Re: [Freesurfer] Hippocampal Subfield error
External Email - Use Caution Okay. I tried the following file. HCA8133362_V1_MR.zip ftp> put HCA8133362_V1_MR.zip 200 PORT command successful. Consider using PASV. 425 Failed to establish connection. ftp> ftp> put HCA8133362_V1_MR.zip 200 PORT command successful. Consider using PASV. 553 Could not create file. I am unsure if it was uploaded correctly. If so please look at the Take a look at the hippocampal-subfields-T2-highres.log for the command that failed. For some reason, the T2 and Highres versions seemed to work for different subjects. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcal...@umd.edu 443-254-6298 On Fri, May 28, 2021 at 4:10 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Please compress the whole subject directory and upload it to the ftp > https://secure-web.cisco.com/17V8syWMVTKaaQhcS6MhcEk3ryPp1_XzTsJDwNhfnSpz5-qvlgwXye9h8Wsj7x3_zJeLzSMUfnEaJ8Ldw1zydmk8KhfVAankUo_IbE_zsAf8gLNkiRi8azFWqXuzO-lryPPpJkHys9g515JC0hcgmKgauj0MtTcD3AQKHQM3qSkJOyxE1U8RqxtApS3DCtnle9jb4xNv9jSwcB_CWJ106fC6zUaH4CWT1ZwEfHHCZSyQYREOeVnE-99eLF3-o3el6kA6jWnyaW23ZBAUTiaMCTA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFtpFileExchange > Cheers, > /E > > Juan Eugenio Iglesias > Senior research fellow > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > http://secure-web.cisco.com/1XIQD_seUELoMBl32vITG_77ibtO3YwKokZL9vz-PcxXYRKf3CfhTe9-zVIwpP0gO9cpwQY2C4871TrcCqjugL2aWgMRVvRNDJKGRV7gnceJnYmyG46kw49v-Fwb6BxqwRCRl8y7svy9w3AGhwSm62l7gv2mDj8d8Q_zLIsKzO1FfcpyTKrpNb8kW6SL7dyErUDRn2ALuoAkuFpVFc5Hig8jaSByrZYV5CtqnjQ9sSiAOkwqi7z3eij1-tn_auVTh4qiJvU0JV4ASqtLlZChaQA/http%3A%2F%2Fwww.jeiglesias.com > > On May 28, 2021, at 15:35, Daniel Davidson Callow wrote: > > External Email - Use Caution > > Sure, what is the best way to share it with you? and which folders/files > should I send? > > On Fri, May 28, 2021 at 3:28 PM Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> wrote: > >> It seems the linear registration is dying. Would you mind sharing the >> subject, please? >> Cheers, >> /E >> Juan Eugenio Iglesias >> Senior research fellow >> CMIC (UCL), MGH (HMS) and CSAIL (MIT) >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> http://secure-web.cisco.com/1XIQD_seUELoMBl32vITG_77ibtO3YwKokZL9vz-PcxXYRKf3CfhTe9-zVIwpP0gO9cpwQY2C4871TrcCqjugL2aWgMRVvRNDJKGRV7gnceJnYmyG46kw49v-Fwb6BxqwRCRl8y7svy9w3AGhwSm62l7gv2mDj8d8Q_zLIsKzO1FfcpyTKrpNb8kW6SL7dyErUDRn2ALuoAkuFpVFc5Hig8jaSByrZYV5CtqnjQ9sSiAOkwqi7z3eij1-tn_auVTh4qiJvU0JV4ASqtLlZChaQA/http%3A%2F%2Fwww.jeiglesias.com >> <http://secure-web.cisco.com/1gT1t332MrjlumWoLsCvCODpcjL_Q7MljRoRdHSVXsW_jLPgjmaoLw7W3F0bWnNAuU_i6YcvUn1CduipTCLoLmI28KrJsxObJ-pJjn0aT42elUDeQDY-VOqdDAsm_XCSLk6O0cQQsHQZ_WeLdLkkSP0ZqAF22pxtjRYWOS_mGB4DgjcwDWt2LSx_Vl4dfFH7q6x0dS6wAUxGejm01T0GyOn03KUjtR1Y7XZ1AVi0U9kSfev4sOmBR8c1iZDmEC4jy_1ZRJ6fDyEI8ZlK8tFektA/http%3A%2F%2Fwww.jeiglesias.com> >> >> >> On May 28, 2021, at 12:20, Daniel Davidson Callow >> wrote: >> >> External Email - Use Caution >> >> Hello Juan, >> >> I am using data from the HCP aging dataset which has a T1 and a >> high-resolution hippocampal scan (T2). >> >> Yes, it does seem that the T2 and T1's are roughly aligned to each other. >> It seems like it has something to do with the creation of the >> tmp/hippoSF_T1T2_v21_highres_left/ folder where the program is expecting >> something to be produced that is not there/hasn't been produced. >> >> Again, here is an example of the code output/error. >> >> @ linenum = 1 >> cd /data/bswift-1/dcallow/aging/freesurfer >> set subj= ( HCA8587705_V1_MR ) >> rm: No match. >> rm -rf >> /a/ha-nfs-2-ib/export/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/IsRunning.lh+rh >> cd /data/bswift-1/dcallow/aging/freesurfer >> echo HCA8587705_V1_MR >> HCA8587705_V1_MR >> segmentHA_T2.sh HCA8587705_V1_MR >> /data/bswift-1/dcallow/aging/imaging/HCA8587705_V1_MR/unprocessed/TSE_HiResHp/HCA8587705_V1_MR_TSE_HiResHp.nii.gz >> highres 1 >> # >> #@# Hippocampal Subfields processing (T1+T2) left Fri May 28 12:05:35 EDT >> 2021 >> -- >> Setting up environment variables >> --- >> INFO: error loading libraries in default configuration, trying with MCR >> libraries only >> LD_LIBRARY_PATH is >> .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//
Re: [Freesurfer] Hippocampal Subfield error
External Email - Use Caution Sure, what is the best way to share it with you? and which folders/files should I send? On Fri, May 28, 2021 at 3:28 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > It seems the linear registration is dying. Would you mind sharing the > subject, please? > Cheers, > /E > Juan Eugenio Iglesias > Senior research fellow > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > http://secure-web.cisco.com/1gT1t332MrjlumWoLsCvCODpcjL_Q7MljRoRdHSVXsW_jLPgjmaoLw7W3F0bWnNAuU_i6YcvUn1CduipTCLoLmI28KrJsxObJ-pJjn0aT42elUDeQDY-VOqdDAsm_XCSLk6O0cQQsHQZ_WeLdLkkSP0ZqAF22pxtjRYWOS_mGB4DgjcwDWt2LSx_Vl4dfFH7q6x0dS6wAUxGejm01T0GyOn03KUjtR1Y7XZ1AVi0U9kSfev4sOmBR8c1iZDmEC4jy_1ZRJ6fDyEI8ZlK8tFektA/http%3A%2F%2Fwww.jeiglesias.com > > On May 28, 2021, at 12:20, Daniel Davidson Callow wrote: > > External Email - Use Caution > > Hello Juan, > > I am using data from the HCP aging dataset which has a T1 and a > high-resolution hippocampal scan (T2). > > Yes, it does seem that the T2 and T1's are roughly aligned to each other. > It seems like it has something to do with the creation of the > tmp/hippoSF_T1T2_v21_highres_left/ folder where the program is expecting > something to be produced that is not there/hasn't been produced. > > Again, here is an example of the code output/error. > > @ linenum = 1 > cd /data/bswift-1/dcallow/aging/freesurfer > set subj= ( HCA8587705_V1_MR ) > rm: No match. > rm -rf > /a/ha-nfs-2-ib/export/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/IsRunning.lh+rh > cd /data/bswift-1/dcallow/aging/freesurfer > echo HCA8587705_V1_MR > HCA8587705_V1_MR > segmentHA_T2.sh HCA8587705_V1_MR > /data/bswift-1/dcallow/aging/imaging/HCA8587705_V1_MR/unprocessed/TSE_HiResHp/HCA8587705_V1_MR_TSE_HiResHp.nii.gz > highres 1 > # > #@# Hippocampal Subfields processing (T1+T2) left Fri May 28 12:05:35 EDT > 2021 > -- > Setting up environment variables > --- > INFO: error loading libraries in default configuration, trying with MCR > libraries only > LD_LIBRARY_PATH is > .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswif$Registering > norm.mgz to additional volume > No more processes. > ERROR: could not open > /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh > for reading > ERROR: loading > /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh > as MGH > Warning: File > '/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh' > not found. > [^H> In myMRIread at 64 > In segmentSubjectT1T2_autoEstimateAlveusML at 186]^H > Attempt to reference field of non-structure array. > > Error in segmentSubjectT1T2_autoEstimateAlveusML (line 188) > MATLAB:nonStrucReference > @#@FSTIME 2021:05:28:12:05:35 > run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 7.49 S 0.61 U 6.79 P > 98% M 283156 F 0 R 84320 W 0 c 2392 w 9596 I 0 O 85080 L 5$@#@FSLOADPOST > 2021:05:28:12:05:42 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 > 60.45 53.15 38.08 > Linux compute-4-33.bswift.umd.edu > <http://secure-web.cisco.com/1sqdwOUu2B9k20N1ZAF2G3AjMOwj2lJePh4GNFQiYhImRJsLReMbcU3SXEBp36HD81jqxGdU8a11rJylMhtgbY4fajAEU2pMYsr0DVpWBlkaOMa76fsceUrIl9aQQGsiXc4t6jAY6yGgeO2kzpjftDgTb1eWEbDGuGccb2HunIGkKRrj0yIIhMCUBXNMsPGxCpYhRthsOcBxVagqqmQZxB5PmjkPPc4BKyyMN_eLiZEjt4ui6aNQG76WiX_3leabsXT0Dc4AQ7eKoT8OWNqqHcQ/http%3A%2F%2Fcompute-4-33.bswift.umd.edu> > 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64 > x86_64 x86_64 GNU/Linux > > T2 hippocampal subfields exited with ERRORS at Fri May 28 12:05:42 EDT 2021 > > For more details, see the log file > /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/hippocampal-subfields-T2.highres.log > > > Any ideas what might be causing this error. Again, it seems to be working > for a small subset of participants however, the majority are failing with > this error. > *Daniel Callow* > *PhD Student, Neuroscience and Cognitive Science* > Exercise for Brain Health Lab > University of Maryland, College Park > dcal...@umd.edu > 443-254-6298 > > > > On Fri, May 28, 2021 at 9:32 AM Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> wrote: > > Dear Daniel, >> >> Are the T2s and T1s roughly aligned in RAS (physical coordinates)? In >> other word
Re: [Freesurfer] Hippocampal Subfield error
External Email - Use Caution
Hello Juan,
I am using data from the HCP aging dataset which has a T1 and a
high-resolution hippocampal scan (T2).
Yes, it does seem that the T2 and T1's are roughly aligned to each other.
It seems like it has something to do with the creation of the
tmp/hippoSF_T1T2_v21_highres_left/ folder where the program is expecting
something to be produced that is not there/hasn't been produced.
Again, here is an example of the code output/error.
@ linenum = 1
cd /data/bswift-1/dcallow/aging/freesurfer
set subj= ( HCA8587705_V1_MR )
rm: No match.
rm -rf
/a/ha-nfs-2-ib/export/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/IsRunning.lh+rh
cd /data/bswift-1/dcallow/aging/freesurfer
echo HCA8587705_V1_MR
HCA8587705_V1_MR
segmentHA_T2.sh HCA8587705_V1_MR
/data/bswift-1/dcallow/aging/imaging/HCA8587705_V1_MR/unprocessed/TSE_HiResHp/HCA8587705_V1_MR_TSE_HiResHp.nii.gz
highres 1
#
#@# Hippocampal Subfields processing (T1+T2) left Fri May 28 12:05:35 EDT
2021
--
Setting up environment variables
---
INFO: error loading libraries in default configuration, trying with MCR
libraries only
LD_LIBRARY_PATH is
.:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswif$Registering
norm.mgz to additional volume
No more processes.
ERROR: could not open
/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh
for reading
ERROR: loading
/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh
as MGH
Warning: File
'/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh'
not found.
[^H> In myMRIread at 64
In segmentSubjectT1T2_autoEstimateAlveusML at 186]^H
Attempt to reference field of non-structure array.
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 188)
MATLAB:nonStrucReference
@#@FSTIME 2021:05:28:12:05:35
run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 7.49 S 0.61 U 6.79 P
98% M 283156 F 0 R 84320 W 0 c 2392 w 9596 I 0 O 85080 L 5$@#@FSLOADPOST
2021:05:28:12:05:42 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
60.45 53.15 38.08
Linux compute-4-33.bswift.umd.edu 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May
29 04:45:43 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Fri May 28 12:05:42 EDT 2021
For more details, see the log file
/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/hippocampal-subfields-T2.highres.log
Any ideas what might be causing this error. Again, it seems to be working
for a small subset of participants however, the majority are failing with
this error.
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu
443-254-6298
On Fri, May 28, 2021 at 9:32 AM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:
> Dear Daniel,
>
> Are the T2s and T1s roughly aligned in RAS (physical coordinates)? In
> other words: do they (roughly) overlap when you open them together in
> Freeview?
>
> Cheers,
>
> /E
>
> Juan Eugenio Iglesias
> Senior research fellow
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
> http://secure-web.cisco.com/1M43tYnBIwe0As03lwnAGcBzSZfvIXhP_UsjatHKyZUaaQ4wSAHDh_rwH1615JlqcHfPYywTwRzVbI_to9hVZq--leXJy2p4Zrh_mUI3lNII4SXa870Dh3HPFfDvztZQqR8Lzb5jZgrooucfAyVmWEBNMCuB8-mMhkfQpliBwpQ4AlrLgpwXKROaATxslozZ45t7me-SsaBv2pGfPGHhefMDQiyWYTTwRkiWX5UsaBqKv7GznpWuae2cijb7yGp0Ot534fYLsrPfsPuzrmK7NMQ/http%3A%2F%2Fwww.jeiglesias.com
>
> On May 28, 2021, at 07:53, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am running into errors when running
>
> segmentHA_T2.sh ${subj}
> /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
>
> Approximately 10% of my subjects are being processed but for some reason,
> the majority fail to execute. Here is an output from the error log.
> --
> USER dcallow
> HOST compute-4-32.bswift.umd.edu
> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
> PROCESSID 4033
> PROCESSOR x86_64
> OS Linux
> Linux compute-4-32.bswift.umd.edu
> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9
[Freesurfer] Hippocampal Subfield error
External Email - Use Caution
Hello,
I am running into errors when running
segmentHA_T2.sh ${subj}
/data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
Approximately 10% of my subjects are being processed but for some reason,
the majority fail to execute. Here is an output from the error log.
--
USER dcallow
HOST compute-4-32.bswift.umd.edu
PROCESSID 4033
PROCESSOR x86_64
OS Linux
Linux compute-4-32.bswift.umd.edu
2.6.32-754.35.1.el6.x86_64
#1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
--
#
#@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT
2021
--
Setting up environment variables
---
INFO: error loading libraries in default configuration, trying with MCR
libraries only
LD_LIBRARY_PATH is
.:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering
norm.mgz to additional volume
makeIsotropic WARNING: not different enough, won't reslice!
No more processes.
ERROR: could not open
/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
for reading
ERROR: loading
/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
as MGH
Warning: File
'/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh'
not found.
[^H> In myMRIread at 64
In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H
Attempt to reference field of non-structure array.
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211)
MATLAB:nonStrucReference
@#@FSTIME 2021:05:27:21:39:51
run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61
P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST
2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
31.22 29.74 28.95
Linux compute-4-32.bswift.umd.edu
2.6.32-754.35.1.el6.x86_64
#1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT 2021
I am also getting a matlab_crash_dump file
Segmentation violation detected at Thu May 27 21:51:52 2021
Configuration:
Crash Decoding : Disabled
Current Visual : None
Default Encoding : US-ASCII
GNU C Library : 2.12 stable
MATLAB Architecture: glnxa64
MATLAB Root: /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux
MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29
04:45:43 EDT 2020 x86_64
Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
Software OpenGL: 0
Virtual Machine: Java 1.7.0_11-b21 with Oracle Corporation Java
HotSpot(TM) 64-Bit Server VM mixed mode
Window System : No active display
Fault Count: 1
Abnormal termination:
Segmentation violation
Stack Trace (from fault):
[ 0] 0x7f2b30f06213
/lib64/libpthread.so.0+00033299 pthread_join+0035
[ 1] 0x7f2a9f4d847d
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
2] 0x7f2a9f4d8cac
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
3] 0x7f2a9f5cae63
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
4]
[Freesurfer] (no subject)
External Email - Use Caution
Hello,
I am running into errors when running
segmentHA_T2.sh ${subj}
/data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
Approximately 10% of my subjects are being processed but for some reason,
the majority fail to execute. Here is an output from the error log.
--
USER dcallow
HOST compute-4-32.bswift.umd.edu
PROCESSID 4033
PROCESSOR x86_64
OS Linux
Linux compute-4-32.bswift.umd.edu
2.6.32-754.35.1.el6.x86_64
#1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
--
#
#@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT
2021
--
Setting up environment variables
---
INFO: error loading libraries in default configuration, trying with MCR
libraries only
LD_LIBRARY_PATH is
.:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering
norm.mgz to additional volume
makeIsotropic WARNING: not different enough, won't reslice!
No more processes.
ERROR: could not open
/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
for reading
ERROR: loading
/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
as MGH
Warning: File
'/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh'
not found.
[^H> In myMRIread at 64
In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H
Attempt to reference field of non-structure array.
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211)
MATLAB:nonStrucReference
@#@FSTIME 2021:05:27:21:39:51
run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61
P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST
2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
31.22 29.74 28.95
Linux compute-4-32.bswift.umd.edu
2.6.32-754.35.1.el6.x86_64
#1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT 2021
I am also getting a matlab_crash_dump file
Segmentation violation detected at Thu May 27 21:51:52 2021
Configuration:
Crash Decoding : Disabled
Current Visual : None
Default Encoding : US-ASCII
GNU C Library : 2.12 stable
MATLAB Architecture: glnxa64
MATLAB Root: /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux
MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29
04:45:43 EDT 2020 x86_64
Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
Software OpenGL: 0
Virtual Machine: Java 1.7.0_11-b21 with Oracle Corporation Java
HotSpot(TM) 64-Bit Server VM mixed mode
Window System : No active display
Fault Count: 1
Abnormal termination:
Segmentation violation
Stack Trace (from fault):
[ 0] 0x7f2b30f06213
/lib64/libpthread.so.0+00033299 pthread_join+0035
[ 1] 0x7f2a9f4d847d
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
2] 0x7f2a9f4d8cac
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
3] 0x7f2a9f5cae63
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
4]
[Freesurfer] dt_recon registration check
External Email - Use Caution
Hello,
I have run through dt_recon and want to use anatomically based
segmentations (aseg) to create ROIs for the diffusion-weighted data using
mri_vol2vol.
I ran
mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz --inv
--interp nearest --o
$subj_dir/dtrecon/${subj}.${cond}./aparc+aseg2diff.nii.gz --reg
$subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
Which worked.
I now want to quality check and make sure the ROIs I make from the
aseg2diff segmentation is accurately aligned in diffusion space (such as
making sure the hippocampal ROIs for aseg are actually going to overlay the
hippocampal region of the diffusion data). My question is what is the best
way to quality check for quality registration between the diffusion and
anatomical data?
Best,
*Daniel 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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[Freesurfer] anat2dti error after dt_recon
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}.${cond}/register.dat --no-save-reg
to get the anatomical segmentations into diffusion space. However, when
running the above code I get the following error message?
echo subj = AES139 , cond = Rest
subj = AES139 , cond = Rest
set echo
cd /Volumes/DANIEL/dti_freesurf
mri_vol2vol --mov
/Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/lowb.nii.gz --targ
/Volumes/DANIEL/dti_freesurf/diffusion_recons/AES139.Rest/mri/aparc+aseg.mgz
--inv --interp nearest --o
/Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/aparc+aseg2diff.nii.gz
--reg /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
--no-save-reg
regio_read_register(): No such file or directory
Could not open /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
Matrix from regfile:
MatrixPrint: mat = NULL!
No such file or directory
I have attached an example register.dat file in case that is the issue.
also the output for ls -l register.dat
-rwxrwxrwx 1 administrator staff 323 Feb 18 13:59 register.dat
Any advice with troubleshooting is greatly appreciated!
Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu
443-254-6298
register.dat
Description: Binary data
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[Freesurfer] dt_recon issue
External Email - Use Caution
Thanks for pointing that out! Unfortunately after making the change
dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/${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 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 $LF
tee -a
echo
exit 1 ;
exit 1
Again the DICOM files are named image01.dcm through image65.dcm. These
were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. I
assume there is an issue with how I am naming the input volumes for
dt_recon. Any advice on how I should structure this command would be
greatly appreciated!
Thanks,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu
443-254-6298
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
On Wed, Feb 13, 2019 at 3:04 PM fsbuild wrote:
> Hello Daniel.
>
> It looks like you need a slash in front of Volumes for the path after —I
> /Volumes
>
> - R.
>
> On Feb 13, 2019, at 14:44, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to run dt_recon on my dti data using the following script.
>
> dt_recon --debug --i
> Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
> --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
>
>
> with the following error
>
> echo "ERROR: cannot find $InputVol"
> echo ERROR: cannot find
> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> ERROR: cannot find
> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> goto error_exit ;
>
> the DICOM files are named image01.dcm through image65.dcm
>
> These were 64 gradient images acquired on a SIEMENS scanner with 1 bo
> image. Any advice on how I should structure this command would be greatly
> appreciated!
>
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> dcal...@umd.edu
> 443-254-6298
>
> ___
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>
>
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[Freesurfer] dt_recon issue
External Email - Use Caution
Hello,
I am trying to run dt_recon on my dti data using the following script.
dt_recon --debug --i
Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s
${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
with the following error
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 ;
the DICOM files are named image01.dcm through image65.dcm
These were 64 gradient images acquired on a SIEMENS scanner with 1 bo
image. Any advice on how I should structure this command would be greatly
appreciated!
*Daniel 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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