Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?
There's a line break after:
set dcmlist = (APOE.124.dwi.nii.gz APOE.158.dwi.nii.gz APOE.215.dwi.nii.gz
APOE.269.dwi.nii.gz
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent: Monday, October 7, 2019 10:21 AM
To: Freesurfer support list
Subject: [Freesurfer] TRACULA - input Nifti instead of DICOM?
External Email - Use Caution
Hello Anastasia,
I am following up on my previous email about running TRACULA on my subject's
NIFTI DWI images instead of dicoms and am running into the following issues
which I have had before when trying to use NIFTI files instead of dicoms.
Too many ('s.
ERROR: must specify as many DWI dicoms as subjects
The number of subjects and dwi's listed should all be the same? I have included
the dmrirc file to this email as a reference. Any ideas what could be leading
to this issue? Is it the way I am naming or referencing the DWI images?
Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
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[Freesurfer] TRACULA - input Nifti instead of DICOM?
External Email - Use Caution
Hello Anastasia,
I am following up on my previous email about running TRACULA on my
subject's NIFTI DWI images instead of dicoms and am running into the
following issues which I have had before when trying to use NIFTI files
instead of dicoms.
Too many ('s.
ERROR: must specify as many DWI dicoms as subjects
The number of subjects and dwi's listed should all be the same? I have
included the dmrirc file to this email as a reference. Any ideas what could
be leading to this issue? Is it the way I am naming or referencing the DWI
images?
Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
#
# dmrirc.long.example
#
# This example is applicable to longitudinal studies, where DWI data from
# multiple time points are available for each subject. For a simple example
# with a single DWI data set per subject, see dmrirc.example instead.
#
# This file contains commands that will be run by trac-all before an analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#$Author: zkaufman $
#$Date: 2016/12/20 17:04:05 $
#$Revision: 1.3.2.1 $
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_pin/
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
set dtroot = /Volumes/DANIEL/dti_pin/trac
# Subject IDs (one per time point per subject)
#
set subjlist = (APOE.124 APOE.125 APOE.126 APOE.127 APOE.129 APOE.132 APOE.134 APOE.136 APOE.139 APOE.141 APOE.143 APOE.144 APOE.145 APOE.147 APOE.148 APOE.149 APOE.150 APOE.151 APOE.153 APOE.155 APOE.156 APOE.157 APOE.158 APOE.159 APOE.160 APOE.166 APOE.167 APOE.168 APOE.169 APOE.171 APOE.174 APOE.176 APOE.177 APOE.180 APOE.183 APOE.187 APOE.188 APOE.190 APOE.196 APOE.197 APOE.199 APOE.203 APOE.209 APOE.212 APOE.215 APOE.221 APOE.227 APOE.228 APOE.229 APOE.230 APOE.231 APOE.234 APOE.235 APOE.237 APOE.240 APOE.243 APOE.249 APOE.250 APOE.251 APOE.252 APOE.253 APOE.254 APOE.256 APOE.259 APOE.260 APOE.262 APOE.269 APOE.270 APOE.275 APOE.276 APOE.278 APOE.279 APOE.289 APOE.299 APOE.324 APOE.401 APOE.404 APOE.405 APOE.406 APOE.408 APOE.428 APOE.432 APOE.445 APOE.453 APOE.460 APOE.465 APOE.469 APOE.470)
# In case you want to analyze only Huey and Louie
# Default: Run analysis on all time points and subjects
#1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88
set runlist = (1)
# Input diffusion DICOMs (file names relative to dcmroot)
# 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 = /Volumes/DANIEL/PIN/DTI/
set dcmlist = (APOE.124.dwi.nii.gz APOE.158.dwi.nii.gz APOE.215.dwi.nii.gz APOE.269.dwi.nii.gz
APOE.125.dwi.nii.gz APOE.159.dwi.nii.gz APOE.221.dwi.nii.gz APOE.270.dwi.nii.gz
APOE.126.dwi.nii.gz APOE.160.dwi.nii.gz APOE.227.dwi.nii.gz APOE.275.dwi.nii.gz
APOE.127.dwi.nii.gz APOE.166.dwi.nii.gz APOE.228.dwi.nii.gz APOE.276.dwi.nii.gz
APOE.129.dwi.nii.gz APOE.167.dwi.nii.gz APOE.229.dwi.nii.gz APOE.278.dwi.nii.gz
APOE.132.dwi.nii.gz APOE.168.dwi.nii.gz APOE.230.dwi.nii.gz APOE.279.dwi.nii.gz
APOE.134.dwi.nii.gz APOE.169.dwi.nii.gz APOE.231.dwi.nii.gz APOE.289.dwi.nii.gz
APOE.136.dwi.nii.gz APOE.171.dwi.nii.gz APOE.234.dwi.nii.gz APOE.299.dwi.nii.gz
APOE.139.dwi.nii.gz APOE.174.dwi.nii.gz APOE.235.dwi.nii.gz APOE.324.dwi.nii.gz
APOE.141.dwi.nii.gz APOE.176.dwi.nii.gz APOE.237.dwi.nii.gz APOE.401.dwi.nii.gz
APOE.143.dwi.nii.gz APOE.177.dwi.nii.gz APOE.240.dwi.nii.gz APOE.404.dwi.nii.gz
APOE.144.dwi.nii.gz APOE.180.dwi.nii.gz APOE.243.dwi.nii.gz APOE.405.dwi.nii.gz
APOE.145.dwi.nii.gz APOE.183.dwi.nii.gz APOE.249.dwi.nii.gz APOE.406.dwi.nii.gz
APOE.147.dwi.nii.gz APOE.187.dwi.nii.gz APOE.250.dwi.nii.gz APOE.408.dwi.nii.gz
APOE.148.dwi.nii.gz APOE.188.dwi.nii.gz APOE.251.dwi.nii.gz APOE.428.dwi.nii.gz
APOE.149.dwi.nii.gz APOE.190.dwi.nii.gz
Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?
Nifti files don't store that info. You'd have to get the gradient table and b-values either from the dicom header or from the scanner. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Daniel Callow Sent: Friday, September 27, 2019 11:32 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - input Nifti instead of DICOM? External Email - Use Caution Gotcha. I was wondering if it would be possible to extract the bvecs and bval files directly from the Nifti file, however, it seems like based on the documentation that this is not possible and I will have to specify the bvals and bvecs and make sure they are formatted correctly for TRACULA. Thanks for the reply! Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2...@gmail.com<mailto:ddcc2...@gmail.com> 443-254-6298 On Fri, Sep 27, 2019 at 11:26 AM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Yes. Please check out the instructions in the tutorial on how to specify your input DWIs and let us know if you have any questions: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Daniel Callow mailto:ddcc2...@gmail.com>> Sent: Friday, September 27, 2019 10:31:19 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA - input Nifti instead of DICOM? External Email - Use Caution Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work? Best, Daniel Callow -- Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2...@gmail.com<mailto:ddcc2...@gmail.com> 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?
External Email - Use Caution Gotcha. I was wondering if it would be possible to extract the bvecs and bval files directly from the Nifti file, however, it seems like based on the documentation that this is not possible and I will have to specify the bvals and bvecs and make sure they are formatted correctly for TRACULA. Thanks for the reply! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Fri, Sep 27, 2019 at 11:26 AM Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > Yes. Please check out the instructions in the tutorial on how to specify > your input DWIs and let us know if you have any questions: > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Friday, September 27, 2019 10:31:19 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] TRACULA - input Nifti instead of DICOM? > > > External Email - Use Caution > > Hello I was given a dataset already in Nifti format that I would like to > run Tracula on. Is it possible to input Nifti files in the config file > instead of DICOMs? How would this work? > > Best, > Daniel Callow > -- > *Daniel Callow* > *PhD Student, Neuroscience and Cognitive Science* > Exercise for Brain Health Lab > University of Maryland, College Park > *ddcc2...@gmail.com * > 443-254-6298 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?
Yes. Please check out the instructions in the tutorial on how to specify your input DWIs and let us know if you have any questions: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Daniel Callow Sent: Friday, September 27, 2019 10:31:19 AM To: Freesurfer support list Subject: [Freesurfer] TRACULA - input Nifti instead of DICOM? External Email - Use Caution Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work? Best, Daniel Callow -- Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2...@gmail.com<mailto:ddcc2...@gmail.com> 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] TRACULA - input Nifti instead of DICOM?
External Email - Use Caution Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work? Best, Daniel Callow -- *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
