subject:"\[Freesurfer\] Hippocampal Subfield error"

Re: [Freesurfer] Hippocampal Subfield error

2021-05-28 Thread Daniel Davidson Callow

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
>> 
>>
>>
>> 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:

Re: [Freesurfer] Hippocampal Subfield error

2021-05-28 Thread Iglesias Gonzalez, Juan E.

Please compress the whole subject directory and upload it to the ftp
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On May 28, 2021, at 15:35, Daniel Davidson Callow 
mailto:dcal...@umd.edu>> 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. 
mailto: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://www.jeiglesias.com

On May 28, 2021, at 12:20, Daniel Davidson Callow 
mailto:dcal...@umd.edu>> 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
 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. 
mailto: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

Re: [Freesurfer] Hippocampal Subfield error

2021-05-28 Thread Daniel Davidson Callow

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
> 
> 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)
>>
> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be* 
>>

Re: [Freesurfer] Hippocampal Subfield error

2021-05-28 Thread Iglesias Gonzalez, Juan E.

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://www.jeiglesias.com

On May 28, 2021, at 12:20, Daniel Davidson Callow 
mailto:dcal...@umd.edu>> 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
 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. 
mailto: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)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com

On May 28, 2021, at 07:53, Daniel Davidson Callow 
mailto:dcal...@umd.edu>> 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.

Re: [Freesurfer] Hippocampal Subfield error

2021-05-28 Thread Daniel Davidson Callow

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
> 
> PROCESSID 4033
> PROCESSOR x86_64
> OS Linux
> Linux compute-4-32.bswift.umd.edu
>

Re: [Freesurfer] Hippocampal Subfield error

2021-05-28 Thread Iglesias Gonzalez, Juan E.

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://www.jeiglesias.com

On May 28, 2021, at 07:53, Daniel Davidson Callow 
mailto:dcal...@umd.edu>> 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
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

[Freesurfer] Hippocampal Subfield error

2021-05-28 Thread Daniel Davidson Callow

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]

Re: [Freesurfer] Hippocampal Subfield Error

2018-02-27 Thread Iglesias Gonzalez, Eugenio

Hi Theo,
Sorry for not being more clear; I meant hippocampal-subfields-T1.log, which 
should be in the directory “scripts”.
Cheers,
/Eugenio



--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "AKUDJEDU, 
THEOPHILUS" <t.akudje...@nuigalway.ie>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 27 February 2018 at 15:31
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal Subfield Error





Dear Eugenio,

Attached as requested.

Thanks

Theo
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Re: [Freesurfer] Hippocampal Subfield Error

2018-02-27 Thread Iglesias Gonzalez, Eugenio

Dear Theo,
Would you mind sending up the log of the hippocampal subfields as well?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "AKUDJEDU, 
THEOPHILUS" <t.akudje...@nuigalway.ie>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 27 February 2018 at 11:13
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal Subfield Error


Dear Eugenio,



I executed the command below and it exited with errors (log files attached.



Thanks



Theo

recon-all -all -s CHRM2001 -hippocampal-subfields-T1
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Hippocampal Subfield Error

2018-02-26 Thread Iglesias Gonzalez, Eugenio

Dear Theo,
Can you please provide us with the command you executed, and the complete 
output logs?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "AKUDJEDU, 
THEOPHILUS" <t.akudje...@nuigalway.ie>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 26 February 2018 at 12:39
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal Subfield Error


Hi All,



I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield 
segmentation but exited with errors.



The content of the recon-all.error file is below.




SUBJECT CHRM2001
DATE Sun Feb 25 00:34:13 GMT 2018
USER 15233963
HOST psych-sl03
PROCESSOR x86_64
OS Linux
Linux psych-sl03 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
/opt/ohpc/pub/apps/freesurfer/6.0.0/bin/recon-all
PWD /home/15233963/freesurfer/SUBJECTS/CHRM2001/label
CMD mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a 
./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab CHRM2001 rh white






Will be glad if you can provide guidance.



Cheers



Theo



___

Theophilus Akudjedu

BSc, MSc, PhD Candidate

Room 202 Comerford Suite,

Clinical Science Institute,

Department of Psychiatry,

National University of Ireland, Galway



Phone: +353 838329602

Email: t.akudje...@nuigalway.ie<mailto:t.akudje...@nuigalway.ie>

   rasni...@gmail.com<mailto:rasni...@gmail.com>



[mage removed by sender.]

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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] Hippocampal Subfield Error

2018-02-26 Thread AKUDJEDU, THEOPHILUS

Hi All,


I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield 
segmentation but exited with errors.


The content of the recon-all.error file is below.



SUBJECT CHRM2001
DATE Sun Feb 25 00:34:13 GMT 2018
USER 15233963
HOST psych-sl03
PROCESSOR x86_64
OS Linux
Linux psych-sl03 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
/opt/ohpc/pub/apps/freesurfer/6.0.0/bin/recon-all
PWD /home/15233963/freesurfer/SUBJECTS/CHRM2001/label
CMD mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a 
./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab CHRM2001 rh white




Will be glad if you can provide guidance.


Cheers


Theo


___

Theophilus Akudjedu

BSc, MSc, PhD Candidate

Room 202 Comerford Suite,

Clinical Science Institute,

Department of Psychiatry,

National University of Ireland, Galway


Phone: +353 838329602

Email: t.akudje...@nuigalway.ie

   rasni...@gmail.com



[https://ci6.googleusercontent.com/proxy/b9-AoNc-V0v85TZ_pj6puJTgX7uWBNlZdohjQM11hVJywIAEwXEGsHgEnDPLCI7oFsH_DknZswzkpzUMsK1_yk3OwzRkUZZ73VRhQq1-TF2aFt-1u2fB2jnkmTrpvirljLd9ciRy-A_D1eiTBaS6Xak0JKNMiKL1sBIdRVKUiqrLEkqWzllvsRAPy9j9Ed1nWXu4-QUpob0nkuM=s0-d-e1-ft#https://docs.google.com/uc?export=download=0Bw-d1Byh7ldEU2czeGlfMjNVOTg=0Bw-d1Byh7ldENkZtSlhueGFHdTFhVVFSa25xSmNvNGs4QXdNPQ]

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Hippocampal Subfield error

Re: [Freesurfer] Hippocampal Subfield error

Re: [Freesurfer] Hippocampal Subfield error

Re: [Freesurfer] Hippocampal Subfield error

Re: [Freesurfer] Hippocampal Subfield error

Re: [Freesurfer] Hippocampal Subfield error

[Freesurfer] Hippocampal Subfield error

Re: [Freesurfer] Hippocampal Subfield Error

Re: [Freesurfer] Hippocampal Subfield Error

Re: [Freesurfer] Hippocampal Subfield Error

[Freesurfer] Hippocampal Subfield Error

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