.gz... >> cp /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons/118/**Diffusion_Recons/118.bvecs >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig.mghdti.bvecs >> cp /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons/118/**Diffusion_Recons/118.bvals >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig.mghdti.bvals >> flip4fsl /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig.nii.gz >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig_flip.nii.gz >> INFO: input image orientation is LAS >> INFO: input image determinant is -6.8719 >> fslswapdim /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_orig.nii.gz >> x y z /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig_flip.nii.gz >> fslorient -forceradiological >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig_flip.nii.gz >> INFO: found >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig.mghdti.bvals, >> converting to FSL format >> INFO: found >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig.mghdti.bvecs, >> converting to FSL format >> mv -f/autofs/space/dali_003/**users/BW_project_DTI/** >> FreeSurfer_5.3_Data/diffusion_**recons//118/dmri/dwi_orig_** >> flip.mghdti.bvecs >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/bvecs >> mv -f/autofs/space/dali_003/**users/BW_project_DTI/** >> FreeSurfer_5.3_Data/diffusion_**recons//118/dmri/dwi_orig_** >> flip.mghdti.bvals >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/bvals >> eddy_correct >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_orig_flip.nii.gz >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi.nii.gz 0 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0000 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0001 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0002 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0003 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0004 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0005 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0006 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0007 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0008 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0009 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0010 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0011 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0012 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0013 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0014 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0015 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0016 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0017 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0018 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0019 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0020 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0021 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0022 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0023 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0024 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0025 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0026 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0027 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0028 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0029 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0030 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0031 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0032 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0033 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0034 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0035 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0036 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0037 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0038 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0039 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0040 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0041 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0042 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0043 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0044 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0045 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0046 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0047 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0048 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0049 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0050 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0051 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0052 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0053 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0054 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0055 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0056 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0057 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0058 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0059 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0060 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0061 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0062 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0063 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0064 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0065 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0066 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0067 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0068 >> processing /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_* >> *Data/diffusion_recons//118/**dmri/dwi_tmp0069 >> mv -f /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/bvecs >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/bvecs.norot >> xfmrot /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi.ecclog >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/bvecs.norot >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/bvecs >> ln -sf /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi.nii.gz >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/data.nii.gz >> awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file >> or directory) >> mri_concat --i >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_frame.nii.gz --mean --o >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/lowb.nii.gz >> niiRead(): error opening file >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_frame.nii.gz >> ninputs = 1 >> Checking inputs >> ERROR: reading >> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_** >> Data/diffusion_recons//118/**dmri/dwi_frame.nii.gz >> Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC >> 2013 x86_64 x86_64 x86_64 GNU/Linux >> >> trac-preproc exited with ERRORS at Mon Aug 12 17:30:05 EDT 2013 >> >> As always - thanks for your help, >> >> best, >> >> Alan >> >> Martinos Center. >> >> >> >> > > 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 Freesurfer@nmr.mgh.harvard.edu 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.
