Why do you want to use a '$'?
On Wed, 14 Aug 2013, Alan Francis wrote:
Hi Anastasia: Yes the path that you pointed out is the one I presently use. Is there no way to use the '$' as a substitute? thanks, Alan On Wed, Aug 14, 2013 at 1:46 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote: Alan - Where is the location that has plenty of space? You should set your SUBJECTS_DIR to that location, e.g., setenv SUBJECTS_DIR /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons On Wed, 14 Aug 2013, Alan Francis wrote: Hi Anastasia/ FreeSurfers I did not use the conventional path usr/local/freesurfer. since there is very little disc space in this location. Alternately I set the environment at a location where is plenty of disc space and then sourced it. For the SUBJECTS_DIR I set the environment without using the dollar sign $. The Freesurfer recons and Tracula ran without problem and saved the processed data to this location. So the FReeSurfer recons and tracula data are in the same location. Now I am trying to use the dollar sign, so that I can extract the trac data, but I keep getting the 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. thanks, Alan On Wed, Aug 14, 2013 at 1:08 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote: Where did you get this command line? You should set the SUBJECTS_DIR to the location on disk where your freesurfer recons are. On Wed, 14 Aug 2013, Alan Francis wrote: 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/200 90224_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/200 90224_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 $ readingfrom/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200 90224_1 4110 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.b ve cs /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.b va ls /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. 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