Hi Anastasia- it is attached- one note is that it is actually a .txt file but i
just copied and pasted it into an RTF from our group’s cluster for this purpose.
On Jun 7, 2017, at 4:43 PM, Simon, Katrina R
<katsi...@sas.upenn.edu<mailto:katsi...@sas.upenn.edu>> wrote:
Hi Anastasia, when running -prior, I am getting the following error:
/tmp/subj33.surfaces/BPD0067A.23694.txt: No such file or directory.
Is this something created during one of the earlier stages of preprocessing?
My corresponding output file looks like this:
INFO: SUBJECTS_DIR is /data/picsl/mackey_group/BPD
INFO: Diffusion root is /data/picsl/mackey_group/BPD/
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
trac-preproc -c
/data/picsl/mackey_group/BPD//surfaces/BPD0067A/scripts/dmrirc.local -log
/data/picsl/mackey_group/BPD//surfaces/BPD0067A/scripts/trac-all.log -cmd
/data/picsl/mackey_group/BPD//surfaces/BPD0067A/scripts/trac-all.cmd
#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-preproc
#-------------------------------------
#@# Priors Wed Jun 7 16:26:51 EDT 2017
Thanks
Katrina
On Jun 7, 2017, at 3:58 PM, Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Katrina - It looks like the last stage of the pre-processing did not run for
some reason. You can run that one stage only with trac-all -prior. If that
runs, then you can run trac-all -path (no need to rerun trac-all -bedp).
Best,
a.y
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Simon, Katrina R
[katsi...@sas.upenn.edu<mailto:katsi...@sas.upenn.edu>]
Sent: Wednesday, June 07, 2017 1:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA -path issue
Hi Anastasia, thanks for your response.
The entire log file is attached. Let me know if you think you need anything
else.
Best
Katrina
On Jun 6, 2017, at 9:33 PM, Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Katrina - Most likely the problem occurred earlier in the process, so the
real error is hiding earlier in the log file. Can you please the entire
scripts/trac-all.log file?
Thanks,
a.y
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Simon, Katrina R
[katsi...@sas.upenn.edu<mailto:katsi...@sas.upenn.edu>]
Sent: Tuesday, June 06, 2017 3:41 PM
To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA -path issue
Hi all, I am running TRACULA on free surfer 6.0.0 and have done the 1st and 2nd
step and am getting stuck on the last step with the following error.
Loading atlas reference volume from
/data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
niiRead(): error opening file
/data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
ERROR: Could not read
/data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
Linux compute-0-12.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
This file is not in the dlabel/mni folder- is this because of something going
wrong in the 1st and 2nd steps? Or could it be a problem with loading the atlas
reference volume? I have tried this with multiple subjects and am getting the
same issue for each one.
Any help would be appreciated.
Thanks,
Katrina
Katrina Simon
Research Specialist- Mackey Lab
University of Pennsylvania Department of Psychology
katsi...@sas.upenn.edu<mailto:katsi...@sas.upenn.edu>
(215) 573-1670
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{\rtf1\ansi\ansicpg1252\cocoartf1404\cocoasubrtf470
{\fonttbl\f0\fswiss\fcharset0 Helvetica;}
{\colortbl;\red255\green255\blue255;}
\margl1440\margr1440\vieww10800\viewh8400\viewkind0
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0
\f0\fs24 \cf0 # FreeSurfer SUBJECTS_DIR\
# T1 images and FreeSurfer segmentations are expected to be found here\
#\
setenv SUBJECTS_DIR $SUBJECTS_DIR\
\
# Output directory where trac-all results will be saved\
# Default: Same as SUBJECTS_DIR\
#\
set dtroot = $SUBJECTS_DIR/\
\
# Subject IDs\
#\
set subjlist = ( surfaces/BPD0067A )\
\
# Input diffusion DICOMs\
# If original DICOMs don't exist, these can be in other image format\
# but then the gradient table and b-value table must be specified (see below)\
#\
\
set dcmroot = $SUBJECTS_DIR/dicoms/\
\
set dcmlist = ( BPD0067A/001_000011_000001.dcm)\
\
# Diffusion gradient tables (if there is a different one for each scan)\
# Must be specified if they cannot be read from the DICOM headers\
# The tables must have either three columns, where each row is a gradient vector\
# or three rows, where each column is a gradient vector\
# There must be as many gradient vectors as volumes in the diffusion data set\
# Default: Read from DICOM header\
#\
set bveclist = ( $SUBJECTS_DIR/niftis/BPD0067A/dti.bvec )\
\
# Diffusion b-value tables (if there is a different one for each scan)\
# Must be specified if they cannot be read from the DICOM headers\
# There must be as many b-values as volumes in the diffusion data set\
# Default: Read from DICOM header\
#\
set bvallist = ( $SUBJECTS_DIR/niftis/BPD0067A/dti.bval)\
\
set doeddy = 1\
set dorotbvecs = 1\
set usemaskanat = 1\
set thrbet = 0.3\
set doregflt = 0\
set doregbbr = 1\
set doregmni = 1\
set doregcvs = 0\
\
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 ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)}_______________________________________________
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