[Freesurfer] HBT hippocampal segmentation
External Email - Use Caution Hello, I was just asked by a reviewer how the head body and tail of the Freesurfer subfield segmentation is determined. I know that there is no differentiation of the tail, however, there are differentiations between the head and body of the different subfields. Are there specific anatomical boundary rules that drive the algorithm to differentiate between head and body in the HBT segmentation output. Thank you for any guidance you can provide! Best, *Daniel Callow* *Graduate 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] b0 to T1’s co-registration without b0 inhommogeneities
External Email - Use Caution Hello, I am trying to do a within-subject co-registration between b0 volumes and T1's for my subjects. This is an old dataset that does not have anything for correcting b0 inhomogeneities. The registration using --dti and normal parameters for bbregister led to "okay" within-subject registration. I am wondering if modifying the --dof (like 12) option for bbregister or applying some type of linear/nonlinear registration might improve the registration? 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
External Email - Use Caution Hello, I am trying to do a within-subject co-registration between b0 volumes and T1's for my subjects. This is an old dataset that does not have anything for correcting b0 inhomogeneities. The registration using --dti and normal parameters for bbregister led to "okay" within-subject registration. I am wondering if modifying the --dof (like 12) option for bbregister or applying some type of linear/nonlinear registration might improve the registration? 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA error - MRISread could not open file
External Email - Use Caution Hello, It isn't an error with recon-all, at least I don't think it is. Recon-all ran without error and the file that Tracula is trying to access seems to be where it is supposed to be. It seems like Tracula is having an issue opening the lh.white file. I just included the recon-all log for that subject to show that recon-all hadn't had any issues. Do you still think it would have to do with recon-all? It seems to have to do with the way Tracula is trying to read the file? 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 On Thu, Oct 10, 2019 at 9:14 AM Yendiki, Anastasia wrote: > Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula > error" in the subject line if you want the developers of the structural > stream to look into it. > > a.y > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Thursday, October 10, 2019 9:01:25 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] TRACULA error - MRISread could not open file > > > External Email - Use Caution > > Hello, > > I am running tracula on some of my DTI data and have had no issues for > most of my subjects. However, for one of them I get the following error > after mri_segreg > > MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not > open file > > Loading mov > > Extracting frame 0 > > Projecting LH Surfs > > Loading lh.white surf > > No such file or directory > > > It doesn't make sense that I am getting this error because when looking in > that exact folder I see the following > > > [255a-280:freesurfer_pin/APOE.269/surf] amos% ls > > lh.area lh.smoothwm.FI.crv rh.area > rh.smoothwm.FI.crv > > lh.curv lh.smoothwm.H.crv rh.curv > rh.smoothwm.H.crv > > lh.defect_borders lh.smoothwm.K.crv rh.defect_borders > rh.smoothwm.K.crv > > lh.defect_chull lh.smoothwm.K1.crv rh.defect_chull > rh.smoothwm.K1.crv > > lh.defect_labelslh.smoothwm.K2.crv rh.defect_labels > rh.smoothwm.K2.crv > > lh.inflated lh.smoothwm.S.crv rh.inflated > rh.smoothwm.S.crv > > lh.inflated.H lh.smoothwm.nofix rh.inflated.H > rh.smoothwm.nofix > > lh.inflated.K lh.sphere rh.inflated.K rh.sphere > > lh.inflated.nofix lh.sphere.reg rh.inflated.nofix rh.sulc > > lh.orig lh.sulc rh.orig rh.white.H > > lh.orig.nofix lh.white.H rh.orig.nofix rh.white.K > > lh.qsphere.nofixlh.white.K rh.qsphere.nofix > rh.white.preaparc > > lh.smoothwm lh.white.preaparc rh.smoothwm > rh.white.preaparc.H > > lh.smoothwm.BE.crv lh.white.preaparc.H rh.smoothwm.BE.crv > rh.white.preaparc.K > > lh.smoothwm.C.crv lh.white.preaparc.K rh.smoothwm.C.crv > > > It looks like the file it can't open is there? I have attached the log > file for recon-all and trac-all the subject in case it might help. > > > Thank you, > *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
[Freesurfer] TRACULA error - MRISread could not open file
External Email - Use Caution Hello, I am running tracula on some of my DTI data and have had no issues for most of my subjects. However, for one of them I get the following error after mri_segreg MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not open file Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf No such file or directory It doesn't make sense that I am getting this error because when looking in that exact folder I see the following [255a-280:freesurfer_pin/APOE.269/surf] amos% ls lh.area lh.smoothwm.FI.crv rh.area rh.smoothwm.FI.crv lh.curv lh.smoothwm.H.crv rh.curv rh.smoothwm.H.crv lh.defect_borders lh.smoothwm.K.crv rh.defect_borders rh.smoothwm.K.crv lh.defect_chull lh.smoothwm.K1.crv rh.defect_chull rh.smoothwm.K1.crv lh.defect_labelslh.smoothwm.K2.crv rh.defect_labels rh.smoothwm.K2.crv lh.inflated lh.smoothwm.S.crv rh.inflated rh.smoothwm.S.crv lh.inflated.H lh.smoothwm.nofix rh.inflated.H rh.smoothwm.nofix lh.inflated.K lh.sphere rh.inflated.K rh.sphere lh.inflated.nofix lh.sphere.reg rh.inflated.nofix rh.sulc lh.orig lh.sulc rh.orig rh.white.H lh.orig.nofix lh.white.H rh.orig.nofix rh.white.K lh.qsphere.nofixlh.white.K rh.qsphere.nofix rh.white.preaparc lh.smoothwm lh.white.preaparc rh.smoothwm rh.white.preaparc.H lh.smoothwm.BE.crv lh.white.preaparc.H rh.smoothwm.BE.crv rh.white.preaparc.K lh.smoothwm.C.crv lh.white.preaparc.K rh.smoothwm.C.crv It looks like the file it can't open is there? I have attached the log file for recon-all and trac-all the subject in case it might help. Thank you, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 recon-all-status.log Description: Binary data trac-all.error Description: Binary data trac-all.log Description: Binary data ___ 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 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.g
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
[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] TRACULA - OrientLAS issue for a subject
External Email - Use Caution For reference, I think the issue had to do with the orientation of these two subjects. I added tome code to use 3dwarp -deoblique to the dwi_orig.nii.gz and then ran orientLAS and it worked this time. The only thing I am unsure about is if this will nulify the bvals and bvecs I have and ruin later preprocessing steps? This is the only solution to the problem I have found thus far though. *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] TRACULA - OrientLAS issue for a subject
External Email - Use Caution Hello, An additional one of my subjects (2/66) is having the exact same issue. I can send his dcminfo.dat information and .log info if that might help with troubleshooting the issue? I have still had no luck determining why OrientLAS in TRACULA doesn't seem to be working for these two subjects. 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA - runlist longer than subject list
External Email - Use Caution Sorry I did not see your reply (having issues getting notifications from the freesurfer list). The error seemed to be an issue with the version I was using, which wasn't reading the subject list correctly. Wanted to make sure I posted a solution. Thank you for your help! *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 Thu, Aug 8, 2019 at 9:07 AM Daniel Callow wrote: > Hello, > > When trying to run TRACULA on my data I keep getting the following error. > > domainname: Command not found. > > INFO: SUBJECTS_DIR is /Volumes/DANIEL/freesurfer_Tracy > > INFO: Diffusion root is /Volumes/DANIEL/dti_Tracy/trac > > Actual FREESURFER_HOME /Applications/freesurfer > > INFO: FreeSurfer build stamps do not match > > Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc > > Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > INFO: current FREESURFER_HOME does not match that of previous processing. > > Current: /Applications/freesurfer > > Previous: /Applications/freesurfer_dev > > /Volumes/DANIEL/trac-all -c > /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/dmrirc.local -log > /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.log -cmd > /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.cmd > > domainname: Command not found. > > ERROR: run list is longer than subject list > > > I have never had this issue before and have tried multiple options for the > run list from () to (1 2 3) to include a number for every subject. However, > I always get this error. > > > I wonder if there is some issue with the formatting this go around that > could be causing the issue but I can't find it. > > > Below is what I have for the initial part of my dmrirc folder. > > > *# FreeSurfer SUBJECTS_DIR* > > *# T1 images and FreeSurfer segmentations are expected to be found here* > > *# * > > setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_Tracy/ > > > *# Output directory where trac-all results will be saved* > > *# Default: Same as SUBJECTS_DIR* > > *#* > > set dtroot = /Volumes/DANIEL/dti_Tracy/trac > > > *# Subject IDs (one per time point per subject)* > > *#* > > set subjlist = (HMN002 HMN003 HMN005 HMN006 HMN007 HMN011 HMN014 HMN018 > HMN020 HMN021 HMN022 HMN025 HMN029 HMN035 HMN037 HMN039 HMN045 HMN050 > HMN055 HMN057 HMN060 HMN064 HMN065 HMN069 HMN072 HMN073 HMN079 HMN085 > HMN087 HMN088 HMN095 HMN097 HMN098 HMN099 HMN101 HMN102 HMN103 HMN105 > HMN108 HMN110 HMN112 HMN113 HMN115 HMN118 HMN120 HMN121 HMN123 HMN135 > HMN141 HMN144 HMN152 HMN156 HMN160 HMN163 HMN175 HMN180 HMN186 HMN187 > HMN189 HMN190 HMN191 HMN193 HMN195 HMN196 HMN200 HMN201) > > > *# Longitudinal base template subject IDs (one for each time point above)* > > *#* > > set baselist = () > > > *# 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* > > > set runlist = () > > > *# 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/Tracy/HMN_W1 > > set dcmlist = ( HMN002/image01.dcm HMN003/image01.dcm > HMN005/image01.dcm HMN006/image01.dcm HMN007/image01.dcm > HMN011/image01.dcm HMN014/image01.dcm HMN018/image01.dcm > HMN020/image01.dcm HMN021/image01.dcm HMN022/image01.dcm > HMN025/image01.dcm HMN029/image01.dcm HMN035/image01.dcm > HMN037/image01.dcm HMN039/image01.dcm HMN045/image01.dcm > HMN050/image01.dcm HMN055/image01.dcm HMN057/image01.dcm > HMN060/image01.dcm HMN064/image01.dcm HMN065/image01.dcm > HMN069/image01.dcm HMN072/image01.dcm HMN073/image01.dcm > HMN079/image01.dcm HMN085/image01.dcm HMN087/image01.dcm > HMN088/image01.dcm HMN095/image01.dcm HMN097/image01.dcm > HMN098/image01.dcm HMN099/image01.dcm HMN101/image01.dcm > HMN102/image01.dcm HMN103/image01.dcm HMN105/image01.dcm > HMN108/image01.dcm HMN110/image01.dcm HMN112/image01.dcm > HMN113/image01.dcm HMN115/image01.dcm HMN118/image01.dcm > HMN120/image01.dcm HMN121/image01.dcm HMN123/i
[Freesurfer] TRACULA - OrientLAS issue for a subject
External Email - Use Caution Hello, I am running TRACULA on my data set and am having issues with one of my subjects. For this subject, I get the following error. INFO: input image orientation is LIS INFO: input image determinant is 18.4229 rdc_new: Undefined variable. rdc_new: Undefined variable. rdc_new: Undefined variable. ny_new: Undefined variable. I have attached the dcminfo.dat file of this subject. It seems like mri_info is having trouble either extracting or writing cdc, rdc, and sdc values from this subject's dcminfo.dat file? Any idea why this might be? I have looked through this subjects dcminfo.dat file and compared it to others but have been unable to identify the issue. I have also included the trac-all log for this subject. Some advice on what the issue might be would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 dcminfo.dat Description: Binary data trac-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] TRACULA - runlist longer than subject list
External Email - Use Caution Hello, When trying to run TRACULA on my data I keep getting the following error. domainname: Command not found. INFO: SUBJECTS_DIR is /Volumes/DANIEL/freesurfer_Tracy INFO: Diffusion root is /Volumes/DANIEL/dti_Tracy/trac Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /Applications/freesurfer_dev /Volumes/DANIEL/trac-all -c /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/dmrirc.local -log /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.log -cmd /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.cmd domainname: Command not found. ERROR: run list is longer than subject list I have never had this issue before and have tried multiple options for the run list from () to (1 2 3) to include a number for every subject. However, I always get this error. I wonder if there is some issue with the formatting this go around that could be causing the issue but I can't find it. Below is what I have for the initial part of my dmrirc folder. *# FreeSurfer SUBJECTS_DIR* *# T1 images and FreeSurfer segmentations are expected to be found here* *# * setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_Tracy/ *# Output directory where trac-all results will be saved* *# Default: Same as SUBJECTS_DIR* *#* set dtroot = /Volumes/DANIEL/dti_Tracy/trac *# Subject IDs (one per time point per subject)* *#* set subjlist = (HMN002 HMN003 HMN005 HMN006 HMN007 HMN011 HMN014 HMN018 HMN020 HMN021 HMN022 HMN025 HMN029 HMN035 HMN037 HMN039 HMN045 HMN050 HMN055 HMN057 HMN060 HMN064 HMN065 HMN069 HMN072 HMN073 HMN079 HMN085 HMN087 HMN088 HMN095 HMN097 HMN098 HMN099 HMN101 HMN102 HMN103 HMN105 HMN108 HMN110 HMN112 HMN113 HMN115 HMN118 HMN120 HMN121 HMN123 HMN135 HMN141 HMN144 HMN152 HMN156 HMN160 HMN163 HMN175 HMN180 HMN186 HMN187 HMN189 HMN190 HMN191 HMN193 HMN195 HMN196 HMN200 HMN201) *# Longitudinal base template subject IDs (one for each time point above)* *#* set baselist = () *# 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* set runlist = () *# 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/Tracy/HMN_W1 set dcmlist = ( HMN002/image01.dcm HMN003/image01.dcm HMN005/image01.dcm HMN006/image01.dcm HMN007/image01.dcm HMN011/image01.dcm HMN014/image01.dcm HMN018/image01.dcm HMN020/image01.dcm HMN021/image01.dcm HMN022/image01.dcm HMN025/image01.dcm HMN029/image01.dcm HMN035/image01.dcm HMN037/image01.dcm HMN039/image01.dcm HMN045/image01.dcm HMN050/image01.dcm HMN055/image01.dcm HMN057/image01.dcm HMN060/image01.dcm HMN064/image01.dcm HMN065/image01.dcm HMN069/image01.dcm HMN072/image01.dcm HMN073/image01.dcm HMN079/image01.dcm HMN085/image01.dcm HMN087/image01.dcm HMN088/image01.dcm HMN095/image01.dcm HMN097/image01.dcm HMN098/image01.dcm HMN099/image01.dcm HMN101/image01.dcm HMN102/image01.dcm HMN103/image01.dcm HMN105/image01.dcm HMN108/image01.dcm HMN110/image01.dcm HMN112/image01.dcm HMN113/image01.dcm HMN115/image01.dcm HMN118/image01.dcm HMN120/image01.dcm HMN121/image01.dcm HMN123/image01.dcm HMN135/image01.dcm HMN141/image01.dcm HMN144/image01.dcm HMN152/image01.dcm HMN156/image01.dcm HMN160/image01.dcm HMN163/image01.dcm HMN175/image01.dcm HMN180/image01.dcm HMN186/image01.dcm HMN187/image01.dcm HMN189/image01.dcm HMN190/image01.dcm HMN191/image01.dcm HMN193/image01.dcm HMN195/image01.dcm HMN196/image01.dcm HMN200/image01.dcm HMN201/image01.dc) Any help debugging the issue would be greatly appreciated! *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] segmentHA_T1.sh error
External Email - Use Caution Hello, When trying to run segmentHA_T1.sh I keep getting the following error log that I am having a lot of trouble debugging. Matlab 2014b is installed. Any help or guidance would be greatly appreciated! -- USER dcallow HOST compute-4-9.bswift.umd.edu PROCESSID 8771 PROCESSOR x86_64 OS Linux ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Linux compute-4-9.bswift.umd.edu 2.6.32-754.15.3.el6.x86_64 #1 SMP Thu Jun 13 22:49:44 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux -- freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc setenv SUBJECTS_DIR /homes/dcallow/freesurfer_Tracy cd /a/ha-nfs-1-ib/export/home/bswift/dcallow /homes/dcallow/freesurfer_dev/bin/segmentHA_T1.sh HMN002 # #@# Hippocampal Subfields processing (T1) left Sun Aug 4 15:08:35 EDT 2019 -- Setting up environment variables --- DYLD_LIBRARY_PATH is .:/homes/dcallow/freesurfer_dev/MCRv84//runtime/maci64:/homes/dcallow/freesurfer_dev/MCRv84//bin/maci64:/homes/dcallow/freesurfer_dev/MCRv84//sys/os/maci64:/hom$ /homes/dcallow/freesurfer_dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: /homes/dcallow/freesurfer_dev/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/s$ @#@FSTIME 2019:08:04:15:08:35 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 0.07 S 0.00 U 0.00 P 15% M 1360 F 0 R 2250 W 0 c 13 w 171 I 40 O 0 L 0.12 0.68 0.88 @#@FSLOADPOST 2019:08:04:15:08:35 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.12 0.68 0.88 Linux compute-4-9.bswift.umd.edu 2.6.32-754.15.3.el6.x86_64 #1 SMP Thu Jun 13 22:49:44 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Sun Aug 4 15:08:36 EDT 2019 *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
Re: [Freesurfer] TRACULA incorporate topup instead of field map?
External Email - Use Caution Thank you! And glad to hear it’s in the works for the newest version. Best, Daniel On Tue, Jul 30, 2019 at 12:50 PM Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > Hi Daniel - It'll be easier to just preprocess the data before passing > them to trac-all. Topup will be incorporated to the preprocessing for the > next version release. Of course you can replace that part of the script > yourself if you prefer - you'll have to also combine the AP and PA outputs > etc etc. > > Best, > a.y > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Tuesday, July 30, 2019 8:44:32 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] TRACULA incorporate topup instead of field map? > > > External Email - Use Caution > > Hello, > > I have previously used field map correction for b0 inhomogeneities when > running TRACULA, however my new data set has A>P and P>A encoding. I know > that topup has been shown to perform slightly better than filed map > correction. I wonder if it would be possible to manually edit the > ($dob0) then # B0-inhomogeneity "correction" > part of the code and run topup instead of epidewarp.fsl? I am trying to > determine how feasible this is and was wondering if this had been tried by > others? > > If not, does it make more sense to process the data with topup separately > and then incorporate it into TRACULA? > > Thank you for any guidance you can provide, > *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 -- *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
Re: [Freesurfer] segmentHA_T2.sh longitudinal version?
External Email - Use Caution In that case, would you suggest one to use segmentHA_T1_long.sh instead of segmentHA_T2.sh (cross-sectional) if one has longitudinal data and T2 high-resolution data? Would one be expected to provide superior results? 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 On Tue, Jul 30, 2019 at 9:27 AM Daniel Callow wrote: > Thank you for the prompt answer! > *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 Tue, Jul 30, 2019 at 9:18 AM Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk> wrote: > >> External Email - Use Caution >> >> Dear Daniel, >> >> Such a script doesn’t exist yet (it’s in the to-do list). The reason why >> it’s not a straightforward extension of segmentHA_T1.sh is that resampling >> the anisotropic T2s to a common space is not a good idea, given the >> differences in orientation. There are ways of getting around this problem; >> I just haven’t found the time to do it, yet… >> >> Cheers, >> >> /Eugenio >> >> >> >> -- >> >> Juan Eugenio Iglesias >> >> Senior research fellow >> >> CMIC (UCL), MGH (HMS) and CSAIL (MIT) >> >> http://www.jeiglesias.com >> >> >> >> >> >> *From: * on behalf of Daniel >> Callow >> *Reply-To: *Freesurfer support list >> *Date: *Monday, 29 July 2019 at 21:48 >> *To: *Freesurfer support list >> *Subject: *[Freesurfer] segmentHA_T2.sh longitudinal version? >> >> >> >> *External Email - Use Caution* >> >> Hello, >> >> >> >> I have recently used segmentHA_T1_long.sh and was pleased with the >> segmentation results. However, I now have a longitudinal data set that has >> additional T2 high-resolution scans of the hippocampus as well as T1's. I >> know there is a segmentHA_T2.sh script to incorporate these types of scans. >> However, there doesn't seem to be a longitudinal version for this. Is this >> something that is being worked on? Or is there another reason that T2 >> should not be used with longitudinal analysis? >> >> >> >> Thank you for any advice you can provide, >> >> >> >> *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] segmentHA_T2.sh longitudinal version?
External Email - Use Caution Thank you for the prompt answer! *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 Tue, Jul 30, 2019 at 9:18 AM Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > External Email - Use Caution > > Dear Daniel, > > Such a script doesn’t exist yet (it’s in the to-do list). The reason why > it’s not a straightforward extension of segmentHA_T1.sh is that resampling > the anisotropic T2s to a common space is not a good idea, given the > differences in orientation. There are ways of getting around this problem; > I just haven’t found the time to do it, yet… > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > *From: * on behalf of Daniel > Callow > *Reply-To: *Freesurfer support list > *Date: *Monday, 29 July 2019 at 21:48 > *To: *Freesurfer support list > *Subject: *[Freesurfer] segmentHA_T2.sh longitudinal version? > > > > *External Email - Use Caution* > > Hello, > > > > I have recently used segmentHA_T1_long.sh and was pleased with the > segmentation results. However, I now have a longitudinal data set that has > additional T2 high-resolution scans of the hippocampus as well as T1's. I > know there is a segmentHA_T2.sh script to incorporate these types of scans. > However, there doesn't seem to be a longitudinal version for this. Is this > something that is being worked on? Or is there another reason that T2 > should not be used with longitudinal analysis? > > > > Thank you for any advice you can provide, > > > > *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
[Freesurfer] TRACULA incorporate topup instead of field map?
External Email - Use Caution Hello, I have previously used field map correction for b0 inhomogeneities when running TRACULA, however my new data set has A>P and P>A encoding. I know that topup has been shown to perform slightly better than filed map correction. I wonder if it would be possible to manually edit the ($dob0) then # B0-inhomogeneity "correction" part of the code and run topup instead of epidewarp.fsl? I am trying to determine how feasible this is and was wondering if this had been tried by others? If not, does it make more sense to process the data with topup separately and then incorporate it into TRACULA? Thank you for any guidance you can provide, *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] segmentHA_T2.sh longitudinal version?
External Email - Use Caution Hello, I have recently used segmentHA_T1_long.sh and was pleased with the segmentation results. However, I now have a longitudinal data set that has additional T2 high-resolution scans of the hippocampus as well as T1's. I know there is a segmentHA_T2.sh script to incorporate these types of scans. However, there doesn't seem to be a longitudinal version for this. Is this something that is being worked on? Or is there another reason that T2 should not be used with longitudinal analysis? Thank you for any advice you can provide, *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
Re: [Freesurfer] TRACULA for kids/children
External Email - Use Caution Thank you for your response. We may have some children slightly younger so I am not sure if the method would still apply. Does that mean my suggested edit of changing the mni template to a different template wouldn’t work. I appreciate your input and quick response! Kind regards, Daniel Callow On Mon, Jul 29, 2019 at 6:43 PM Yendiki, Anastasia wrote: > Hi Daniel - What is the age range you're interested in? We have used > tracula with children as young as 5 (see example ref below). Keep in mind > that tracula is not a traditional template-based approach that needs > perfect alignment to a template, because it finds tracts based on their > relative position with respect to the labels in the individual aparc+aseg, > rather than their absolute coordinates in some template space. > > https://www.ncbi.nlm.nih.gov/m/pubmed/24269273/ > > For neonates, we have a new training set of manually labeled tracts in > neonates that can be used by tracula. That option, however is not yet in > the official freesurfer release. > > https://www.ncbi.nlm.nih.gov/m/pubmed/31132451/ > > a.y > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Monday, July 29, 2019 6:31:37 PM > *To:* Freesurfer support list > *Subject:* [Freesurfer] TRACULA for kids/children > > > External Email - Use Caution > > Hello, > > Is it possible to run TRACULA on baby/children brain scans? If so how > would one go about doing this? > > Could I just change > > set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > > to a different baby/child atlas? If not how would I go about this? > > 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 > _______ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *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] TRACULA for kids/children
External Email - Use Caution Hello, Is it possible to run TRACULA on baby/children brain scans? If so how would one go about doing this? Could I just change set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz to a different baby/child atlas? If not how would I go about this? 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Trac-all error
External Email - Use Caution Thank you for the reply. I guess it is possible that there were some issues with compiling, however I have been using it for a while without issue. I will look into that issue further. Thanks for all your help and feedback! Best, Daniel Callow On Thu, Jul 4, 2019 at 8:42 AM Yendiki, Anastasia wrote: > It's not an issue of compatibility. The tkregister2 executable doesn't > exist in whatever version you're sourcing when you run tracula. As far as I > can see, it should be there in both the stable6 and dev versions. Any > chance that something went wrong when you built the dev version on your > system and tkregister2 did not compile? > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Thursday, July 4, 2019 8:24:32 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Trac-all error > > > External Email - Use Caution > > When running on freesurfer 6.0 I get the following pop-up screen as well. > > *“tkregister2.bin” is not optimized for your Mac and needs to be updated.* > > This software will not work with future versions of macOS and needs to be > updated to improve compatibility. Contact the developer for more > information. > > > Just FYI. It does work on the freesurfer 6.0 version despite the pop-up. > It seems like trac-all is not compatible with the development version then? > > > 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 > > > On Thu, Jul 4, 2019 at 8:08 AM Daniel Callow wrote: > > Hello Anastasia, > > I was running this on freesurfer's dev version. I will try running it on > freesurfer 6.0. > > Best, > *Daniel Callow* > *PhD Student, Neuroscience and Conitive Science* > Exercise for Brain Health Lab > University of Maryland, College Park > *ddcc2...@gmail.com * > 443-254-6298 > > > On Thu, Jul 4, 2019 at 4:26 AM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > > Hi Daniel - Yes, this seems to be the problem: " tkregister2: Command not > found." What version of freesurfer are you using? > > > a.y > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Wednesday, July 3, 2019 2:06:27 PM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Trac-all error > > > External Email - Use Caution > > Hello, > > I am running trac-all preproc with the following code > > setenv FREESURFER_HOME /Applications/freesurfer_dev > > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > *#Must set SUBJECTS_DIR to where data is or else uses what was set up when > installing freesurfer* > > setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons > > > *#Must set up configuration file - see trac-all-config-file in > dti_analysis compository* > > *#In configuration file can change number of subject to perform analysis > on each cluster* > > > *#RUN FIRST* > trac-all -prep -c /Volumes/DANIEL/dmrirc.long.MCIP.example.sh > > > *and the attached configuration file. * > > *However, I get the following error.* > > #@# Intra-subject registration Tue Jul 2 18:21:42 EDT 2019 > > mri_convert > /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > > mri_convert > /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > > > $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ > > reading from > /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz... > > TR=9.62, TE=3.90, TI=450.00, flip angle=12.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... > > orientLAS > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz > > INFO: input image orientation is LIA > > INFO: input image determinant is -1 > > mri_convert -o
Re: [Freesurfer] Trac-all error
External Email - Use Caution Hello Anastasia, I was running this on freesurfer's dev version. I will try running it on freesurfer 6.0. Best, *Daniel Callow* *PhD Student, Neuroscience and Conitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Thu, Jul 4, 2019 at 4:26 AM Yendiki, Anastasia wrote: > Hi Daniel - Yes, this seems to be the problem: " tkregister2: Command not > found." What version of freesurfer are you using? > > > a.y > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Wednesday, July 3, 2019 2:06:27 PM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Trac-all error > > > External Email - Use Caution > > Hello, > > I am running trac-all preproc with the following code > > setenv FREESURFER_HOME /Applications/freesurfer_dev > > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > *#Must set SUBJECTS_DIR to where data is or else uses what was set up when > installing freesurfer* > > setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons > > > *#Must set up configuration file - see trac-all-config-file in > dti_analysis compository* > > *#In configuration file can change number of subject to perform analysis > on each cluster* > > > *#RUN FIRST* > trac-all -prep -c /Volumes/DANIEL/dmrirc.long.MCIP.example.sh > > > *and the attached configuration file. * > > *However, I get the following error.* > > #@# Intra-subject registration Tue Jul 2 18:21:42 EDT 2019 > > mri_convert > /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > > mri_convert > /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > > > $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ > > reading from > /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz... > > TR=9.62, TE=3.90, TI=450.00, flip angle=12.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... > > orientLAS > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz > > INFO: input image orientation is LIA > > INFO: input image determinant is -1 > > mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 > -oc -6.32147 -1.97853 6.55573 -rt nearest > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz > > mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 > -oc -6.32147 -1.97853 6.55573 -rt nearest > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz > > > $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ > > reading from > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... > > TR=9.62, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > Reslicing using nearest > > writing to > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz... > > tkregister2 --mov > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > --targ > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz > --regheader --noedit --fslregout > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anatorig2anat.mat > --reg > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anat2anatorig.dat > > tkregister2: Command not found. > > Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 > 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Tue Jul 2 18:21:47 EDT 2019 > > > #---
[Freesurfer] Trac-all error
External Email - Use Caution Hello, I am running trac-all preproc with the following code setenv FREESURFER_HOME /Applications/freesurfer_dev source $FREESURFER_HOME/SetUpFreeSurfer.csh *#Must set SUBJECTS_DIR to where data is or else uses what was set up when installing freesurfer* setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons *#Must set up configuration file - see trac-all-config-file in dti_analysis compository* *#In configuration file can change number of subject to perform analysis on each cluster* *#RUN FIRST* trac-all -prep -c /Volumes/DANIEL/dmrirc.long.MCIP.example.sh *and the attached configuration file. * *However, I get the following error.* #@# Intra-subject registration Tue Jul 2 18:21:42 EDT 2019 mri_convert /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz mri_convert /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz... TR=9.62, TE=3.90, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... orientLAS /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -6.32147 -1.97853 6.55573 -rt nearest /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -6.32147 -1.97853 6.55573 -rt nearest /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... TR=9.62, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Reslicing using nearest writing to /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz... tkregister2 --mov /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz --targ /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anatorig2anat.mat --reg /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anat2anatorig.dat tkregister2: Command not found. Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jul 2 18:21:47 EDT 2019 #- /Applications/freesurfer_dev/bin/trac-preproc #- #@# Inter-subject registration (base template) Tue Jul 2 18:21:49 EDT 2019 cp /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat /Volumes/DANIEL/dti_freesurf_MCIP/trac/base_MCIP0006/dmri/xfms cp: /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat: No such file or directory cp: /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat: No such file or directory Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jul 2 18:21:49 EDT 2019 *What might be causing the issue? Does it seem like tkregister2 isn't working?* *Thank you for help or assistance you can provide.* *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
[Freesurfer] Citing the development version for use of hippocampal/amygdala sub-field segmentation
External Email - Use Caution Hello, I used the longitudinal HippocampalSubfieldsAndNucleiOfAmygdala <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala?action=fullsearch=180=linkto%3A%22HippocampalSubfieldsAndNucleiOfAmygdala%22> pipeline to create subject-specific hippocampal ROI's for a paper I am preparing for submission. I would like to know what the best way to cite this technique is. This is what I currently have in my methods section. Subjects T1-weighted anatomical images were processed with the FreeSurfer image analysis suite (http://surfer.nmr.mgh.harvard.edu/, version 6.0) and Automated hippocampal subfield segmentation was performed for each subjects T1 weighted image using the Freesurfer longitudinal hippocampal subfield segmentation program(Iglesias et al., 2015, 2016). Do I need to cite my use of the development version? And if so how is the best way to go about doing this? 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tractstats2table error
External Email - Use Caution Sorry, I realized I used the pathstats.byvoxel.txt instead of pathstats.overall.txt. Attached is the correct .txt file and the new error I get from the python script called by tractstats2table pathstats.overall.txt Parsing the .stats files Building the table.. Traceback (most recent call last): File "/Applications/freesurfer_dev/bin/tractstats2table", line 368, in r1c1, rows, columns, table = sanitize_table(options, pretable) File "/Applications/freesurfer_dev/bin/tractstats2table", line 260, in sanitize_table if not 1 == len(pthwyset.keys()): File "/Applications/freesurfer_dev/bin/datastruct_utils.py", line 281, in keys return self.__ksl[:] TypeError: 'dict_keys' object is not subscriptable *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 Mon, May 13, 2019 at 9:04 AM Daniel Callow wrote: > Hello, > > I just ran trac-all on my data and am trying to use tractstats2table to > run some tract-based group level analysis. > > I have created a text file with the full paths to each conditions stats > file (attached below and tried to run the following command > > tractstats2table --load-pathstats-from-file > /Volumes/DANIEL/trac/stats_info/stats_rh.unc.txt --overall --tablefile > /Volumes/DANIEL/trac/stats_info/rh.unc.All.table > > > However, I get the following error message. > > > Parsing the .stats files > > Traceback (most recent call last): > > File "/Applications/freesurfer_dev/bin/tractstats2table", line 347, in > > > pathway_subj, measure_value_map = parsed.parse() > > File "/Applications/freesurfer_dev/bin/fsutils.py", line 288, in parse > > val = float(strlist[1]) > > ValueError: could not convert string to float: 'y' > > > Could someone please provide me some guidance on how to troubleshoot this? > > > *Daniel Callow* > *PhD Student, Neuroscience and Cognitive Science* > Exercise for Brain Health Lab > University of Maryland, College Park > *ddcc2...@gmail.com * > 443-254-6298 > /Volumes/DANIEL/trac/Ex.AES101.long.base_AES101/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES101.long.base_AES101/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES102.long.base_AES102/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES102.long.base_AES102/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES104.long.base_AES104/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES104.long.base_AES104/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES107.long.base_AES107/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES107.long.base_AES107/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES108.long.base_AES108/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES108.long.base_AES108/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES109.long.base_AES109/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES109.long.base_AES109/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES110.long.base_AES110/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES110.long.base_AES110/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES111.long.base_AES111/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES111.long.base_AES111/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES113.long.base_AES113/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES113.long.base_AES113/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES114.long.base_AES114/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES114.long.base_AES114/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES115.long.base_AES115/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES115.long.base_AES115/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES116.long.base_AES116/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES116.long.base_AES116/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES117.long.base_AES117/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Rest.AES117.long.base_AES117/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt /Volumes/DANIEL/trac/Ex.AES118.long.base_AES118/dpath/rh
[Freesurfer] tractstats2table error
External Email - Use Caution Hello, I just ran trac-all on my data and am trying to use tractstats2table to run some tract-based group level analysis. I have created a text file with the full paths to each conditions stats file (attached below and tried to run the following command tractstats2table --load-pathstats-from-file /Volumes/DANIEL/trac/stats_info/stats_rh.unc.txt --overall --tablefile /Volumes/DANIEL/trac/stats_info/rh.unc.All.table However, I get the following error message. Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer_dev/bin/tractstats2table", line 347, in pathway_subj, measure_value_map = parsed.parse() File "/Applications/freesurfer_dev/bin/fsutils.py", line 288, in parse val = float(strlist[1]) ValueError: could not convert string to float: 'y' Could someone please provide me some guidance on how to troubleshoot this? *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 /Volumes/DANIEL/trac/Ex.AES101.long.base_AES101/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES101.long.base_AES101/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES102.long.base_AES102/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES102.long.base_AES102/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES104.long.base_AES104/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES104.long.base_AES104/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES107.long.base_AES107/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES107.long.base_AES107/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES108.long.base_AES108/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES108.long.base_AES108/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES109.long.base_AES109/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES109.long.base_AES109/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES110.long.base_AES110/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES110.long.base_AES110/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES111.long.base_AES111/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES111.long.base_AES111/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES113.long.base_AES113/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES113.long.base_AES113/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES114.long.base_AES114/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES114.long.base_AES114/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES115.long.base_AES115/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES115.long.base_AES115/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES116.long.base_AES116/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES116.long.base_AES116/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES117.long.base_AES117/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES117.long.base_AES117/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES118.long.base_AES118/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES118.long.base_AES118/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES119.long.base_AES119/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES119.long.base_AES119/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES120.long.base_AES120/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES120.long.base_AES120/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES121.long.base_AES121/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES121.long.base_AES121/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES122.long.base_AES122/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES122.long.base_AES122/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES123.long.base_AES123/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Rest.AES123.long.base_AES123/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.byvoxel.txt /Volumes/DANIEL/trac/Ex.AES124.lo
[Freesurfer] trac-all -prep b0 inhomogeneity correction error
External Email - Use Caution Hello Doug, When running trac-all -prep and including b0 inhomogeneity correction with epidewarp.fsl I get the following error. FSL Version is $FSLVersion, must be 3.X or 4.X or 5.X Looking at the epidewarp.fsl source code I see that the error is occurring because of this section of the code. set FSLVersion = `cat $FSLDIR/etc/fslversion`; set FSLVerMaj = `echo $FSLVersion | cut -c 1` echo FSLVersion $FSLVersion echo FSLVerMaj $FSLVerMaj if($FSLVerMaj == 3) then set FSLPre = avw set DilFlag = -dil set FSLToFloat = avwmaths_32R set FSLToFloatFlag = () else if($FSLVerMaj == 4) then set FSLPre = fsl set DilFlag = -dilM set FSLToFloat = (fslmaths) set FSLToFloatFlag = (-odt float) else if($FSLVerMaj == 5) then set FSLPre = fsl set DilFlag = -dilM set FSLToFloat = (fslmaths) set FSLToFloatFlag = (-odt float) else echo "FSL Version is $FSLVersion, must be 3.X or 4.X or 5.X" exit 1; endif Since fsl is now at version 6.0.1 would epidewarp.fsl be compatible with this version? Could I simply include else if($FSLVerMaj == 6) then set FSLPre = fsl set DilFlag = -dilM set FSLToFloat = (fslmaths) set FSLToFloatFlag = (-odt float) or are these paramaters different under fsl 6.x+? 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] epidewarp.fsl error in trac-all script
External Email - Use Caution Hello freesurfer developers, When running trac-all the script seems to be getting tripped up on the epidewarp.fsl portion of the script and throwing a weird error about the fsl version? I am running trac-all -prep with bo homogeneity correction included in the configuration file. I get the following error. writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz... orientLAS /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 10 mri_convert -oni 96 -onj 96 -onk 53 -oid -0.998405 -0.0247418 0.0507528 -ojd 4.61648e-10 0.898878 0.438199 -okd 0.0564624 -0.4375 0.897444 -oc 2.21634 10.523 31.9495 -rt nearest /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz mri_convert.bin -oni 96 -onj 96 -onk 53 -oid -0.998405 -0.0247418 0.0507528 -ojd 4.61648e-10 0.898878 0.438199 -okd 0.0564624 -0.4375 0.897444 -oc 2.21634 10.523 31.9495 -rt nearest /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz normalizing out_i_direction: (-0.998405, -0.0247418, 0.0507528) -> (-0.998405, -0.0247418, 0.0507528) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz... TR=560.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998405, -0.0247418, 0.0507528) j_ras = (-4.61648e-10, -0.898878, -0.438199) k_ras = (0.0564624, -0.4375, 0.897444) Reslicing using nearest writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz... mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/phase/TE7.38_image01.dcm > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0info.dat fslroi /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_eddy.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/lowb.nii.gz 0 1 epidewarp.fsl --mag /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0mag.nii.gz --dph /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz --exf /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/lowb.nii.gz --epi /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_eddy.nii.gz --tediff 2.4600 --esp 0.7 --vsm /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/vsm.nii.gz --epidw /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi.nii.gz FSLVersion 6.0.1 FSLVerMaj 6 FSL Version is 6.0.1, must be 3.X or 4.X or 5.X Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Sat Apr 20 14:56:02 EDT 2019 Does this mean there is an issue with the trac-all script that makes it incompatable with fsl? I notice the --vsm /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/vsm.nii.gz portion of the epidewarp.fsl script was not created. Everything else that should go into it was created. Can anyone give me some guidance on why this might be happening? 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] trac-all running -jobs issue error
direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value /bin/rm: cannot remove `_tmp.*': No such file or directory /bin/rm: cannot remove `_ref*': No such file or directory /cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 83: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/ ys:/cell_root/software/fsl/new/sys/bin/remove_ext: No such file or directory /cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 84: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: [: -eq: unary operator expected Usage: fslroi fslroi fslroi Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Cannot open volume _tmp for reading! /cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 95: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$ Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value /bin/rm: cannot remove `_tmp.*': No such file or directory /bin/rm: cannot remove `_ref*': No such file or directory Linux compute-4-28.bswift.umd.edu 2.6.32-696.30.1.el6.x86_64 #1 SMP Fri May 18 11:50:44 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Apr 19 15:45:56 EDT 2019 Any idea why the script might be throwing this error? 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] issue running trac-all longitudinal
External Email - Use Caution Sorry, that fix did not infact fix the problem. I am still getting the following error. writing to /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mv -f /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Ex/image01.dcm > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dcminfo.dat mv -f /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvecs.tmp /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs mv -f /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvals.tmp /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvals orientLAS /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort ERROR: input file must be in NIfTI format Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Thu Apr 18 15:12:04 EDT 2019 Any help you can provide with debugging would be greatly appreciated. *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, Apr 19, 2019 at 8:04 AM Daniel Callow wrote: > Disabling root system integrity protection seems to have solved the > problem. > *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 Thu, Apr 18, 2019 at 6:12 PM Daniel Callow wrote: > >> Sorry, the beginning of the email seems to have been cut off. I was >> trying to run trac-all on one of my subjects to troubleshoot running the >> following command. >> >> trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh >> >> >> I posted the errors and attached the dmrirc file I used below. >> >> >> There seems to be an issue with >> >> >> >> >> >> writing to >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz... >> >> Saving bvals and bvecs >> >> mv -f >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs >> >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs >> >> mri_probedicom --i >> /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Ex/image01.dcm > >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dcminfo.dat >> >> mv -f >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvecs.tmp >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs >> >> mv -f >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvals.tmp >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvals >> >> orientLAS >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz >> >> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz >> >> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address >> >> Referenced from: >> /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib >> >> Expected in: /usr/lib/libSystem.B.dylib >> >> >> dyld: Symbol not found: ___emutls_get_address >> >> Referenced from: >> /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib >> >> Expected in: /usr/lib/libSystem.B.dylib >> >> >> Abort >> >> ERROR: input file must be in NIfTI format >> >> >> The error does not seem to be due to dwi_orig.nii.gz being missing as I see >> it in the folderr after it has been written there in a previous command. >> >> >> >> >> >> >> What could be leading to these issues? >> >> *Daniel Ca
Re: [Freesurfer] issue running trac-all longitudinal
External Email - Use Caution Disabling root system integrity protection seems to have solved the problem. *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 Thu, Apr 18, 2019 at 6:12 PM Daniel Callow wrote: > Sorry, the beginning of the email seems to have been cut off. I was trying > to run trac-all on one of my subjects to troubleshoot running the following > command. > > trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh > > > I posted the errors and attached the dmrirc file I used below. > > > There seems to be an issue with > > > > > > > > > writing to > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz... > > Saving bvals and bvecs > > mv -f > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs > > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs > > mri_probedicom --i > /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Ex/image01.dcm > > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dcminfo.dat > > mv -f > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvecs.tmp > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs > > mv -f > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvals.tmp > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvals > > orientLAS > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz > > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz > > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > > Referenced from: > /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > dyld: Symbol not found: ___emutls_get_address > > Referenced from: > /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > Abort > > ERROR: input file must be in NIfTI format > > > The error does not seem to be due to dwi_orig.nii.gz being missing as I see > it in the folderr after it has been written there in a previous command. > > > > > > > What could be leading to these issues? > > *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 Thu, Apr 18, 2019 at 3:18 PM Daniel Callow wrote: > >> Hello, >> >> trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh with the >> attached configuration file. >> >> >> I get the following error message >> >> >> >> INFO: no Siemens slice order reversal detected (good!). >> >> TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 >> >> i_ras = (-1, -0, 0) >> >> j_ras = (-0, -1, 0) >> >> k_ras = (-0, -0, 1) >> >> writing to >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz... >> >> Saving bvals and bvecs >> >> mv -f >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs >> >> mri_probedicom --i >> /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/image01.dcm >> > >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dcminfo.dat >> >> mv -f >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvecs.tmp >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs >> >> mv -f >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvals.tmp >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvals >> >> orientLAS >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz >> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz >> >> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address >> >> Referenced from: >> /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib >> >> Expected in: /usr/lib/libSystem.B.dylib >> >> >> dyld: Symbol not found: ___emutls_get_address >> >> Referenced fro
Re: [Freesurfer] issue running trac-all longitudinal
External Email - Use Caution Sorry, the beginning of the email seems to have been cut off. I was trying to run trac-all on one of my subjects to troubleshoot running the following command. trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh I posted the errors and attached the dmrirc file I used below. There seems to be an issue with writing to /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mv -f /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Ex/image01.dcm > /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dcminfo.dat mv -f /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvecs.tmp /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs mv -f /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvals.tmp /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvals orientLAS /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort ERROR: input file must be in NIfTI format The error does not seem to be due to dwi_orig.nii.gz being missing as I see it in the folderr after it has been written there in a previous command. What could be leading to these issues? *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 Thu, Apr 18, 2019 at 3:18 PM Daniel Callow wrote: > Hello, > > trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh with the > attached configuration file. > > > I get the following error message > > > > INFO: no Siemens slice order reversal detected (good!). > > TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 > > i_ras = (-1, -0, 0) > > j_ras = (-0, -1, 0) > > k_ras = (-0, -0, 1) > > writing to > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz... > > Saving bvals and bvecs > > mv -f > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs > > mri_probedicom --i > /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/image01.dcm > > > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dcminfo.dat > > mv -f > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvecs.tmp > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs > > mv -f > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvals.tmp > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvals > > orientLAS > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz > > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > > Referenced from: > /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > dyld: Symbol not found: ___emutls_get_address > > Referenced from: > /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > Abort > > ERROR: input file must be in NIfTI format > > Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 > 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Thu Apr 18 15:16:47 EDT 2019 > > > > and after that I get > > > -- > > SUBJECT base_AES101 > > DATE Thu Apr 18 15:11:44 EDT 2019 > > USER amos > > HOST 255a-280.umd.edu > > PROCESSOR x86_64 > > OS Darwin > > Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 > 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64 > > $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ > > /Applicat
[Freesurfer] issue running trac-all longitudinal
External Email - Use Caution Hello, trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh with the attached configuration file. I get the following error message INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mv -f /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/image01.dcm > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dcminfo.dat mv -f /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvecs.tmp /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs mv -f /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvals.tmp /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvals orientLAS /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort ERROR: input file must be in NIfTI format Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Thu Apr 18 15:16:47 EDT 2019 and after that I get -- SUBJECT base_AES101 DATE Thu Apr 18 15:11:44 EDT 2019 USER amos HOST 255a-280.umd.edu PROCESSOR x86_64 OS Darwin Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ /Applications/freesurfer//bin/trac-preproc PWD /Volumes/DANIEL/dti_freesurf CMD cp /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/mni2anatorig.mat /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/anatorig2mni.mat /Volumes/DANIEL/dti_freesurf/trac/base_AES101/dmri/xfms Any idea what might be causing the issue? 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/ # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Volumes/DANIEL/dti_freesurf/trac # Subject IDs (one per time point per subject) # set subjlist = (Ex.AES101 Rest.AES101) # Longitudinal base template subject IDs (one for each time point above) # set baselist = (base_AES101 base_AES101) # In case you want to analyze only Huey and Louie # Default: Run analysis on all time points and subjects # set runlist = () # 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/dti_freesurf/diffusio
Re: [Freesurfer] Creating anatomical ROI's
External Email - Use Caution
Thank you Doug!
*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 Tue, Apr 9, 2019 at 11:03 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Try using mri_binarize with the hipsubfields as input and using --match
> 231 232
> This will create a mask of all voxels that match the numbers
>
> On 4/8/2019 8:49 PM, Daniel Callow wrote:
>
> External Email - Use Caution
> Hello,
>
> I am trying to create ROI volumes from the hippocampal subfields I get from
>
> mri_vol2vol --mov
> /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lowb.nii.gz --targ
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz
> --inv --interp nearest --o
> /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lhipp2diff.nii.gz
> --reg /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/register.dat
> --no-save-reg
>
> so that I can merge specific hippocampal subfields I want together into a
> single ROI (like --id 231 and --id 232). However, when looking through the
> freesurfer options like mri_vol2vol there isn't an option to index to
> specific segments of the lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz
> volume
> I have converted into dti space.
>
> My plan is to combine the head and body segments and extract average
> diffusion information from the combined mask.
>
> Anything that can help get me in the right direction would be greatly
> appreciated!
>
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com *
> 443-254-6298
>
>
> ___
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>
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[Freesurfer] Creating anatomical ROI's
External Email - Use Caution
Hello,
I am trying to create ROI volumes from the hippocampal subfields I get from
mri_vol2vol --mov
/Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lowb.nii.gz --targ
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz
--inv --interp nearest --o
/Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lhipp2diff.nii.gz
--reg /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/register.dat
--no-save-reg
so that I can merge specific hippocampal subfields I want together into a
single ROI (like --id 231 and --id 232). However, when looking through the
freesurfer options like mri_vol2vol there isn't an option to index to
specific segments of the
lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz volume
I have converted into dti space.
My plan is to combine the head and body segments and extract average
diffusion information from the combined mask.
Anything that can help get me in the right direction would be greatly
appreciated!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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Re: [Freesurfer] dt_recon ERROR: DTIloadBValues
External Email - Use Caution
It might be an issue with the current freesurfer dev version because when I
change it back to the Freesurfer 6.0 version it works perfectly fine? And
has no issues reading them.
On Tue, Apr 2, 2019 at 1:51 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> It is having problems reading both the bvals and the bvecs
>
> On 4/2/19 9:34 AM, Daniel Callow wrote:
>
> > External Email - Use Caution
> >
> > Hello,
> >
> > I am running dt_Recon with the following specifications and am running
> > into this issue? I wasn't running into this issue previously. Two
> > changes I made are I added the --eres-save flag and I am running the
> > code on the dev version instead of the freesurfer6.0 version. Any idea
> > what could be contributing to this issue?
> >
> > I am running the following
> >
> > mri_convert image01.dcm
> > /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/dwi.nii.gz
> >
> >
> >
> > dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i
> > /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/dwi.nii.gz
> > --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --eres-save
> > --o /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}
> >
> >
> > and get an error at this point
> >
> >
> >
> > #@#---
> >
> > Fitting Tensors
> >
> > Mon Apr1 15:16:29 EDT 2019
> >
> > cd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES114.Rest
> >
> > mri_glmfit --y
> > /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz
> > --glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 --nii.gz
> > --dti dwi.bvals dwi.voxel_space.bvecs --eres-save
> >
> >
> > $Id: mri_glmfit.c,v 1.246 2017/02/15 21:04:18 greve Exp $
> >
> > cwd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES114.Rest
> >
> > cmdline mri_glmfit --y
> > /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz
> > --glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 --nii.gz
> > --dti dwi.bvals dwi.voxel_space.bvecs --eres-save
> >
> > sysnameDarwin
> >
> > hostname 255a-280.umd.edu <http://255a-280.umd.edu>
> >
> > machinex86_64
> >
> > user amos
> >
> > FixVertexAreaFlag = 1
> >
> > UseMaskWithSmoothing 1
> >
> > OneSampleGroupMean 0
> >
> > y/Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz
> >
> > logyflag 1
> >
> > usedti1
> >
> > glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114
> >
> > IllCondOK 0
> >
> > ReScaleX 1
> >
> > DoFFx 0
> >
> > Creating output directory
> /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114
> >
> > Loading y from
> > /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz
> >
> > ... done reading.
> >
> > Using DTI
> >
> > Loading BValues from dwi.bvals
> >
> > ERROR: DTIloadBValues(dwi.bvals): could not scan value(s)
> >
> > Found 65 bvalues
> >
> > ERROR: DTIloadBValues(dwi.bvals): could not scan value(s)
> >
> > Loading BVectors from dwi.voxel_space.bvecs
> >
> > ERROR: DTIloadBValues(dwi.voxel_space.bvecs): could not scan value(s)
> >
> > Found 0 bvectorss
> >
> > ERROR: DTIloadBValues: no bvectors found in dwi.voxel_space.bvecs
> >
> >
> >
> > 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
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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[Freesurfer] dt_recon ERROR: DTIloadBValues
External Email - Use Caution
Hello,
I am running dt_Recon with the following specifications and am running into
this issue? I wasn't running into this issue previously. Two changes I made
are I added the --eres-save flag and I am running the code on the dev
version instead of the freesurfer6.0 version. Any idea what could be
contributing to this issue?
I am running the following
mri_convert image01.dcm
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/dwi.nii.gz
dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/dwi.nii.gz
--s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --eres-save --o
/Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}
and get an error at this point
#@#---
Fitting Tensors
Mon Apr 1 15:16:29 EDT 2019
cd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES114.Rest
mri_glmfit --y
/Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz --glmdir
/Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 --nii.gz --dti dwi.bvals
dwi.voxel_space.bvecs --eres-save
$Id: mri_glmfit.c,v 1.246 2017/02/15 21:04:18 greve Exp $
cwd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES114.Rest
cmdline mri_glmfit --y
/Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz --glmdir
/Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 --nii.gz --dti dwi.bvals
dwi.voxel_space.bvecs --eres-save
sysname Darwin
hostname 255a-280.umd.edu
machine x86_64
user amos
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz
logyflag 1
usedti 1
glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114
Loading y from
/Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz
... done reading.
Using DTI
Loading BValues from dwi.bvals
ERROR: DTIloadBValues(dwi.bvals): could not scan value(s)
Found 65 bvalues
ERROR: DTIloadBValues(dwi.bvals): could not scan value(s)
Loading BVectors from dwi.voxel_space.bvecs
ERROR: DTIloadBValues(dwi.voxel_space.bvecs): could not scan value(s)
Found 0 bvectorss
ERROR: DTIloadBValues: no bvectors found in dwi.voxel_space.bvecs
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
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Re: [Freesurfer] segmentHA_T1.sh
External Email - Use Caution
Thank you for the suggestion. Is it possible to just calculate
certain sub-field volumes such as the head body and tail as opposed to all
of them?
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
On Mon, Apr 1, 2019 at 1:22 PM Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:
> External Email - Use Caution
>
> How about quantifyHAsubregions.sh?
>
> Cheers,
>
> /E
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
> *From: * on behalf of Daniel
> Callow
> *Reply-To: *Freesurfer support list
> *Date: *Monday, 1 April 2019 at 13:19
> *To: *Freesurfer support list
> *Subject: *[Freesurfer] segmentHA_T1.sh
>
>
>
> *External Email - Use Caution*
>
> I thought a solution like this might work but there seems to be an issue
> reading in the file.
>
>
>
> I tried using mri_segstats on the .mgz file like this to create the stats
> file as this is what I do for my dt_recon results however it doesn't seem
> to work when I just want the volume stats?
>
>
>
> mri_segstats --seg
> /Volumes/DANIEL/freesurf/${cond}.${subj}.long.base_${subj}/mri/lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz
> --ctab /Applications/freesurfer_dev/FreeSurferColorLUT.txt --id 226 --id
> 231 --id 232 --sum
> ${SUBJECTS_DIR}/${cond}.${subj}/stats/lhipp_volume.stats
>
>
>
>
>
> Any ideas on how to make this work or a potential other work around.
>
>
>
> Best,
>
> *Daniel Callow*
>
> *PhD Student, Neuroscience and Cognitive Science*
>
> Exercise for Brain Health Lab
>
> University of Maryland, College Park
>
> *ddcc2...@gmail.com *
>
> 443-254-6298
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[Freesurfer] segmentHA_T1.sh
External Email - Use Caution
I thought a solution like this might work but there seems to be an issue
reading in the file.
I tried using mri_segstats on the .mgz file like this to create the stats
file as this is what I do for my dt_recon results however it doesn't seem
to work when I just want the volume stats?
mri_segstats --seg
/Volumes/DANIEL/freesurf/${cond}.${subj}.long.base_${subj}/mri/lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz
--ctab /Applications/freesurfer_dev/FreeSurferColorLUT.txt --id 226 --id 231
--id 232 --sum ${SUBJECTS_DIR}/${cond}.${subj}/stats/lhipp_volume.stats
Any ideas on how to make this work or a potential other work around.
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
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[Freesurfer] segmentHA_T1.sh
External Email - Use Caution Hello, I have finished running segmentHA_T1.sh on my data and have gotten all the .mgz and .txt files in my mri folder. I would like to collect all the hippocampal volumes and get them into a table to run stats on. When reading the documentation it says that It will also produce files in the stats folder called hipposubfields.[lr]h.T1.v2x.stats and amygdalar-nuclei.[lr]h.T1.v2x.stats. These can be compiled across subject with, eg, asegstats2table --statsfile=hipposubfields.lh.T1.v21.stats --tablefile=hipposubfields.lh.T1.v21.dat ... However, the stats folders for my subjects do not have these files in the stats folder. Just the usual aseg.stats lh.aparc.a2009s.stats lh.aparc.DKTatlas.stats lh.aparc.pial.stats lh.aparc.stats lh.BA_exvivo.stats lh.BA_exvivo.thresh.stats lh.curv.stats lh.w-g.pct.stats rh.aparc.a2009s.stats rh.aparc.DKTatlas.stats rh.aparc.pial.stats rh.aparc.stats rh.BA_exvivo.stats rh.BA_exvivo.thresh.stats rh.curv.stats rh.w-g.pct.stats wmparc.stats Is there a way to get the correct stats files in my stats folder so I can use the suggested command? Or is there a way to extract the information from the .txt files? Any help you can provide would be greatly appreciated! *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] segmentHA_T1_long.sh HBT issue
External Email - Use Caution The issue was that I was using the freesurfer 6.0 version of freeview and not the development version. Thanks for your help Eugenio! 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] segmentHA_T1_long.sh HBT issue
External Email - Use Caution Hello, To add to my original post it seems the issue is I am not able to look at these merged images or that the HBT file write out seems to be wrong? I don't know how to post a picture to the listserve so someone can determine if I am just looking at it incorrectly in freeview? Any help is greatly appreciated! 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] segmentHA_T1_long.sh HBT issue
External Email - Use Caution Hello, I have run *segmentHA_T1_long.sh from the developer freesurfer version and am looking to segment and visualize the head body and tail of the left and right hippocampus.* *However, when looking at the lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz and other files for each subject I see only amygdala and subfield segmentations. How do I use the outputs to create a head body and tail segmentation that I can visualize and extract values from?* *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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentHA_T1_long.sh error {Disarmed}
External Email - Use Caution Hi Eugenia, I did not get any other output. I think it was an issue with runtime. I closed out Matlab and reran the script and had no issues. I think the problem may have had to do with the fact that I already had a different version of Matlab up when running the script. Best, Daniel On Mon, Mar 25, 2019 at 9:23 AM Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > External Email - Use Caution > > Hi Daniel, > > Can you please give us some more information? How did you call the script? > Did you get any other output? Did the running case complete without errors? > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > > > Research staff > > Martinos Center for Biomedical Imaging > > Massachusetts General Hospital > > > > Research Affiliate > > Computer Science and Artificial Intelligence Laboratory (CSAIL) > > Massachusetts Institute of Technology > > > > Lecturer on Radiology > > Harvard Medical School > > > > http://www.jeiglesias.com > > > > > > *From: * on behalf of Daniel > Callow > *Reply-To: *Freesurfer support list > *Date: *Sunday, 24 March 2019 at 13:28 > *To: *Freesurfer support list > *Subject: *[Freesurfer] segmentHA_T1_long.sh error > > > > *External Email - Use Caution* > > Hello, > > > > When trying to run the segmentHA_T1_long.sh command on my data I get the > following error log posted below (I ran several versions of a for loop and > got issues with all of them). I closed out the matlab browsers and am > retrying the code again to see if it is reproducible and so afar it is > running. I just wanted to get an idea if this is a known problem. > > > > Best, > > Daniel > > > > > >Segmentation violation detected at Sat Mar 23 18:31:18 2019 > > > > > > Configuration: > > Crash Decoding : Disabled > > Current Visual : Quartz > > Default Encoding : ISO-8859-1 > > MATLAB Architecture: maci64 > > MATLAB Root: /Applications/freesurfer_dev/MCRv84 > > MATLAB Version : 8.4.0.150421 (R2014b) > > Operating System : Darwin 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct > 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 > > Processor ID : x86 Family 6 Model 44 Stepping 2, GenuineIntel > > Software OpenGL: 0 > > Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java > HotSpot(TM) 64-Bit Server VM mixed mode > > Window System : Quartz > > > > Fault Count: 1 > > > > > > Abnormal termination: > > Segmentation violation > > > > Register State (from fault): > > RAX = 7f9c4806f000 RBX = 7f9c4806f000 > > RCX = 79ab52d0 RDX = 00011392e97e > > RSP = 7f9c4806f000 RBP = 9b6309ab52d0 > > RSI = 7f9c47637ba0 RDI = > > > >R8 = 7f9c4a0a3270 R9 = 7f9c4806f000 > > R10 = 00011e59176a R11 = > > R12 = 79ab5330 R13 = 00011377c3c7 > > R14 = 79ab53a0 R15 = 00011e591777 > > > > RIP = 0001188c5f40 RFL = 7f9c4a0a3270 > > > >CS = 9b6300305bc3 FS = 00011e59176a GS = 7f9c4806f1e8 > > > > Stack Trace (from fault): > > [ 0] 0x0001075f6e64 > /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00028260 > _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052 > > [ 1] 0x0001075faa2a > /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00043562 > _ZN2fl4test17terminate_handledEv+0906 > > [ 2] 0x0001075fa477 > /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwfl.dylib+00042103 > _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119 > > [ 3] 0x00010c443b7a > /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00387962 > _Z32mnRunPathDependentInitializationv+3146 > > [ 4] 0x00010c443e58 > /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00388696 > _Z32mnRunPathDependentInitializationv+3880 > > [ 5] 0x00010c441733 > /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00378675 > mnFatalSignalHandler+0275 > > [ 6] 0x7fffbac1cb3a > /usr/lib/s
[Freesurfer] segmentHA_T1_long.sh error
_ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE3runEv+0023 [ 76] 0x00010c401f90 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00118672 _ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+0032 [ 77] 0x000105114005 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+1205 [ 78] 0x00010dbeba65 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+0501 [ 79] 0x0001051e3a45 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693 [ 80] 0x0001051df152 /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+0834 [ 81] 0x0001051dee5e /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+0078 [ 82] 0x00010c40218f /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+0095 [ 83] 0x00010c40249f /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+0335 [ 84] 0x00010c3e8d1b /Applications/freesurfer_dev/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+0059 [ 85] 0x7fffbac2693b /usr/lib/system/libsystem_pthread.dylib+00014651 _pthread_body+0180 [ 86] 0x7fffbac26887 /usr/lib/system/libsystem_pthread.dylib+00014471 _pthread_body+ [ 87] 0x7fffbac2608d /usr/lib/system/libsystem_pthread.dylib+00012429 thread_start+0013 If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/ A technical support engineer might contact you with further information. Thank you for your help. *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
Re: [Freesurfer] segmentHA_T1_long.sh: Command not found.
External Email - Use Caution
Sorry,
I realized I did not have the path to freesurfer in my script set to
the dev version. It was set to the FS6.0 version.
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
On Sat, Mar 23, 2019 at 4:39 PM Daniel Callow wrote:
> Hello,
>
> I am trying to use the segmentHA_T1_long.sh command on my longitudinal
> data. I have already run all the previous steps and have even successfully
> run longHippoSubfieldsT1.sh. However I want to use the segmentHA version to
> get my hippocampal segmentations.
>
> I assume the issue has something to do with the script not being in the
> FS6.0 version I downloaded? When looking at the literature for installation
> all I could find was info on installing runtime which I already have.
>
> Any help debugging the issue would be greatly appreciated.
>
> Below is the code I ran.
>
> #!/bin/tcsh
>
>
> setenv FREESURFER_HOME /Applications/freesurfer
>
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
>
> foreach subj (MCIP0031 MCIP0032 MCIP0033 MCIP0035 MCIP0036 MCIP0041
> MCIP0048 MCIP0052 MCIP0053 MCIP0054 MCIP0055 MCIP0058 MCIP0061)
>
>
> setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_MCIP
>
>
> segmentHA_T1_long.sh base_${subj}
>
>
> end
>
>
> I get the following error.
>
>
> [hlhp-105:/Volumes/DANIEL/freesurfer_MCIP] administrator%
> ./recon-all_longitudinal_hippo.sh
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
> segmentHA_T1_long.sh: Command not found.
>
>
> *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
>
___
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[Freesurfer] segmentHA_T1_long.sh: Command not found.
External Email - Use Caution
Hello,
I am trying to use the segmentHA_T1_long.sh command on my longitudinal
data. I have already run all the previous steps and have even successfully
run longHippoSubfieldsT1.sh. However I want to use the segmentHA version to
get my hippocampal segmentations.
I assume the issue has something to do with the script not being in the
FS6.0 version I downloaded? When looking at the literature for installation
all I could find was info on installing runtime which I already have.
Any help debugging the issue would be greatly appreciated.
Below is the code I ran.
#!/bin/tcsh
setenv FREESURFER_HOME /Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
foreach subj (MCIP0031 MCIP0032 MCIP0033 MCIP0035 MCIP0036 MCIP0041
MCIP0048 MCIP0052 MCIP0053 MCIP0054 MCIP0055 MCIP0058 MCIP0061)
setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_MCIP
segmentHA_T1_long.sh base_${subj}
end
I get the following error.
[hlhp-105:/Volumes/DANIEL/freesurfer_MCIP] administrator%
./recon-all_longitudinal_hippo.sh
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
segmentHA_T1_long.sh: Command not found.
*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
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all could not read surface file error
External Email - Use Caution Hello, During recon-all I keep running into the same error for one of my subjects. #@# Make White Surf rh Fri Mar 22 00:57:11 EDT 2019 /Volumes/DANIEL/freesurfer/Rest.AES118/scripts \n mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs Rest.AES118 rh \n using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/filled.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/brain.finalsurfs.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/../mri/aseg.presurf.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/wm.mgz... 25155 bright wm thresholded. 1843 bright non-wm voxels segmented. reading original surface position from /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig... mris_make_surfaces: could not read surface file /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig ERROR: reading /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig Read 0 bytes, expected 1 Argument list too long Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 recon-all -s Rest.AES118 exited with ERRORS at Fri Mar 22 00:57:16 EDT 2019 For more details, see the log file /Volumes/DANIEL/freesurfer/Rest.AES118/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks for any help you can provide with debugging! *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
Re: [Freesurfer] recon-all error
External Email - Use Caution Hello Andrew, I tried deleting the files and running the recon-all script again and found I no longer got the nu_correct error. However, I am now getting the following error (which I have seen before). #@# Make White Surf rh Thu Mar 21 13:52:31 EDT 2019 /Volumes/DANIEL/freesurfer/Rest.AES118/scripts \n mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs Rest.AES118 rh \n using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/filled.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/brain.finalsurfs.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/../mri/aseg.presurf.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/wm.mgz... 25155 bright wm thresholded. 1843 bright non-wm voxels segmented. reading original surface position from /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig... mris_make_surfaces: could not read surface file /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig ERROR: reading /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig Read 0 bytes, expected 1 Argument list too long Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 recon-all -s Rest.AES118 exited with ERRORS at Thu Mar 21 13:52:36 EDT 2019 For more details, see the log file /Volumes/DANIEL/freesurfer/Rest.AES118/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting It seems that when I run this subject sometimes it runs no problem, but when I try again on the exact same subject Dicoms I may or may not get an error. Any ideas what could be causing this/these errors? 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 On Tue, Mar 19, 2019 at 4:51 PM Hoopes, Andrew wrote: > It’s only happening for one subject, right? nu_correct isn’t actually a > freesurfer tool, it’s an mni tool. I would try to troubleshoot this by > installing a newer version of minc for osx: > http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/minc-toolkit-1.9.16-20180117-Darwin-10.8-x86_64.dmg > > > > Then, set the following BEFORE sourcing freesurfer and try rerunning the > failed recon: > > > > export MINC_BIN_DIR=/opt/minc/1.9.16/bin > > export MINC_LIB_DIR=/opt/minc/1.9.16/lib > > > > best > > Andrew > > > > > > *From: * on behalf of Daniel > Callow > *Reply-To: *FS Help > *Date: *Tuesday, March 19, 2019 at 4:14 PM > *To: *FS Help > *Subject: *Re: [Freesurfer] recon-all error > > > > *External Email - Use Caution* > > Hi Andrew, > > > > I am on a mac pro running Sierra 10.12.6 > > > > 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 > > > > > > On Tue, Mar 19, 2019 at 2:40 PM Hoopes, Andrew > wrote: > > Hi Daniel, I’ve never seen this error before. I assume you’re on a mac – > what version are you using? > > Andrew > > > > > > *From: * on behalf of Daniel > Callow > *Reply-To: *FS Help > *Date: *Tuesday, March 19, 2019 at 10:45 AM > *To: *FS Help > *Subject: *[Freesurfer] recon-all error > > > > *External Email - Use Caution* > > Hello, > > I am trying to run recon-all on a dataset and am running into errors with > one of my subjects. > > > > I get an error at the following point > > > > Iteration 1 Tue Mar 19 10:11:08 EDT 2019 > > nu_correct -clobber ./tmp.mri_nu_correct.mni.40972/nu0.mnc > ./tmp.mri_nu_correct.mni.40972/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.40972/0/ -iterations 1000 -distance 50 > > [administra...@hlhp-105.umd.edu:/Volumes/DANIEL/freesurfer/Ex.AES118/mri/] > [2019-03-19 10:11:09] running: > > /Applications/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask > -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nok
Re: [Freesurfer] recon-all error
External Email - Use Caution Hi Andrew, I am on a mac pro running Sierra 10.12.6 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 On Tue, Mar 19, 2019 at 2:40 PM Hoopes, Andrew wrote: > Hi Daniel, I’ve never seen this error before. I assume you’re on a mac – > what version are you using? > > Andrew > > > > > > *From: * on behalf of Daniel > Callow > *Reply-To: *FS Help > *Date: *Tuesday, March 19, 2019 at 10:45 AM > *To: *FS Help > *Subject: *[Freesurfer] recon-all error > > > > *External Email - Use Caution* > > Hello, > > I am trying to run recon-all on a dataset and am running into errors with > one of my subjects. > > > > I get an error at the following point > > > > Iteration 1 Tue Mar 19 10:11:08 EDT 2019 > > nu_correct -clobber ./tmp.mri_nu_correct.mni.40972/nu0.mnc > ./tmp.mri_nu_correct.mni.40972/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.40972/0/ -iterations 1000 -distance 50 > > [administra...@hlhp-105.umd.edu:/Volumes/DANIEL/freesurfer/Ex.AES118/mri/] > [2019-03-19 10:11:09] running: > > /Applications/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask > -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp > -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ > ./tmp.mri_nu_correct.mni.40972/nu0.mnc > ./tmp.mri_nu_correct.mni.40972/nu1.imp > > > > > Processing:.Done > > > Processing:.Done > > > Processing:.Done > > > Processing:.Done > > > Processing:.Done > > > Processing:.Done > > > Processing:.Done > > > Processing:.Done > > > Processing:.Done > > > Processing:.Done > > ncvarget: ncid 4; varid 6: Argument list too long > > miicv_get: MINC package entry point > > nu_estimate_np_and_em: crashed while running mincmath (termination > status=768) > > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=768) > > ERROR: nu_correct > > Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 > 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 > > > > recon-all -s Ex.AES118 exited with ERRORS at Tue Mar 19 10:11:18 EDT 2019 > > > > For more details, see the log file > /Volumes/DANIEL/freesurfer/Ex.AES118/scripts/recon-all.log > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > Any help you can provide for troubleshooting would be greatly appreciated. > > *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
[Freesurfer] recon-all error
External Email - Use Caution Hello, I am trying to run recon-all on a dataset and am running into errors with one of my subjects. I get an error at the following point Iteration 1 Tue Mar 19 10:11:08 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ -iterations 1000 -distance 50 [administra...@hlhp-105.umd.edu:/Volumes/DANIEL/freesurfer/Ex.AES118/mri/] [2019-03-19 10:11:09] running: /Applications/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.imp Processing:.Done Processing:.Done Processing:.Done Processing:.Done Processing:.Done Processing:.Done Processing:.Done Processing:.Done Processing:.Done Processing:.Done ncvarget: ncid 4; varid 6: Argument list too long miicv_get: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 recon-all -s Ex.AES118 exited with ERRORS at Tue Mar 19 10:11:18 EDT 2019 For more details, see the log file /Volumes/DANIEL/freesurfer/Ex.AES118/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any help you can provide for troubleshooting would be greatly appreciated. *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] dt_recon multiple dti scans
External Email - Use Caution Hello Doug, If I collected 3 dti scans at each time point and I wanted to know how would I go about incorporating them all into dt_recon to improve my SNR? Could I just pull all the DICOMS into 1 folder? Or process each one separately? Thanks, Daniel -- *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
Re: [Freesurfer] mri_segstats issue with hippocampal subfields
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Never mind. I see that I can use those to id #'s to call
from FreeSurferColorLUT.txt.
I assume that those Id's are consistent for both left and right hippocampus.
Thanks for the help!
*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 Wed, Mar 6, 2019 at 1:09 PM Daniel Callow wrote:
> Hi Doug,
>
> Thank you for your reply!
>
>
> Unfortunately when I run the same code as before but by calling to
> /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
> instead of /Applications/freesurfer/FreeSurferColorLUT.txt and using the
> assosciated --id #'s as shown below
>
> mri_segstats --seg
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
> --mul 1000 --ctab
> /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
> --id 226 --id 205 --id 206 --id 208 --id 209 --id 210 --i
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./radialdiff-masked.nii.gz
> --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.radialdiff.stats
>
>
>
> I get the following error.
>
>
> Loading /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest./rhipp2diff.nii.gz
>
> CTABreadASCII(/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt):
> badly formed file
>
> No such file or directory
>
> ERROR: reading
> /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
>
>
> any idea how I could make it a formed file that is compatible?
>
>
> 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
>
>
> On Wed, Mar 6, 2019 at 12:56 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt
>> The first number should be the one you are looking for.
>>
>> On 3/6/19 12:26 PM, Daniel Callow wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hello,
>> >
>> > I am trying to extract stats from the hippocampal subfield volumes
>> > that I have warped to diffusion space.
>> >
>> > mri_vol2vol --mov
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz
>> > --targ
>> >
>> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz
>>
>> > --inv --interp nearest --o
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
>> > --reg
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat
>> > --no-save-reg
>> >
>> >
>> > Then I run
>> >
>> >
>> > mri_segstats --seg
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
>> > --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id
>> > 552 --id 556 --id 557 --id 558 --i
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz
>> > --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats
>> >
>> >
>> > using the --i id# from FreeSurferColorLUT.txt.
>> >
>> >
>> > However, looking at the values of the hippocampal subfield volume I
>> > see that the Id's are all in the 200's?
>> >
>> >
>> > Is there a txt file that has the labelings like in
>> > FreeSurferColorLUT.txt for these hippocampal subfields?
>> >
>> >
>> > Thank you for any help you can provide!
>> >
>> > *Daniel Callow*
>> > /PhD Student, Neuroscience and Cognitive Science/
>> > Exercise for Brain Health Lab
>> > University of Maryland, College Park
>> > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>_
>> > 443-254-6298
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>
>
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Re: [Freesurfer] mri_segstats issue with hippocampal subfields
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Hi Doug,
Thank you for your reply!
Unfortunately when I run the same code as before but by calling to
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
instead of /Applications/freesurfer/FreeSurferColorLUT.txt and using the
assosciated --id #'s as shown below
mri_segstats --seg
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
--mul 1000 --ctab
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
--id 226 --id 205 --id 206 --id 208 --id 209 --id 210 --i
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./radialdiff-masked.nii.gz
--sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.radialdiff.stats
I get the following error.
Loading /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest./rhipp2diff.nii.gz
CTABreadASCII(/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt):
badly formed file
No such file or directory
ERROR: reading
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
any idea how I could make it a formed file that is compatible?
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
On Wed, Mar 6, 2019 at 12:56 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt
> The first number should be the one you are looking for.
>
> On 3/6/19 12:26 PM, Daniel Callow wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I am trying to extract stats from the hippocampal subfield volumes
> > that I have warped to diffusion space.
> >
> > mri_vol2vol --mov
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz
> > --targ
> >
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz
>
> > --inv --interp nearest --o
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
> > --reg
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat
> > --no-save-reg
> >
> >
> > Then I run
> >
> >
> > mri_segstats --seg
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
> > --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id
> > 552 --id 556 --id 557 --id 558 --i
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz
> > --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats
> >
> >
> > using the --i id# from FreeSurferColorLUT.txt.
> >
> >
> > However, looking at the values of the hippocampal subfield volume I
> > see that the Id's are all in the 200's?
> >
> >
> > Is there a txt file that has the labelings like in
> > FreeSurferColorLUT.txt for these hippocampal subfields?
> >
> >
> > Thank you for any help you can provide!
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>_
> > 443-254-6298
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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[Freesurfer] mri_segstats issue with hippocampal subfields
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Hello,
I am trying to extract stats from the hippocampal subfield volumes that I
have warped to diffusion space.
mri_vol2vol --mov
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz
--inv --interp nearest --o
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
--reg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat
--no-save-reg
Then I run
mri_segstats --seg
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
--ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id 552
--id 556 --id 557 --id 558 --i
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz
--sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats
using the --i id# from FreeSurferColorLUT.txt.
However, looking at the values of the hippocampal subfield volume I see
that the Id's are all in the 200's?
Is there a txt file that has the labelings like in FreeSurferColorLUT.txt
for these hippocampal subfields?
Thank you for any help you can provide!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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[Freesurfer] citing freesurfer
External Email - Use Caution Hello, How should I go about properly citing freesurfer if I am using dt_recon for dti analysis? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dt_recon field map for eddy correct
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Hi Doug,
I was looking at the dt_recon code and was wondering if it would be
possible to incorporate a field map into the eddy_correct portion? I tried
to test it on one subject and tried to add --field=$pathtofieldmap to the
eddy_correct command however I got the following error.
cd /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./ectmp
eddy_correct /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi.nii
/Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi-ec.nii 0
--field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi-ec_tmp
Unrecognised interpolation method:
--field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi-ec_tmp0001
Unrecognised interpolation method:
--field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed
I probably did this in a silly way. I wonder if and how I could add a field
map I created to the eddy_correct command in dt_recon.
Below is what I tried to change
set fec = $OutDir/dwi-ec.nii
if($DoEddyCorrect) then
echo "#@#---" | tee -a $LF
echo "Eddy/Motion Correct" | tee -a $LF
date | tee -a $LF
set ectmp = $OutDir/ectmp
mkdir -p $ectmp
pushd $ectmp > /dev/null
set cmd = (eddy_correct $f $fec $ECRefTP
*--field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed*)
#set cmd = ($cmd; mri_convert ${fec:r} $fec)
#set cmd = ($cmd; rm -f ${fec:r})
#set cmd = (cp $f $fec)
echo "cd `pwd`" | tee -a $LF
echo $cmd | tee -a $LF
$cmd|& tee -a $LF
if($status) exit 1;
if(! -e $fec) then
echo "ERROR: when running eddy_correct" | tee -a $LF
exit 1;
endif
popd > /dev/null
rm -r $ectmp
echo "" | tee -a $LF
echo "" | tee -a $LF
else
echo "#@#---" | tee -a $LF
echo "Skipping Eddy/Motion Correct" | tee -a $LF
set fec = $f
endif
Thanks for any help you can provide,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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Re: [Freesurfer] dt_recon --> tbss
External Email - Use Caution I was also running an ROI analysis based on the recon-all segmentations so I figured I could use the FA results and skip the process of running through the whole tbss process. I also found dt_recon's ability to determine bvals and bvecs from the dcm without needing to create the txt files that fsl needed made the preprocessing steps simpler and less likely to lead to human error in the process. *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 Thu, Feb 28, 2019 at 3:05 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > no idea. If you want to use tbss, why not use FSL to do the dti analysis > from the start? > > On 2/26/19 10:27 AM, Daniel Callow wrote: > > > > External Email - Use Caution > > > > Hello, > > > > I am working through dt_recon troubleshooting (One subjects > > registration to anatomical is skewed leading to incorrect masking of > > that subjects FA image). I would like to use the dt_recon's FA outputs > > and input them into FSL's tbss pipeline. My question is are there any > > steps I should take converting or modifying the FA images so they are > > compatible with the tbss pipeline. My intention was to take the > > dt_recon fa or fa-masked into the tbss_1_preproc command? > > > > Are there any considerations I should take into account? > > > > 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 > > > > ___ > > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] MD with dt_recon
External Email - Use Caution Thank you! *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 Thu, Feb 28, 2019 at 2:56 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > sorry, yes, that is right > > On 2/27/19 2:18 PM, Daniel Callow wrote: > > > > External Email - Use Caution > > > > Sorry, I just found in a previous post by doug that ADC is the same as > MD? > > *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 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
[Freesurfer] MD with dt_recon
External Email - Use Caution Sorry, I just found in a previous post by doug that ADC is the same as MD? *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] MD with dt_recon?
External Email - Use Caution Hello, There is no mean diffusivity output with dt_recon. How would you suggest to create MD images? Could you simply divide the adc.nii.gz map by 3? 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mask-FA mri_vol2vol issue - followup
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Hello,
I am still having the same issue as in my previous post. I have
successfully run dt_recon and upon looking at the images there seems to be
no issue with the registrations of outputs including the FA, lowb and other
images.
I wanted to mask my FA images using the wmparc.mgz image from recon-all
using
mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv --interp
nearest --o
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz
--reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
This works perfectly for all of my subjects except 2 of them. These
subjects seem to have normal lowb, wmparc, and FA images compared to the
other 58 subjects. However, the wmparc2diff that is created from
mri_vol2vol has significantly shifted away from the lowb and fa so that
when I try to mask the fa with
mri_mask $subj_dir/dtrecon/${subj}.${cond}./fa.nii.gz
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz
$subj_dir/dtrecon/${subj}.${cond}./fa-masked.nii.gz
It cuts a large part of the brain off and masks incorrectly.
Is there a way to troubleshoot the registration of wmparc to wmparc2diff? I
am not sure why the registration is so off?
Any troubleshooting help for why the registration of the segmentation to
diffusion space is so poor (or if the issue is registration from diffusion
space to anatomical space) would be greatly appreciated.
Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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[Freesurfer] dt_recon --> tbss
External Email - Use Caution Hello, I am working through dt_recon troubleshooting (One subjects registration to anatomical is skewed leading to incorrect masking of that subjects FA image). I would like to use the dt_recon's FA outputs and input them into FSL's tbss pipeline. My question is are there any steps I should take converting or modifying the FA images so they are compatible with the tbss pipeline. My intention was to take the dt_recon fa or fa-masked into the tbss_1_preproc command? Are there any considerations I should take into account? Best *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dt_recon and mri_vol2vol issue
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Hello freesurfer experts,
I am running dt_recon with the following script
dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image01.dcm
--s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}.
and mri_vol2vol to get the wmparc and aseg.mgz files in my lowb space with
the script below
mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv --interp
nearest --o
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz
--reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/aseg.mgz --inv --interp
nearest --o $subj_dir/dtrecon/${subj}.${cond}./aseg2diff.nii.gz --reg
$subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
However, one of my subjects shows a major issue with the mri_vol2vol
registration (for most of the subject scans it seems to work no problem).
When looking at the wmparc2diff.mgz I created, it is apparent that the
registration of the wmparc to wmparc2diff space actually causes
wmparc2diff.mgz to be further from the lowb than wmparc is (the brain is
shifted severely to the right). This same registration issue occurs for
aseg.mgz.
When I look at fa-tal.nii.gz it is poorly registered (again worse than FA
overlayed on aseg or wmparc which happens to be pretty close without
dt_recon). I assume this means there is an issue with the register.dat file
for this subject? If so is there any way to troubleshoot the issue and get
a correct register.dat file from dt_recon?
For reference, the following commands and registration steps have worked
for other subjects, as well as this same subject's scans under a different
condition. At first glance there don't seem to be any specific issues with
the anatomical or diffusion images before the registration attempt.
Any advice with troubleshooting would be greatly appreciated.
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
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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Re: [Freesurfer] Partial Volume Correction for FA map
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It is a volume based study so I will continue to use mgx .25.
Thank you!
*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 Mon, Feb 25, 2019 at 1:42 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> When you specify the --seg, just use gtmseg.mgz and not the whole path.
> For mgx, I'd need to know what you intend to do with it. Is it a
> surface-based study? If so, then I'd go with .01 in stead of .25
>
> On 2/25/19 11:05 AM, Daniel Callow wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I am currently trying to run PVC for my adc images using the following
> > script.
> >
> > mri_gtmpvc --i
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./adc-masked.nii.gz
> > --reg
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.lta
> > --psf 0 --seg
> >
> /Applications/freesurfer/subjects/Freesurfer_output/${subj}.${cond}.fsoutput/mri/gtmseg.mgz
>
> > --default-seg-merge --auto-mask PSF .01 --mgx .25 --o
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./adc.gtmpvc.output
> > --no-rescale
> >
> >
> > What would I need to change in order to accurately perform PVC on FA
> > images? Would the --mgx flag need to be changed?
> >
> >
> >
> > Best,
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>_
> > 443-254-6298
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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[Freesurfer] Partial Volume Correction for FA map
External Email - Use Caution
Hello,
I am currently trying to run PVC for my adc images using the following
script.
mri_gtmpvc --i
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./adc-masked.nii.gz
--reg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.lta
--psf 0 --seg
/Applications/freesurfer/subjects/Freesurfer_output/${subj}.${cond}.fsoutput/mri/gtmseg.mgz
--default-seg-merge --auto-mask PSF .01 --mgx .25 --o
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./adc.gtmpvc.output
--no-rescale
What would I need to change in order to accurately perform PVC on FA
images? Would the --mgx flag need to be changed?
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
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[Freesurfer] Issue posting to Freesurfer support
External Email - Use Caution Hello, I am signed up to post emails to Freesurfer support list < freesurfer@nmr.mgh.harvard.edu> which I have cced in this email. However, when I submit my questions they do not seem to show up or go to the listserv. Is there someone I could contact to help with this? 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Issue posting to the listserve
External Email - Use Caution Hello, When trying to post to the freesurfer listserv with this account my emails don't seem to go through. When using my university email dcal...@umd.edu it works. Unfortunately, I don't get and can't respond to responses to emails I submit from that email so I would like to fix the issue I am having with posting to the listserv with my ddcc2...@gmail.com email address. Thank you, *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
Re: [Freesurfer] anat2dti error after dt_recon
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Hi Douglas!
Thank you for the response. I figured out it was simply an issue with the
pathing to the register.dat file!
Thanks,
*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 Tue, Feb 19, 2019 at 3:52 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> what do you get when you run
> ls -l /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
>
> On 2/19/19 8:44 AM, Daniel Davidson Callow wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I ran a successful dt_recon and then wanted to use
> >
> > mri_vol2vol --mov $subj_dir/dtrecons/${subj}.${cond}/lowb.nii.gz
> > --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz
> > --inv --interp nearest --o
> > $subj_dir/dtrecons/${subj}.${cond}/aparc+aseg2diff.nii.gz --reg
> > $subj_dir/dtrecon/${subj}.${cond}/register.dat --no-save-reg
> >
> >
> > to get the anatomical segmentations into diffusion space. However,
> > when running the above code I get the following error message?
> >
> >
> > echo subj =AES139 , cond =Rest
> >
> > subj =AES139 , cond =Rest
> >
> > set echo
> >
> > cd /Volumes/DANIEL/dti_freesurf
> >
> > mri_vol2vol --mov
> > /Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/lowb.nii.gz --targ
> >
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES139.Rest/mri/aparc+aseg.mgz
>
> > --inv --interp nearest --o
> > /Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/aparc+aseg2diff.nii.gz
> > --reg /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
> > --no-save-reg
> >
> > regio_read_register(): No such file or directory
> >
> > Could not open
> > /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
> >
> >
> > Matrix from regfile:
> >
> > MatrixPrint: mat = NULL!
> >
> > No such file or directory
> >
> >
> > I have attached an example register.dat file in case that is the issue.
> >
> >
> > also the output for ls -l register.dat
> >
> > -rwxrwxrwx1 administratorstaff323 Feb 18 13:59 register.dat
> >
> >
> > Any advice with troubleshooting is greatly appreciated!
> >
> >
> > Best,
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > dcal...@umd.edu <mailto:dcal...@gmail.com>
> > 443-254-6298
> >
> >
> > ___
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] dt_recon error MatrixReadTxT: could not scan value [1][1]
External Email - Use Caution
Thanks!
*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, Feb 15, 2019 at 11:18 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Can you do this in two steps? First, convert the dicom to a volume format
> (eg, mgz or nii.gz) with
> mri_convert image001.dcm dwi.nii.gz
> This may or may not create bvals and bvecs. If not, then you will have to
> supply them. If they are created, look at them and make sure they are right.
> Next run dt_recon specifying the input and the bvals/bvecs
>
> On 2/15/19 9:22 AM, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
> Hello,
>
> I tried to run dt_recon, however, I received the following error message.
> Attached is the error log.
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image01.dcm
> --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon/
>
> MatrixReadTxT: could not scan value [1][1]
>
>
> No such file or directory
>
> WARNING: matlab elment type is 1852050003, which is not a matrix.
>
> mri_glmfit.bin(51624,0x7fffaff913c0) malloc: ***
> mach_vm_map(size=9155227648) failed (error code=3)
>
> *** error: can't allocate region
>
> *** set a breakpoint in malloc_error_break to debug
>
> could not allocate 1684305759 x 1144402954 matrix
>
>
> Cannot allocate memory
>
> mri_glmfit.bin(51624,0x7fffaff913c0) malloc: ***
> mach_vm_map(size=13474447360) failed (error code=3)
>
> *** error: can't allocate region
>
> *** set a breakpoint in malloc_error_break to debug
>
> could not allocate 1684305759 x 1144402954 matrix
>
>
> Cannot allocate memory
>
> unsupported matlab format 540094003 (unknown)
>
>
> Cannot allocate memory
>
> It also seems when dt_Recon is trying to process different subjects in
> parallel they are being processed in the same folder? does this create an
> issue?
>
> Any help you can provide in debugging the issue would be greatly
> appreciated!
>
> Thanks,
> D*aniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> dcal...@umd.edu
> 443-254-6298
>
>
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>
>
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[Freesurfer] dt_recon error log
External Email - Use Caution
Hello, running the following command line script for dt_recon
dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image01.dcm
--s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
MatrixReadTxT: could not scan value [1][1]
could not allocate 1684305759 x 1144402954 matrix
could not allocate 1684305759 x 1144402954 matrix
unsupported matlab format 540094003 (unknown)
Any idea what might be causing this error?
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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Re: [Freesurfer] dt_recon issue
External Email - Use Caution
Hi Douglas,
I was unsure if the emails I had been replying with were going through.
They did not seem to come up on the mailing list so I wasn’t sure if they
had reached you. I recently responded to your question about the ls -l path
output and the —debug output after fixing the path to the input Volumes. I
wonder if you have any idea why this might still produce the same error? Is
it an issue with the setenv or the naming of the DICOM files?. Sorry for
any questions. Any help is greatly appreciated!
On Wed, Feb 13, 2019 at 6:30 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Yes. Can you run it with --debug with the slash in front of "Volumes"?
>
> On 2/13/19 6:25 PM, Daniel Callow wrote:
> >
> > External Email - Use Caution
> >
> >
> > Is this what you mean by no variables??
> >
> > dt_recon --debug --i
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
> > AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
> >
> > *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 Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > can you send the command line without the variables?
> >
> >
> > On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Thanks for pointing that out! Unfortunately after making the change
> > >
> > > dt_recon --debug --i
> > >
> >
> /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
> >
> > > --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
> > >
> > >
> > > I still get the error.
> > >
> > >
> > > ./dt_recon.sh
> > >
> > > mkdir: tutorial_data: File exists
> > >
> > > mkdir: diffusion_recons: File exists
> > >
> > > subj =AES101 , cond =Ex
> > >
> > > mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex:
> > File
> > > exists
> > >
> > > set echo = 1 ;
> > >
> > > breaksw
> > >
> > > breaksw
> > >
> > > end
> > >
> > > end
> > >
> > > while ( $#argv != 0 )
> > >
> > > while ( 6 != 0 )
> > >
> > >
> > > set flag = $argv[1] ; shift ;
> > >
> > > set flag = --i
> > >
> > > shift
> > >
> > >
> > > switch ( $flag )
> > >
> > > switch ( --i )
> > >
> > > if ( $#argv < 1 ) goto arg1err ;
> > >
> > > if ( 5 < 1 ) goto arg1err
> > >
> > > set InputVol = "$argv[1]" ; shift ;
> > >
> > > set InputVol =
> > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> > >
> > > shift
> > >
> > > if ( ! -e "$InputVol" ) then
> > >
> > > if ( ! -e
> > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> > ) then
> > >
> > > echo "ERROR: cannot find $InputVol"
> > >
> > > echo ERROR: cannot find
> > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> > >
> > > ERROR: cannot find
> > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> > >
> > > goto error_exit ;
> > >
> > > goto error_exit
> > >
> > > uname -a | tee -a $LF
> > >
> > > uname -a
> > >
> > > tee -a
> > >
> > > Darwin hlhp-105.umd.edu <http://hlhp-105.umd.edu>
> > <http://hlhp-105.umd.edu> 16.7.0 Darwin Kernel
> > > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018;
> > > root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
> > >
> > > echo "" | & tee -a $LF
> > >
> > > tee -a
> > >
> >
Re: [Freesurfer] dt_recon issue
External Email - Use Caution Here it is. [hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 ) set flag = $argv[1] ; shift ; set flag = --i shift switch ( $flag ) switch ( --i ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then echo "ERROR: cannot find $InputVol" echo ERROR: cannot find /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ERROR: cannot find /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm goto error_exit ; goto error_exit uname -a | tee -a $LF uname -a tee -a Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 echo "" | & tee -a $LF tee -a echo echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF tee -a echo dt_recon exited with ERRORS at `date` date dt_recon exited with ERRORS at Wed Feb 13 18:44:07 EST 2019 echo "" | & tee -a $LF tee -a echo exit 1 ; exit 1 [hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% *aniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Wed, Feb 13, 2019 at 6:31 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > what happens when you run > > ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > On 2/13/19 6:27 PM, Daniel Callow wrote: > > > > External Email - Use Caution > > > > The error output that accompanies the command. > > > > > > administrator% dt_recon --debug --i > > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s > > AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon > > > > set echo = 1 ; > > > > breaksw > > > > breaksw > > > > end > > > > end > > > > while ( $#argv != 0 ) > > > > while ( 6 != 0 ) > > > > > > set flag = $argv[1] ; shift ; > > > > set flag = --i > > > > shift > > > > > > switch ( $flag ) > > > > switch ( --i ) > > > > if ( $#argv < 1 ) goto arg1err ; > > > > if ( 5 < 1 ) goto arg1err > > > > set InputVol = "$argv[1]" ; shift ; > > > > set InputVol = > > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > > > shift > > > > if ( ! -e "$InputVol" ) then > > > > if ( ! -e > > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then > > > > echo "ERROR: cannot find $InputVol" > > > > echo ERROR: cannot find > > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > > > ERROR: cannot find > > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > > > goto error_exit ; > > > > goto error_exit > > > > uname -a | tee -a $LF > > > > uname -a > > > > tee -a > > > > Darwin hlhp-105.umd.edu <http://hlhp-105.umd.edu> 16.7.0 Darwin Kernel > > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; > > root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 > > > > echo "" | & tee -a $LF > > > > tee -a > > > > echo > > > > > > echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF > > > > tee -a > > > > echo dt_recon exited with ERRORS at `date` > > > > date > > > > dt_recon exited with ERRORS at Wed Feb 13 18:26:16 EST 2019 > > > > echo "" | & tee -a $LF > > > > tee -a > > > > echo > > > > > > exit 1 ; > > > > exit 1 > > * > > * > > * > > * > > *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 Wed, Feb 13, 2019 at 6:25 PM Daniel Callow > <mailto:ddcc2...@gmail.com>> wrote: > > > > > > Is this what you mean by no va
Re: [Freesurfer] dt_recon issue
External Email - Use Caution
The error output that accompanies the command.
administrator% dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 6 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv < 1 ) goto arg1err ;
if ( 5 < 1 ) goto arg1err
set InputVol = "$argv[1]" ; shift ;
set InputVol =
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
shift
if ( ! -e "$InputVol" ) then
if ( ! -e /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
) then
echo "ERROR: cannot find $InputVol"
echo ERROR: cannot find
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
ERROR: cannot find
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
goto error_exit ;
goto error_exit
uname -a | tee -a $LF
uname -a
tee -a
Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10
20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
echo "" | & tee -a $LF
tee -a
echo
echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
tee -a
echo dt_recon exited with ERRORS at `date`
date
dt_recon exited with ERRORS at Wed Feb 13 18:26:16 EST 2019
echo "" | & tee -a $LF
tee -a
echo
exit 1 ;
exit 1
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow wrote:
>
> Is this what you mean by no variables??
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
> AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
>
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com *
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> can you send the command line without the variables?
>>
>>
>> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Thanks for pointing that out! Unfortunately after making the change
>> >
>> > dt_recon --debug --i
>> > /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
>> > --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
>> >
>> >
>> > I still get the error.
>> >
>> >
>> > ./dt_recon.sh
>> >
>> > mkdir: tutorial_data: File exists
>> >
>> > mkdir: diffusion_recons: File exists
>> >
>> > subj =AES101 , cond =Ex
>> >
>> > mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File
>> > exists
>> >
>> > set echo = 1 ;
>> >
>> > breaksw
>> >
>> > breaksw
>> >
>> > end
>> >
>> > end
>> >
>> > while ( $#argv != 0 )
>> >
>> > while ( 6 != 0 )
>> >
>> >
>> > set flag = $argv[1] ; shift ;
>> >
>> > set flag = --i
>> >
>> > shift
>> >
>> >
>> > switch ( $flag )
>> >
>> > switch ( --i )
>> >
>> > if ( $#argv < 1 ) goto arg1err ;
>> >
>> > if ( 5 < 1 ) goto arg1err
>> >
>> > set InputVol = "$argv[1]" ; shift ;
>> >
>> > set InputVol =
>> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>> >
>> > shift
>> >
>> > if ( ! -e "$InputVol" ) then
>> >
>> > if ( ! -e
>> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then
>> >
>> > echo "ERROR: cannot find $InputVol"
>> >
>> > echo ERROR: cannot find
>> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>> >
>> > ERROR: cannot find
>> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>> >
>> > goto error_exit ;
>> >
>> > goto error_exit
>> >
>> > uname -a | tee -a $LF
>> >
>> > uname -a
>> >
>> > tee -a
>> >
>> > Darwin hlhp-105.umd.edu <http://hlhp-105.umd.edu> 16.7.0 Darwin Kernel
>> > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018;
>> > root
Re: [Freesurfer] dt_recon issue
External Email - Use Caution
Is this what you mean by no variables??
dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> can you send the command line without the variables?
>
>
> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for pointing that out! Unfortunately after making the change
> >
> > dt_recon --debug --i
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
> > --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
> >
> >
> > I still get the error.
> >
> >
> > ./dt_recon.sh
> >
> > mkdir: tutorial_data: File exists
> >
> > mkdir: diffusion_recons: File exists
> >
> > subj =AES101 , cond =Ex
> >
> > mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File
> > exists
> >
> > set echo = 1 ;
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 6 != 0 )
> >
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --i
> >
> > shift
> >
> >
> > switch ( $flag )
> >
> > switch ( --i )
> >
> > if ( $#argv < 1 ) goto arg1err ;
> >
> > if ( 5 < 1 ) goto arg1err
> >
> > set InputVol = "$argv[1]" ; shift ;
> >
> > set InputVol =
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > shift
> >
> > if ( ! -e "$InputVol" ) then
> >
> > if ( ! -e
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then
> >
> > echo "ERROR: cannot find $InputVol"
> >
> > echo ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > goto error_exit ;
> >
> > goto error_exit
> >
> > uname -a | tee -a $LF
> >
> > uname -a
> >
> > tee -a
> >
> > Darwin hlhp-105.umd.edu <http://hlhp-105.umd.edu> 16.7.0 Darwin Kernel
> > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018;
> > root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
> >
> > tee -a
> >
> > echo dt_recon exited with ERRORS at `date`
> >
> > date
> >
> > dt_recon exited with ERRORS at Wed Feb 13 17:12:30 EST 2019
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > exit 1 ;
> >
> > exit 1
> >
> >
> > Again the DICOM files are named image01.dcm through
> > image65.dcm. These were 64 gradient images acquired on a SIEMENS
> > scanner with 1 bo image. I assume there is an issue with how I am
> > naming the input volumes for dt_recon. Any advice on how I should
> > structure this command would be greatly appreciated!
> >
> >
> > Thanks,
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > dcal...@umd.edu <mailto:dcal...@gmail.com>
> > 443-254-6298
> > *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 Wed, Feb 13, 2019 at 3:04 PM fsbuild > <mailto:fsbu...@contbay.com>> wrote:
> >
> > Hello Daniel.
> >
> > It looks like you need a slash in front of Volumes for the path
> > after —I
> > /Volumes
> >
> > - R.
> >
> >> On Feb 13, 2019, at 14:44, Daniel Davidson Callow
> >> mailto:dcal...@umd.edu>> wrote:
> >>
> >> External Email - Use Caution
> >>
> >>
> >> H
