Re: [Freesurfer] Pipeline errors - matlab
2021-11-21
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
urfer/MCRv84/bin/maci64/libmwmcr.dylib+00015643
_Z26run_init_and_handle_eventsPv+0059*
*[ 17] 0x7fff204208fc
/usr/lib/system/libsystem_pthread.dylib+00026876 _pthread_start+0224*
*[ 18] 0x7fff2041c443
/usr/lib/system/libsystem_pthread.dylib+9283 thread_start+0015*
*If this problem is reproducible, please submit a Service Request via:*
*
http://secure-web.cisco.com/1sFp6ev4em_EM8c3cbPoUE6trXNZE7Efoemg6n7hk6C5IFGAsAMrbbI93SRSR8goYyCUFBY68NYUCsB2ph7cj5aHUrjym28U5j03Gc9dH1qdpLKkKkTVKbZ0E3qVZh9N7uZnkk6meV4_HRjZYlsfzCPOW28OcmRDRsqp_jlQVoJSNMFJACs9sJU6zytyTlb2wQYtDc5vOylv5fqJpLgVgRfBV3RmkgQoO7Rsh8PFHHrJ3oiXFc8OSZfFyOmbJfqyMYh0z1EsxQjZjbDinL21loMrMtfRUYB5ATo6Zo5zQW81mGOqsL0ff8TBFoUk5iEiS53q7767J0edrOObAVLjtNj-uXtcriQ3BOeUlYHY9sxE/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
<http://secure-web.cisco.com/1sFp6ev4em_EM8c3cbPoUE6trXNZE7Efoemg6n7hk6C5IFGAsAMrbbI93SRSR8goYyCUFBY68NYUCsB2ph7cj5aHUrjym28U5j03Gc9dH1qdpLKkKkTVKbZ0E3qVZh9N7uZnkk6meV4_HRjZYlsfzCPOW28OcmRDRsqp_jlQVoJSNMFJACs9sJU6zytyTlb2wQYtDc5vOylv5fqJpLgVgRfBV3RmkgQoO7Rsh8PFHHrJ3oiXFc8OSZfFyOmbJfqyMYh0z1EsxQjZjbDinL21loMrMtfRUYB5ATo6Zo5zQW81mGOqsL0ff8TBFoUk5iEiS53q7767J0edrOObAVLjtNj-uXtcriQ3BOeUlYHY9sxE/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F>*
*A technical support engineer might contact you with further information.*
*Thank you for your help.** This crash report has been saved to disk as
/Users/ajobsaid/matlab_crash_dump.7498-2 ***
*MATLAB is exiting because of fatal error*
*/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 37: 7498 Killed: 9
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args*
*Darwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30
06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64*
*T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST
2021*
Thanks!
Alex
On Tue, Nov 16, 2021 at 12:05 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:
> Dear Alex,
> Can you please send us the full output?
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> Senior research fellow
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
> http://secure-web.cisco.com/1TeCpgrxvt8bIkbdkgpN2XezPTkU9wu3kj7LRtXKjfpCH4FAr1qZOYEySIAtfRiAMln0GtQGZNhkn1BYM1QpBk6OnKYzZONWNgjoaNAucvOavgMVCBoALN7YhYXsPKMEj_555pJQYmhPui4CWnFZXnG8H4B8oNtiaSTTEMT9XGkEOUtM3DGGEBB83ASaZxQ0igRdn7yiC5T5r4E2cD9i7B6Je-g7MFMcwX1LieEwRIBN_G5lcE9GwDGR1gnKLISyPtxUguq65_LCB90hChNZisuw5Hc0D3l3UI8yQ9uEGnGShpVf64uODg3P9SFmKKl4-cK_J_nCFZwG04as-0wwsECMTka4Wqc4teLruG-ySa90/http%3A%2F%2Fwww.jeiglesias.com
>
>
>
> On 12 Nov 2021, at 23:39, Lab of Autism and Developmental Neuroscience, Lab
> of Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer experts!
>
> Hope that you are all well. I am having errors when running hippocampal
> subfields and thalamic subfields. When in the error log for the hippocampal
> pipeline, this is part of the error that I got:
>
> *MATLAB is exiting because of fatal error*
> */Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
> line 37: 7498 Killed: 9
>
> "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
> $args*
> *Darwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30
> 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64*
>
> *T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST
> 2021*
>
> Please let me know if additional info is needed.
>
> Thank you so much,
> Alex
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1wJaTkHwn-VkpF_lNXS_GbWO108NU97mb4KPById3DE3cFcM77Y1ssbd6coJ_io-Q38JKIloIvwOFIRm8GS_9mV1dyghTvzZoanxM34WrKsveQUlbcnfRC_Z_djTFqvxEBdam0HD3Xv0mIM6c7ZFUHqx2-gGClQRCVvkaGyheSpDb8HOAvX-3tva5URaaOJe2YFSIQTTQQk3eUdtAxqiqFmsnQPXO9qSk15yefVdjJx_g622F9aRZa0OAGBb0mIqd4OilACfMxrtPiIc-knzLZDU9WB2AlCuYQNPaHrKbFnh45Na9Ba_f-xqff6WYTctsi4ZgG099Rd6te_Newj21ryM5V-yBWBg2TAxoreWL2S4/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> The i
[Freesurfer] Pipeline errors - matlab
2021-11-12
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution
Hello Freesurfer experts!
Hope that you are all well. I am having errors when running hippocampal
subfields and thalamic subfields. When in the error log for the hippocampal
pipeline, this is part of the error that I got:
*MATLAB is exiting because of fatal error*
*/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 37: 7498 Killed: 9
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args*
*Darwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30
06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64*
*T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST
2021*
Please let me know if additional info is needed.
Thank you so much,
Alex
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] LGI - output issue
2021-08-19
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution It worked! Thank you so much for fixing this. I am also trying to open ?h.pial-outer-smoothed file. How should I proceed with either freeview or tksurferfv? Haven't found any info regarding this on the wiki! Again, thank you so much for your help! All the best On Wed, Aug 18, 2021 at 11:37 PM Hoopes, Andrew wrote: > This is fixed in v7.2, but if you want to patch your current freesurfer > distribution, you can try these commands: > > > > cd $FREESURFER_HOME/bin > > sudo mv fsvglrun fsvglrun.backup > > sudo curl -O > https://secure-web.cisco.com/1efCCkX86LzSzP4WTrfKmXAn_UMOkClX1vXHyTzq468M8EqFH6ADhRk-mxvzBUdRYKoD8cdJjHKHVpbGLvr1uJiv3c7wTqLU-GD6Czs0AnxCjEJXuXNtKD9i6EYVGk_5daCrvcj9RAllhwgE15SPG3uUcTVERP5m-_ty2zGGaJ_PZHHHqJP70yt9mFG0UoB2up0mAc2y22KCUNbKW2re-1lKZO-mgyuYeie7b2Aug1Hc1_zYNLqi8EHQ2nvmJXDb_zTDo8kiPf5uDKK1lNlWO7g/https%3A%2F%2Fraw.githubusercontent.com%2Ffreesurfer%2Ffreesurfer%2Fdev%2Fscripts%2Ffsvglrun > > sudo chmod +x fsvglrun > > > > best > > Andrew > > > > *From: *freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lab of Autism and > Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < > l...@email.gwu.edu> > *Date: *Tuesday, August 17, 2021 at 2:43 PM > *To: *Freesurfer support list > *Subject: *[Freesurfer] LGI - output issue > > *External Email - Use Caution* > > Good afternoon FreeSurfer experts, > > > > Hope that everyone is well and staying safe! > > > > I tried opening LGI freeview (or tksurferfv) output, and I have been > running into the following issues (see code and error message outputs > below). Any ideas how I could fix this? Please let me know if additional > details are needed. > > > > Bolded code is what I inserted. Outputs are not bolded. > > > > *tksurfer HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi* > > zsh: command not found: tksurfer > > *tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi* > > ERROR: cannot find lh.pial_lgi > > *cd $SUBJECTS_DIR/HAR30303_srs2_2/surf* > > *tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi* > > freeview -f > /Applications/ace_complete/HAR30303_srs2_2/surf/lh.inflated:curvature=/Applications/ace_complete/HAR30303_srs2_2/surf/lh.curv:overlay=lh.pial_lgi:overlay_threshold=2,2,5 > -viewport 3d > > /Applications/freesurfer/bin/fsvglrun: line 20: conditional binary > operator expected > > /Applications/freesurfer/bin/fsvglrun: line 20: syntax error near > `FS_ALLOW_VGLRUN' > > /Applications/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v > FS_ALLOW_VGLRUN ]]; then' > > > > Also within the surf folder, I tried something like: *freesurfer -v > lh.pial_lgi* > > Output in freeview was just a dark screen - tried changing the color map > but nothing improved this issue. > > > > Thank you so much! > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1w_K9KbbLgBqllsForrGBfzuAXbV3OU9tXXqWdiYWs0gi0QU2Y_HpCshevss4iZKtV4AL7GqEJpJXwpfrc66rH9XoR6PTPyDPdAbCP3LZJQK4objb3ASK9g6TCq246qA1aQkG-y-GsJSBXHmt6sQjpwhx5Ll-ndcHwoqB-kaJ-bv-P_v5qLt5uzzMwmKTsms_x4oVDvxSYitGKBjsTGdOGBP5jBbQVotEFm4q6vmyltbTQEo7vZKYEhZTC7BLwJxmbN21qBGwvoWD-fx0KlZmZw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://secure-web.cisco.com/1SCrfC_MElf0HQqPJLs0fR1rpzO4Gcy_67eg7dowxoBuPpXcNIwdRSH5z1IqYg12XGKhtUcV8z40hIVs-6NsQBoTzNkzX5-l7X33LSKLDX9t8POjzkNgZzsMb6SOa34sYOzUjc0hmmWLAwUspLs-IWXNnGooSalIH2kT0EBNbqPspZxdcyk8KbiiTwyLI8FLgASXSod5QlYFZWIQs9m3vog4CblQvWRyRRaFcoG8_vKF-aciLbUh0_1Jo2J6LYE5H2rDc3dLKt7devdXrYpb4jw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] LGI - trouble creating output file for each subject
2021-08-17
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Dr. Douglas, Thank you so much for your response. I just checked in the surf folder of this specific subject and yes, rh.white does exist. Not 100% sure how to check if it's readable for freesurfer - could you please explain? Thank you! On Tue, Aug 17, 2021 at 5:45 PM Douglas N. Greve wrote: > It says that it cannot find > /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white > does that file exist and readable? > > On 8/17/2021 5:12 PM, Lab of Autism and Developmental Neuroscience, Lab of > Autism and Developmental Neuroscience wrote: > > External Email - Use Caution > Hello again FreeSurfer experts, > > I am having some issues creating the output file with the LGI data for > each subject. Could you please help me with this? See below the code (in > bold) that I used and the outputs that I got. Please let me know if you > need additional information! > > *mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i > $SUBJECTS_DIR/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum > rh.DCNL_001_aparc.pial_lgi.stats* > 7.1.0 > cwd > cmdline mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i > /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi > --sum rh.DCNL_001_aparc.pial_lgi.stats > sysname Darwin > hostname CCAPSY-0GYM0XV > machine x86_64 > user ajobsaid > whitesurfname white > UseRobust 0 > Constructing seg from annotation > error: No such file or directory > error: > MRISread(/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white): > could not open file > > The lh or rh.pial_lgi file is located in the surf folder in each subject. > Should I transfer them to the stats folder and try something like > *asegstats2table > -s subjectID --statsfile=rh.pial_lgi --meas mean --tablefile > SubjectID_rh_lgi_final.txt ? * > > Thank you so much!! > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1DNwVxd-qsdBrqXyrK06wVTFL1NFHVIkX9g9qZ1tPXHe_bXhvRbgfYGwOswY7U-JfQcPIgzRWOXSlKQd_DzcdVsH0HEHccoM5KaxAjhN6o6WWZenjwHV0z284LJo8kSVvtX4H7hSb5tuTK4FhURTbvf_USv5Lr7agTE3DW45W76coXm5jzZmuFPpDrFfFCGNxmvwYibxvKMWv_jh8G_tnncibfMsUKpsYlkxeXqSLXU4w4HHSX44PQ-JRxvs8RbgDIwQr_oYp7H8RJyc6o6qOCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://secure-web.cisco.com/1jTZoWxS_YLhTSE13gn9KJXUGwklxPXiEBh53eZWeDPbF_PTL2LhjF69arNoKNtEF5zCj5ts7kriR6j0KZqMarNCNvMPr6y-Jr1rFKkcwX_dNx9o5iKd1x3BT_xuZI_HOz5GMIhnsvkeViA2PYUGRpEx66JYdCnglDyh94CZIf1BAuEL8BZEP6w1fUXNpLhJgp8i2EpM60LGVyvP8xOZfSQTyTNprAAntZqdt_iVGIt-xvKD1jyamVDE_cwBxRf36zYC5kAMBVNJwOrE-yAfK3A/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] LGI - trouble creating output file for each subject
2021-08-17
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Hello again FreeSurfer experts, I am having some issues creating the output file with the LGI data for each subject. Could you please help me with this? See below the code (in bold) that I used and the outputs that I got. Please let me know if you need additional information! *mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i $SUBJECTS_DIR/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum rh.DCNL_001_aparc.pial_lgi.stats* 7.1.0 cwd cmdline mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum rh.DCNL_001_aparc.pial_lgi.stats sysname Darwin hostname CCAPSY-0GYM0XV machine x86_64 user ajobsaid whitesurfname white UseRobust 0 Constructing seg from annotation error: No such file or directory error: MRISread(/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white): could not open file The lh or rh.pial_lgi file is located in the surf folder in each subject. Should I transfer them to the stats folder and try something like *asegstats2table -s subjectID --statsfile=rh.pial_lgi --meas mean --tablefile SubjectID_rh_lgi_final.txt ? * Thank you so much!! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] LGI - output issue
2021-08-17
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Good afternoon FreeSurfer experts, Hope that everyone is well and staying safe! I tried opening LGI freeview (or tksurferfv) output, and I have been running into the following issues (see code and error message outputs below). Any ideas how I could fix this? Please let me know if additional details are needed. Bolded code is what I inserted. Outputs are not bolded. *tksurfer HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi* zsh: command not found: tksurfer *tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi* ERROR: cannot find lh.pial_lgi *cd $SUBJECTS_DIR/HAR30303_srs2_2/surf* *tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi* freeview -f /Applications/ace_complete/HAR30303_srs2_2/surf/lh.inflated:curvature=/Applications/ace_complete/HAR30303_srs2_2/surf/lh.curv:overlay=lh.pial_lgi:overlay_threshold=2,2,5 -viewport 3d /Applications/freesurfer/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then' Also within the surf folder, I tried something like: *freesurfer -v lh.pial_lgi* Output in freeview was just a dark screen - tried changing the color map but nothing improved this issue. Thank you so much! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Help with LGI pipeline output - Freeview
2021-06-21
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear FreeSurfer experts, Hope that everyone is well and having a great Monday. I am having some trouble opening the outputs for the LGI pipeline via Freeview - could someone please help me with this? I tried using + editing the code available on the website *tksurfer my_subject_id lh inflated -overlay lh.pial_lgi*; however it did not work. Thank you so much, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hypothalamus segmentation output
2021-03-16
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Perfect! Thank you so much for the clarification. Stay safe On Tue, Mar 16, 2021 at 11:53 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Alex, > > As explained in the wiki, if you run the module on a FreeSurfer processed > subject, the output will be in the subject’s mri directory, and will be > called: hypothalamic_subunits_seg.v1.mgz > > So you could run something like: > > cd $SUBJECTS_DIR//mri > > freeview nu.mgz hypothalamic_subunits_seg.v1.mgz > > > > If you ran the module on a raw t1 scan, then the output will be wherever > you specified with the flag -o > > > > Kind regards, > > > > Eugenio > > > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1bFVqbSu5YkzvYL_x_m0f_DQcxx0pZQ8vp0u5Bxy2EBQbGbToWGK-wF62O3dsAjQW4L_UiqVdRONNu-gDz2SA65SFAs67GChhvGZbHe39NTU68i1DO0k3FK51fPTaffWcB3IyhBcaD1RzED6clFlJpHU9JHCTSSwfijZZQ1bwS-LmPM3IRNzJbALP55318jrSYPbJ4Tks1VVYQy8REzjYFAs66Db1vN7KXIYAsKn2Q6r9f4qsBVdDTynqgdTOaZtkKVFLGzvpEJyFh7uHTXyHrg/http%3A%2F%2Fwww.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list > *Date: *Tuesday, March 16, 2021 at 23:22 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Hypothalamus segmentation output > > > > *External Email - Use Caution* > > Dear Freesurfer experts, > > > > Hope that you all are well and stay safe. > > > > I would like some help figuring out the code to open the output for the > hypothalamus segmentation (via freeview). Does anyone have this info? I > didn't find it on the website. > > > > Thank you so much! > > > > All the best, > > Alex > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1H38lylt88AJLP0jL_vYdoopjyZHyqCy_wku5EU2mLyZqW5rT5Zj9tXkU5zuHYgeUvkup8DFaC1Go-eavFyTskXU6gJpETLv-YTrnJmMxtc-BmLwkzTo87MUU66dMbMT0kNvcgpg8DGfgw2FUHZHph_QcuWCdgg5nNrXFjx0iHjzUX2mibXJ5jhg3s3oMcvd_7pdQEgjsLn_NKC_WFrakW29b4KwaGnqGdB8g265etNjqheOkpc9bJcuW2QbeQTaQ196RRLyXhZJ5UHNifchvnA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hypothalamus segmentation output
2021-03-16
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, Hope that you all are well and stay safe. I would like some help figuring out the code to open the output for the hypothalamus segmentation (via freeview). Does anyone have this info? I didn't find it on the website. Thank you so much! All the best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1
2021-02-02
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution
Thank you for your help!
I have tested the hypothalamus segmentation on the development version of
FS, and this was the error output that I got (see below). How should I
proceed to fix this?
:~/Documents$ mri_segment_hypothalamic_subunits --s UCL55003_srs2
Using 1 thread
2021-02-02 12:19:04.878273: I
tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports
instructions that this TensorFlow binary was not compiled to use: AVX2
2021-02-02 12:19:04.899000: I
tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency:
295000 Hz
2021-02-02 12:19:04.899178: I
tensorflow/compiler/xla/service/service.cc:150] XLA service 0x20b88f0
executing computations on platform Host. Devices:
2021-02-02 12:19:04.899215: I
tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device
(0): ,
processing 1/1
Traceback (most recent call last):
File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 1464, in
main()
File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 91, in main
threads=args.threads
File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 165, in predict
net = build_model(path_model, model_input_shape, len(label_list))
File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 579, in build_model
net.load_weights(model_file, by_name=True)
File
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/network.py",
line 1514, in load_weights
saving.load_weights_from_hdf5_group_by_name(f, self.layers)
File
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/saving.py",
line 839, in load_weights_from_hdf5_group_by_name
original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'
Also, what's the best way for me to run a second version of Freesurfer on
the same computer? I used a virtualbox, but is there a way to run it
outside of that?
Thank you so much for the help and stay safe,
Alex
On Sat, Jan 30, 2021 at 1:25 PM Douglas N. Greve
wrote:
> It is not in version 7. You'll have to download a development version of
> FS to run it.
>
> On 1/29/2021 9:26 PM, Lab of Autism and Developmental Neuroscience, Lab of
> Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I am having some trouble getting the hypothalamus segmentation recognized
> on the command line for FreeSurfer 7.1.0. Is it even available for this
> version? If not, will it work on the 6.0 or the 7.1.1 version?
>
> Thanks and stay safe!
>
> All the best,
> Alex
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1FvwK2Q4o_omzwWs74PFlbrtdw14YNUieN1tko0x72qG2lFonMDOyPogsE9xKXjzdOhiiIvSZnywyuM4sb84PcVJxtB7o9Hz386ftng3F32Sr0Ng56HRXaaFUpr8XBElvjFj03gxMUtugMnAxC6ltPKMBtb5snr2idR98P1GpObEainrAdTZtbAUz7fBQ5bzS9ztPjMLpX9eKcc0ozLFjjC9iA9g5FTOCTbucNJ5U3dEBOawX2oM9Iq4kkFoC1X3RhXsYa_hVTXr_4lwgWXRoRw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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[Freesurfer] Hypothalamus segmentation - Freesurfer 7.1
2021-01-29
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I am having some trouble getting the hypothalamus segmentation recognized on the command line for FreeSurfer 7.1.0. Is it even available for this version? If not, will it work on the 6.0 or the 7.1.1 version? Thanks and stay safe! All the best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] LGI output question
2020-10-20
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I have performed LGI for one of my subject pools and I was wondering if I can compute the mean area for the different LGI values instead of the area in the output tables? How should I edit the code below to accomplish this? Thank you and stay safe! mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats All the best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question about LGI stats file
2020-08-28
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Understood! Thank you for your help and stay safe. On Tue, Aug 25, 2020 at 11:20 AM Douglas N. Greve wrote: > Yes, do this for each subject. If you put the result in subject/stats then > you can run asegstats2table with --statsfile=lh.aparc.pial_lgi.stats to > get a table across all your subjects > > On 8/24/2020 8:02 PM, Lab of Autism and Developmental Neuroscience, Lab of > Autism and Developmental Neuroscience wrote: > > External Email - Use Caution > Dear FreeSurfer experts, > > Hope this email finds you well. I was wondering if someone could please > help clarify some components of the LGI pipeline. So the wiki tells us the > following command needs to be done to obtain a stats file with the LGI info > for one subject: > > mri_segstats --annot my_subject_id lh aparc --i > $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats > > Should I perform this for each subject and then join them all into one > file? I was hoping that you guys could direct me to some > stats2table command that could do all of this automatically and thus be > less time consuming. Thank you and stay safe > > All the best, > Alex > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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] Question about LGI stats file
2020-08-24
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear FreeSurfer experts, Hope this email finds you well. I was wondering if someone could please help clarify some components of the LGI pipeline. So the wiki tells us the following command needs to be done to obtain a stats file with the LGI info for one subject: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats Should I perform this for each subject and then join them all into one file? I was hoping that you guys could direct me to some stats2table command that could do all of this automatically and thus be less time consuming. Thank you and stay safe All the best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Local GI error with Matlab
2020-08-12
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution
It worked! Thank you so much
On Tue, Aug 11, 2020 at 7:33 AM Douglas N. Greve
wrote:
> Try downloading
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m
> and copying it to $FREESURFER/matlab
>
>
> On 8/10/2020 8:47 PM, Lab of Autism and Developmental Neuroscience, Lab of
> Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> Hope you are all safe and well. I changed the version of the matlab that I
> was using (from 2020a to 2019b) and most errors that I was having were
> fixed after running the LGI command. The only issue that I'm still having
> is the following (see below) - does anyone know how I could fix this? Thank
> you!
>
>
> < M A T L A B (R) >
>
> Copyright 1984-2019 The MathWorks, Inc.
>
> R2019b Update 6 (9.7.0.1434023) 64-bit (maci64)
>
>July 15, 2020
>
>
>
>
> For online documentation, see https://www.mathworks.com/support
>
> For product information, visit www.mathworks.com.
>
>
>
> >> Warning: Argument must be a string scalar or character vector.
>
> > In ver (line 45)
>
> In freesurfer_read_surf (line 70)
>
> In find_corresponding_center_FSformat (line 26)
>
> Error using fprintf
>
> Function is not defined for 'struct' inputs.
>
>
> Error in freesurfer_read_surf (line 70)
>
> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
>
>
> Error in find_corresponding_center_FSformat (line 26)
>
> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>
>
>
> >>
>
> ERROR: find_corresponding_center_FSformat did not complete successfully!
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://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
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[Freesurfer] Local GI error with Matlab
2020-08-10
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution
Dear Freesurfer experts,
Hope you are all safe and well. I changed the version of the matlab that I
was using (from 2020a to 2019b) and most errors that I was having were
fixed after running the LGI command. The only issue that I'm still having
is the following (see below) - does anyone know how I could fix this? Thank
you!
< M A T L A B (R) >
Copyright 1984-2019 The MathWorks, Inc.
R2019b Update 6 (9.7.0.1434023) 64-bit (maci64)
July 15, 2020
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
>> Warning: Argument must be a string scalar or character vector.
> In ver (line 45)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>>
ERROR: find_corresponding_center_FSformat did not complete successfully!
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Re: [Freesurfer] Help with LGI
2020-08-05
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Tim, 1) Here is the output after I type matlab: - Matlab does open, and the following appears on terminal: shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory pwd: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory pwd: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory GVA encoder info: AMD performance mode : 2 GVA encoder info: deleteSCDMetalContext : texture cache hits: 0, misses: 0 2) and /Applications/MATLAB_R2020a/bin/matlab: /Applications/MATLAB_R2020a/bin/matlab: No such file or directory Please let me know if you need more information. Thank you, Alex On Wed, Aug 5, 2020 at 3:42 AM Tim Schäfer wrote: > External Email - Use Caution > > Looks like something is wrong with the Matlab installation. It would be > good to know: > > 1) What happens if you type 'matlab' in your shell? > 2) What happens if you type '/Applications/MATLAB_R2020a/bin/matlab' in > your shell? > > Best, > > Tim > > > On August 4, 2020 at 8:31 PM "Lab of Autism and Developmental > Neuroscience, Lab of Autism and Developmental Neuroscience" < > l...@email.gwu.edu> wrote: > > > > > > External Email - Use Caution > > > > Dear Freesurfer experts, > > > > Just wanted to follow up my last email - does anyone know what might be > > wrong with my code? > > > > Thank you and stay safe, > > Alex > > > > On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental > > Neuroscience, Lab of Autism and Developmental Neuroscience < > > l...@email.gwu.edu> wrote: > > > > > Dear Douglas, > > > > > > Yes, now matlab is correctly set to my freesurfer path, but the > following > > > error occurs when I run localGI (please see below). Any ideas what > might be > > > wrong? Maybe there are some issues with the matlab version or image > > > processing toolbox that I'm using? > > > > > > iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4 > -localGI > > > Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b > > > Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b > > > INFO: SUBJECTS_DIR is /Applications/BAP_complete > > > Actual FREESURFER_HOME /Applications/freesurfer > > > -rw-rw-r-- 1 ajobsaid 982768932 956144 Jun 30 09:20 > > > /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log > > > Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 > > > 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64 > > > /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms > > > /Applications/BAP_complete/nih00024_epoch11_4 > > > /Applications/BAP_complete/nih00024_epoch11_4 > > > #@# white curv lh Fri Jul 31 09:20:05 PDT 2020 > > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > > > mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv > > >Update not needed > > > #@# white area lh Fri Jul 31 09:20:05 PDT 2020 > > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > > > mris_place_surface --area-map ../surf/lh.white ../surf/lh.area > > >Update not needed > > > #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020 > > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > > > mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial > > >Update not needed > > > #@# pial area lh Fri Jul 31 09:20:05 PDT 2020 > > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > > > mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial > > >Update not needed > > > #@# thickness lh Fri Jul 31 09:20:05 PDT 2020 > > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > > > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 > > > ../surf/lh.thickness > > >Update not needed > > > #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020 > > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > > > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 > > > ../surf/lh.thickness > > >Update not needed > > > #@# white curv rh Fri Jul 31 09:20:05 PDT 2020 > > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > > > mris_place_surface
Re: [Freesurfer] Help with LGI
2020-08-04
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, Just wanted to follow up my last email - does anyone know what might be wrong with my code? Thank you and stay safe, Alex On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < l...@email.gwu.edu> wrote: > Dear Douglas, > > Yes, now matlab is correctly set to my freesurfer path, but the following > error occurs when I run localGI (please see below). Any ideas what might be > wrong? Maybe there are some issues with the matlab version or image > processing toolbox that I'm using? > > iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4 -localGI > Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b > Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b > INFO: SUBJECTS_DIR is /Applications/BAP_complete > Actual FREESURFER_HOME /Applications/freesurfer > -rw-rw-r-- 1 ajobsaid 982768932 956144 Jun 30 09:20 > /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log > Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 > 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64 > /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms > /Applications/BAP_complete/nih00024_epoch11_4 > /Applications/BAP_complete/nih00024_epoch11_4 > #@# white curv lh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv >Update not needed > #@# white area lh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --area-map ../surf/lh.white ../surf/lh.area >Update not needed > #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial >Update not needed > #@# pial area lh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial >Update not needed > #@# thickness lh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 > ../surf/lh.thickness >Update not needed > #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 > ../surf/lh.thickness >Update not needed > #@# white curv rh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv >Update not needed > #@# white area rh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --area-map ../surf/rh.white ../surf/rh.area >Update not needed > #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial >Update not needed > #@# pial area rh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial >Update not needed > #@# thickness rh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 > ../surf/rh.thickness >Update not needed > #@# area and vertex vol rh Fri Jul 31 09:20:05 PDT 2020 > cd /Applications/BAP_complete/nih00024_epoch11_4/mri > mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 > ../surf/rh.thickness >Update not needed > /Applications/BAP_complete/nih00024_epoch11_4/surf > # > #@# Local Gyrification Index lh Fri Jul 31 09:20:05 PDT 2020 > \n mris_compute_lgi --i lh.pial \n > = > rm -Rf > /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial > = > = > mkdir -p > /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial > = > = > mris_fill -c -r 1 lh.pial > /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz > = > reading surface from lh.pial... > writing filled volume to > /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... > conforming output volume > setting resolution for int
Re: [Freesurfer] Help with LGI
2020-08-01
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
rivate/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
>> reading filled volume...
closing volume...
morphological closing done.
writing outer surface...
=
mris_extract_main_component
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
=
counting number of connected components...
72876 voxel in cpt #1: X=2 [v=72876,e=218622,f=145748] located at
(-25.312176, -9.845789, 0.428207)
For the whole surface: X=2 [v=72876,e=218622,f=145748]
One single component has been found
nothing to do
done
=
mris_smooth -nw -n 30
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
./lh.pial-outer-smoothed
=
smoothing for 30 iterations
smoothing surface tessellation for 30 iterations...
smoothing complete - recomputing first and second fundamental forms...
=
mris_euler_number ./lh.pial-outer-smoothed
=
euler # = v-e+f = 2g-2: 72876 - 218622 + 145748 = 2 --> 0 holes
F =2V-4: 145748 = 145752-4 (0)
2E=3F:437244 = 437244 (0)
total defect index = 0
=
mris_convert -n lh.pial-outer-smoothed
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc
=
=
find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_37963_.m');
exit
=
< M A T L A B (R) >
Copyright 1984-2020 The MathWorks, Inc.
R2020a Update 3 (9.8.0.1396136) 64-bit (maci64)
May 27, 2020
Warning: Name is nonexistent or not a directory:
/Applications/MATLAB_R2020a/bin
Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a
Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020
Warning: Name is nonexistent or not a directory:
/private/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
>> Warning: Argument must be a string scalar or character vector.
> In ver (line 45)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>>
ERROR: find_corresponding_center_FSformat did not complete successfully!
Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5
00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
recon-all -s nih00024_epoch11_4 exited with ERRORS at Fri Jul 31 09:20:20
PDT 2020
For more details, see the log file
/Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Jul 15, 2020 at 9:46 AM Douglas N. Greve
wrote:
> If you type matlab at the command line, does matlab start?
>
> On 7/12/2020 10:42 PM, Lab of Autism and Developmental Neuroscience, Lab
> of Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I have added Matlab my path and either the same error (please see my first
> email) occurs, or recon-all -s (ID) -localGI command is said to 'not
> exist'. Any other ideas on how to properly solve this problem? Thank you
> and hope everyone is safe!
>
> On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental
> Neuroscience, Lab of Autism and Developmental Neuroscience <
> l...@email.gwu.edu> wrote:
>
>> Dear Douglas,
>>
>> So to accomplish this, should I do the following through matlab?
>>
>> The following code has to be in matlab’s startup.m file:
>> 1
>> 2
>> 3
>> 4
>> 5
>> 6
>> 7
>> 8
>> 9
>> % FreeSurfer -%
>>
>> fshome = getenv('FREESURFER_HOME');
>> fsmatlab = sprintf('%s/matlab',fshome);
>> if (exist(fsmatlab) == 7)
>> path(path,fsmatlab);
>> end
>> clear fshome fsmatlab;
>> %-%
>>
>> Also, if you are getting “ERROR: Matlab is required to run
>> mris_compute_lgi!”, it means your have to add the Matlab pa
Re: [Freesurfer] fsgd file - glmfit error
2020-07-29
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Thank you Douglas! On Tue, Jul 28, 2020 at 9:34 AM Douglas N. Greve wrote: > Try putting 1 after GroupDescriptorFile, ie, > > GroupDescriptorFile 1 > > On 7/28/2020 12:21 PM, Lab of Autism and Developmental Neuroscience, Lab > of Autism and Developmental Neuroscience wrote: > > External Email - Use Caution > Here is my fsgd file. > Thank you! > > > On Mon, Jul 27, 2020 at 8:44 PM Douglas N. Greve > wrote: > >> Please send the fsgd file >> >> On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, Lab >> of Autism and Developmental Neuroscience wrote: >> >> External Email - Use Caution >> Dear Freesurfer experts, >> >> Hope this email finds you well. I am having some trouble with the fsgd >> file for glmfit and I'm confused why. This is the error I'm getting when >> running glmfit: >> >> iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y >> mrip.rh_volume_F7_BNB.00.mgh --fsgd fsgd_8.fsgd --C Cor_2.mtx --surf >> fsaverage rh --cortex --glmdir contrast2.rh_volume_BNB.glmdir >> gdfRead(): reading fsgd_8.fsgd >> ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd) >> iMac-Pro:BAP_complete ajobsaid$ >> >> If needed, I can send you my fsgd file, but I have triple checked the >> design and format of the file (it is saved as .fsgd), and I'm still getting >> this error message. >> >> Thank you, >> Alex >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > listfreesur...@nmr.mgh.harvard.eduhttps://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] fsgd file - glmfit error
2020-07-28
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Here is my fsgd file. Thank you! On Mon, Jul 27, 2020 at 8:44 PM Douglas N. Greve wrote: > Please send the fsgd file > > On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, Lab > of Autism and Developmental Neuroscience wrote: > > External Email - Use Caution > Dear Freesurfer experts, > > Hope this email finds you well. I am having some trouble with the fsgd > file for glmfit and I'm confused why. This is the error I'm getting when > running glmfit: > > iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y > mrip.rh_volume_F7_BNB.00.mgh --fsgd fsgd_8.fsgd --C Cor_2.mtx --surf > fsaverage rh --cortex --glmdir contrast2.rh_volume_BNB.glmdir > gdfRead(): reading fsgd_8.fsgd > ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd) > iMac-Pro:BAP_complete ajobsaid$ > > If needed, I can send you my fsgd file, but I have triple checked the > design and format of the file (it is saved as .fsgd), and I'm still getting > this error message. > > Thank you, > Alex > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 fsgd_8.fsgd Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fsgd file - glmfit error
2020-07-27
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, Hope this email finds you well. I am having some trouble with the fsgd file for glmfit and I'm confused why. This is the error I'm getting when running glmfit: iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y mrip.rh_volume_F7_BNB.00.mgh --fsgd fsgd_8.fsgd --C Cor_2.mtx --surf fsaverage rh --cortex --glmdir contrast2.rh_volume_BNB.glmdir gdfRead(): reading fsgd_8.fsgd ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd) iMac-Pro:BAP_complete ajobsaid$ If needed, I can send you my fsgd file, but I have triple checked the design and format of the file (it is saved as .fsgd), and I'm still getting this error message. Thank you, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Help with LGI
2020-07-12
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution
Dear Freesurfer experts,
I have added Matlab my path and either the same error (please see my first
email) occurs, or recon-all -s (ID) -localGI command is said to 'not
exist'. Any other ideas on how to properly solve this problem? Thank you
and hope everyone is safe!
On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental
Neuroscience, Lab of Autism and Developmental Neuroscience <
l...@email.gwu.edu> wrote:
> Dear Douglas,
>
> So to accomplish this, should I do the following through matlab?
>
> The following code has to be in matlab’s startup.m file:
> 1
> 2
> 3
> 4
> 5
> 6
> 7
> 8
> 9
> % FreeSurfer -%
>
> fshome = getenv('FREESURFER_HOME');
> fsmatlab = sprintf('%s/matlab',fshome);
> if (exist(fsmatlab) == 7)
> path(path,fsmatlab);
> end
> clear fshome fsmatlab;
> %-%
>
> Also, if you are getting “ERROR: Matlab is required to run
> mris_compute_lgi!”, it means your have to add the Matlab path to
> Freesurfer`s $PATH variable for it to run.
>
> To do this automatically when starting FS, just edit the .tcshrc file
> (assuming you run FS from TCSH) adding the location of your Matlab’s bin
> folder:
> 1
> setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
>
>
> Thanks,
> Alex
>
>
>
>
>
>
> On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve
> wrote:
>
>> You need to have matlab in your path so that when you type "matlab" it
>> starts matlab
>>
>> On 7/9/2020 4:58 PM, Lab of Autism and Developmental Neuroscience, Lab of
>> Autism and Developmental Neuroscience wrote:
>>
>> External Email - Use Caution
>> Dear Freesurfer experts,
>>
>> I'm needing some simple help running LGI. After downloading MATLAB +
>> Image processing toolbox and double checking if the ?h.pial file is located
>> in the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command still
>> doesn't work. The output says that I still didn't install matlab onto my
>> computer, so maybe it has something to do with setting
>> $FREESURFER_HOME/matlab in your matlab path setup in your ~/matlab/starup.m
>> script, but I'm unsure how to do this. Please see the output below:
>>
>> Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2 -localGI
>> Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
>> Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
>> INFO: SUBJECTS_DIR is /Applications/ace_complete
>> Actual FREESURFER_HOME /Applications/freesurfer
>> -rw-rw-r-- 1 ajobsaid 982768932 959822 Jul 9 10:50
>> /Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log
>> Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20
>> 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
>> /Applications/ace_complete/HAR30003_srs2_2/mri/transforms
>> /Applications/ace_complete/HAR30003_srs2_2
>> /Applications/ace_complete/HAR30003_srs2_2
>> #@# white curv lh Thu Jul 9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
>>Update not needed
>> #@# white area lh Thu Jul 9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
>>Update not needed
>> #@# pial curv lh Thu Jul 9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
>>Update not needed
>> #@# pial area lh Thu Jul 9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
>>Update not needed
>> #@# thickness lh Thu Jul 9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
>> ../surf/lh.thickness
>>Update not needed
>> #@# area and vertex vol lh Thu Jul 9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
>> ../surf/lh.thickness
>>Update not needed
>> #@# white curv rh Thu Jul 9 12:58:04 PDT 2020
>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
>> mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
>>Update not needed
>> #@# white area rh Thu Jul 9 12:58:04 PDT 2020
>&
Re: [Freesurfer] Help with LGI
2020-07-11
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution
Dear Douglas,
So to accomplish this, should I do the following through matlab?
The following code has to be in matlab’s startup.m file:
1
2
3
4
5
6
7
8
9
% FreeSurfer -%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
%-%
Also, if you are getting “ERROR: Matlab is required to run
mris_compute_lgi!”, it means your have to add the Matlab path to
Freesurfer`s $PATH variable for it to run.
To do this automatically when starting FS, just edit the .tcshrc file
(assuming you run FS from TCSH) adding the location of your Matlab’s bin
folder:
1
setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
Thanks,
Alex
On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve
wrote:
> You need to have matlab in your path so that when you type "matlab" it
> starts matlab
>
> On 7/9/2020 4:58 PM, Lab of Autism and Developmental Neuroscience, Lab of
> Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I'm needing some simple help running LGI. After downloading MATLAB + Image
> processing toolbox and double checking if the ?h.pial file is located in
> the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command still
> doesn't work. The output says that I still didn't install matlab onto my
> computer, so maybe it has something to do with setting
> $FREESURFER_HOME/matlab in your matlab path setup in your ~/matlab/starup.m
> script, but I'm unsure how to do this. Please see the output below:
>
> Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2 -localGI
> Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> INFO: SUBJECTS_DIR is /Applications/ace_complete
> Actual FREESURFER_HOME /Applications/freesurfer
> -rw-rw-r-- 1 ajobsaid 982768932 959822 Jul 9 10:50
> /Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log
> Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20
> 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
> /Applications/ace_complete/HAR30003_srs2_2/mri/transforms
> /Applications/ace_complete/HAR30003_srs2_2
> /Applications/ace_complete/HAR30003_srs2_2
> #@# white curv lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
>Update not needed
> #@# white area lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
>Update not needed
> #@# pial curv lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
>Update not needed
> #@# pial area lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
>Update not needed
> #@# thickness lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
>Update not needed
> #@# area and vertex vol lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
>Update not needed
> #@# white curv rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
>Update not needed
> #@# white area rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
>Update not needed
> #@# pial curv rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
>Update not needed
> #@# pial area rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
>Update not needed
> #@# thickness rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> ../surf/rh.thickness
>Update not needed
> #@# area and vertex vol rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003
[Freesurfer] Help with LGI
2020-07-09
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I'm needing some simple help running LGI. After downloading MATLAB + Image processing toolbox and double checking if the ?h.pial file is located in the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command still doesn't work. The output says that I still didn't install matlab onto my computer, so maybe it has something to do with setting $FREESURFER_HOME/matlab in your matlab path setup in your ~/matlab/starup.m script, but I'm unsure how to do this. Please see the output below: Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2 -localGI Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b INFO: SUBJECTS_DIR is /Applications/ace_complete Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 ajobsaid 982768932 959822 Jul 9 10:50 /Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64 /Applications/ace_complete/HAR30003_srs2_2/mri/transforms /Applications/ace_complete/HAR30003_srs2_2 /Applications/ace_complete/HAR30003_srs2_2 #@# white curv lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv Update not needed #@# white area lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area Update not needed #@# pial curv lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# area and vertex vol lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# white curv rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv Update not needed #@# white area rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area Update not needed #@# pial curv rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed #@# thickness rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed #@# area and vertex vol rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed /Applications/ace_complete/HAR30003_srs2_2/surf # #@# Local Gyrification Index lh Thu Jul 9 12:58:04 PDT 2020 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64 recon-all -s HAR30003_srs2_2 exited with ERRORS at Thu Jul 9 12:58:04 PDT 2020 Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec and mris_anatomical_stats help
2020-05-18
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Hello Freesurfer experts, Just wanted to follow-up from my last email. If any clarification is needed regarding what I'm trying to understand from mris_anatomical_stats, please let me know! Kind regards, Alex On Fri, May 15, 2020 at 8:17 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < l...@email.gwu.edu> wrote: > Dear Freesurfer experts, > > Hope everyone is doing well! Could someone please clarify some things > about mris_anatomical_stats, done after running qdec + mapping label to all > subjects? > From what I can understand, the following code should be used: > > mris_anatomical_stats -l lh.supramarg.label \ > -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh > > But if I created the ".label" file directly on qdec, by "mapping label to > all subjects", and didn't use the mri_label2label code for "target > subjects", how should I work around this to perform mris_anatomical_stat > correctly? > Also, I'm confused on when + where this "lh.thickness" file is created and > stored. > Please let me know if you need any other information about my code or my > qdec output. > > Thank you, > Alex Job Said > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] qdec and mris_anatomical_stats help
2020-05-15
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, Hope everyone is doing well! Could someone please clarify some things about mris_anatomical_stats, done after running qdec + mapping label to all subjects? From what I can understand, the following code should be used: mris_anatomical_stats -l lh.supramarg.label \ -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh But if I created the ".label" file directly on qdec, by "mapping label to all subjects", and didn't use the mri_label2label code for "target subjects", how should I work around this to perform mris_anatomical_stat correctly? Also, I'm confused on when + where this "lh.thickness" file is created and stored. Please let me know if you need any other information about my code or my qdec output. Thank you, Alex Job Said ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Downloading Matlab runtime - ubuntu
2020-05-10
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Thank you Tim! Also I was wondering, how should I specify the version (i.e. R2012b) of matlab in the code - "cd $FREESURFER_HOME/bin && curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr -o fs_install_mcr && chmod +x fs_install_mcr" ? All the best, Alex On Sun, May 10, 2020 at 5:42 AM Tim Schäfer wrote: > External Email - Use Caution > > You do not have write permission to $FREESURFER_HOME, which is > /usr/local/freesurfer/ in your case, it seems. There are 2 options: > > 1) run the command again but put 'sudo ' in front. This should give you > permission to write to that location. > > 2) install FreeSurfer into your user directory, where you have write > access. > > I would recommend option 1) if you have sudo access, especially if several > users should be able to use the FreeSurfer installation. > > Best, > > Tim > > > > On May 10, 2020 at 8:02 AM "Lab of Autism and Developmental > Neuroscience, Lab of Autism and Developmental Neuroscience" < > l...@email.gwu.edu> wrote: > > > > > > External Email - Use Caution > > > > Dear Freesurfer experts, > > > > I'm trying to download runtime for ubuntu using the instructions on the > > website and I'm struggling to resolve this error (seen below). Any ideas > on > > how to fix this? Thank you and hope everyone is safe! > > > > cd $FREESURFER_HOME/bin && curl > > > https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr > > -o > > fs_install_mcr && chmod +x fs_install_mcr > > % Total% Received % Xferd Average Speed TimeTime Time > > Current > > Dload Upload Total SpentLeft > > Speed > > 0 00 00 0 0 0 --:--:-- --:--:-- --:--:-- > > 0Warning: Failed to create the file fs_install_mcr: Permission denied > > 68 1988 68 13710 0 4436 0 --:--:-- --:--:-- --:--:-- > > 4422 > > curl: (23) Failed writing body (0 != 1371) > > alex@ubu19:/usr/local/freesurfer/bin$ fs_install_mcr R2012b > > % Total% Received % Xferd Average Speed TimeTime Time > > Current > > Dload Upload Total SpentLeft > > Speed > > 100 177 100 1770 0 77 0 0:00:02 0:00:02 --:--:-- > > 77 > > Archive: installer.zip > > End-of-central-directory signature not found. Either this file is not > > a zipfile, or it constitutes one disk of a multi-part archive. In the > > latter case the central directory and zipfile comment will be found on > > the last disk(s) of this archive. > > unzip: cannot find zipfile directory in one of installer.zip or > > installer.zip.zip, and cannot find installer.zip.ZIP, period. > > > > Thank you, > > Alex Job Said > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Tim Schäfer > > ___ > 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] Downloading Matlab runtime - ubuntu
2020-05-10
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I'm trying to download runtime for ubuntu using the instructions on the website and I'm struggling to resolve this error (seen below). Any ideas on how to fix this? Thank you and hope everyone is safe! cd $FREESURFER_HOME/bin && curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr -o fs_install_mcr && chmod +x fs_install_mcr % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 0 00 00 0 0 0 --:--:-- --:--:-- --:--:-- 0Warning: Failed to create the file fs_install_mcr: Permission denied 68 1988 68 13710 0 4436 0 --:--:-- --:--:-- --:--:-- 4422 curl: (23) Failed writing body (0 != 1371) alex@ubu19:/usr/local/freesurfer/bin$ fs_install_mcr R2012b % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 177 100 1770 0 77 0 0:00:02 0:00:02 --:--:-- 77 Archive: installer.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive. unzip: cannot find zipfile directory in one of installer.zip or installer.zip.zip, and cannot find installer.zip.ZIP, period. Thank you, Alex Job Said ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_glimfit error - help!
2020-05-01
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution No worries, I'll try to figure it out. Does anyone else have any ideas on what might be wrong? Hope everyone is safe and well! Alex Job On Wed, Apr 29, 2020 at 6:30 PM Douglas N. Greve wrote: > There is some rogue character after the "0" in "Class 0". If you run > od -c fsgd_file.fsgd > It comes out as 312. I have no idea what it is > > On 4/29/2020 6:21 PM, Lab of Autism and Developmental Neuroscience, Lab of > Autism and Developmental Neuroscience wrote: > > External Email - Use Caution > Dear Freesurfer experts, > > I'm having a persistent error with mri_glimfit. The fsgd file isn't being > read correctly, despite following the exact requirements of the wiki. Also, > the output mentions this "carriage returns warning", and despite running > this conversion: cat fsgd_file.fsgd | sed 's/\r/\n/g' > > new.fsgd_file.fsgd, the *new fsgd still doesn't work* (this code somehow > alters the Group Descriptor at the top of the file, giving another error). > I've attached my fsgd file (that I used while running the code below) > Also, please see the full error of the glim_fit below: > > WARNING: carriage returns have been detected in file fsgd_file.fsgd > > Was it created on a Windows computer? > > This may cause an error in reading the FSGD file. > > If so, try running: > > cat fsgd_file.fsgd | sed 's/\r/\n/g' > new.fsgd_file.fsgd > > Then use new.fsgd_file.fsgd > > > INFO: ignoring tag Tile > > INFO: ignoring tag nput > > INFO: ignoring tag nput > > INFO: gd2mtx_method is dods > > Reading source surface > /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf/rh.white > > Number of vertices 163842 > > Number of faces327680 > > Total area 65020.839844 > > AvgVtxArea 0.396851 > > AvgVtxDist 0.717994 > > StdVtxDist 0.193566 > > > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ > > cwd /Applications/freesurfer/BAP/group_analysis_data/qdec > > cmdline mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd > dods --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir > > > sysname Darwin > > hostname CCASPH-A1900447.cloud.ccas.gwu.edu > > machine x86_64 > > user ajobsaid > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y > /Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh > > logyflag 0 > > usedti 0 > > FSGD fsgd_file.fsgd > > labelmask > /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/label/rh.cortex.label > > maskinv 0 > > glmdir rhBAP_thickness.glmdir > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory rhBAP_thickness.glmdir > > Loading y from > /Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh > >... done reading. > > INFO: gd2mtx_method is dods > > Saving design matrix to rhBAP_thickness.glmdir/Xg.dat > > Computing normalized matrix > > Normalized matrix condition is 1e+10 > > Design matrix -- > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+10 > > > > Possible problem with experimental design: > > Check for duplicate entries and/or lack of range of > > continuous variables within a class. > > If you seek help with this problem, make sure to send: > > 1. Your command line: > > mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd dods > --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir > > 2. The FSGD file (if using one) > > 3. And the design matrix above > > Attempting to diagnose further > > SumSq: Min=9997952.00 (col 0), Max=0.00 (col 0) > > ... could not determine the cause of the problem > > > Thanks! > > Alex Job > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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] mri_glimfit error - help!
2020-04-29
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I'm having a persistent error with mri_glimfit. The fsgd file isn't being read correctly, despite following the exact requirements of the wiki. Also, the output mentions this "carriage returns warning", and despite running this conversion: cat fsgd_file.fsgd | sed 's/\r/\n/g' > new.fsgd_file.fsgd, the *new fsgd still doesn't work* (this code somehow alters the Group Descriptor at the top of the file, giving another error). I've attached my fsgd file (that I used while running the code below) Also, please see the full error of the glim_fit below: WARNING: carriage returns have been detected in file fsgd_file.fsgd Was it created on a Windows computer? This may cause an error in reading the FSGD file. If so, try running: cat fsgd_file.fsgd | sed 's/\r/\n/g' > new.fsgd_file.fsgd Then use new.fsgd_file.fsgd INFO: ignoring tag Tile INFO: ignoring tag nput INFO: ignoring tag nput INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf/rh.white Number of vertices 163842 Number of faces327680 Total area 65020.839844 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Applications/freesurfer/BAP/group_analysis_data/qdec cmdline mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd dods --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir sysname Darwin hostname CCASPH-A1900447.cloud.ccas.gwu.edu machine x86_64 user ajobsaid FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh logyflag 0 usedti 0 FSGD fsgd_file.fsgd labelmask /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/label/rh.cortex.label maskinv 0 glmdir rhBAP_thickness.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rhBAP_thickness.glmdir Loading y from /Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to rhBAP_thickness.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 1e+10 Design matrix -- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+10 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd dods --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=9997952.00 (col 0), Max=0.00 (col 0) ... could not determine the cause of the problem Thanks! Alex Job fsgd_file.fsgd Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] matlab runtime error - Hippocampal subfield segmentation
2020-04-24
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I am having trouble installing matlab runtime to be used for hippocampal subfield segmentation. I run the code following the instructions on the website, but nothing is installed. This is what happens: /home/alex/Documents/freesurfer/bin# cd $FREESURFER_HOME/bin && curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr -o fs_install_mcr && chmod +x fs_install_mcr % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 1801 100 18010 0 17485 0 --:--:-- --:--:-- --:--:-- 17485 Any ideas why this isn't loading? Thanks, Alex Job ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Contrast file to be used in mri_glimfit
2020-04-23
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution I tried running mri_glmfit and this error is occurring - WARNING: gdfReadV1: class B, is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 ,,,Gender,Age,AQ_Top_Quart nan nan Class Means of each Continuous Variable 1 B, nan 2 NB, nan INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf/lh.–-glmdir MRISread(/Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf This is probably related to some error in my .mtx file. Thank you, Alex Job On Fri, Apr 24, 2020 at 12:31 AM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < l...@email.gwu.edu> wrote: > Dear Freesurfer experts, > > I am a little bit confused on how I should construct my .mtx file to be > used in mri_glmfit. The following variables are what I have used in my fsgd > file: > GroupDescriptorFile 1 > Title Study > Class B > Class NB > Variables ,,,Gender,Age > Input, Sub_ID,NB,F,71 > Input, Sub_ID, B, F, 80 > > Please let me know if you need more information on my work. Thank you! > > All the best, > Alex Job > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Contrast file to be used in mri_glimfit
2020-04-23
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I am a little bit confused on how I should construct my .mtx file to be used in mri_glmfit. The following variables are what I have used in my fsgd file: GroupDescriptorFile 1 Title Study Class B Class NB Variables ,,,Gender,Age Input, Sub_ID,NB,F,71 Input, Sub_ID, B, F, 80 Please let me know if you need more information on my work. Thank you! All the best, Alex Job ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Aseg file issue
2020-04-09
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Thank you for the information! On Thu, Apr 9, 2020 at 10:38 AM Douglas N. Greve wrote: > Hi, unfortunately, QDEC is no longer being supported. Try using > mris_preproc and mri_glmfit with FSGD files. > > On 4/8/2020 7:03 PM, Lab of Autism and Developmental Neuroscience, Lab of > Autism and Developmental Neuroscience wrote: > > External Email - Use Caution > Dear Freesurfer experts, > > I'm having some difficulty importing my aseg stats data onto QDEC. The > error which I'm getting is seen below (please open the JPEG file). Any > ideas on why this is happening? Thank you! > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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] Hippocampal Subfield Segmentation Error
2020-04-08
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Hello! So I have installed the latest Java, reinstalled the Runtime following the instructions on the Freesurfer website, and have attempted to remove Java.opts files, to then run the analysis. Still nothing has changed. Any other suggestions? Thank you, Alex On Tue, Mar 31, 2020 at 6:17 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Uuuummm this is a tough one. Any ideas, Andrew? Maybe updating java? > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list > *Date: *Tuesday, March 31, 2020 at 17:59 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Hippocampal Subfield Segmentation Error > > > > *External Email - Use Caution* > > Hello Eugenio, > > No I wasn't! When I first tried to run the subfields I wasn't pointed to > downloading a version of Java. I do have Java on the MAC I'm using, but the > error "unable to start JVM because of a bad java option" still appears. Any > other ideas on how to fix this? > > Thanks, > > Alex > > > > On Mon, Mar 30, 2020 at 10:12 AM Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> wrote: > > HI Alex, > > Were you pointed to downloading a version of Java when you first tried to > run > > the subfields? If so, did you follow the instructions? > > Cheers, > > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list > *Date: *Saturday, March 28, 2020 at 02:07 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Hippocampal Subfield Segmentation Error > > > > *External Email - Use Caution* > > Dear Freesurfer experts, > > > > Hope everyone is well! I'm unfortunately continuing to have errors running > the hippocampal subfield segmentation. Apparently it's being caused by > issues with the java.opts files. I tried removing it (as recommended by a > link someone set me from the Matlab help website), but it made no > difference. Please find my code and error message below: > > > > > > > > CCASPH-A1900447:3003 ajobsaid$ recon-all -s Sub_42 > -hippocampal-subfields-T1 > > Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > INFO: SUBJECTS_DIR is /Applications/freesurfer/BAP/3003 > > Actual FREESURFER_HOME /Applications/freesurfer > > -rw-rw-r-- 1 ajobsaid wheel 859204 Mar 24 12:59 > /Applications/freesurfer/BAP/3003/Sub_42/scripts/recon-all.log > > Darwin CCASPH-A1900447.cloud.ccas.gwu.edu 18.7.0 Darwin Kernel Version > 18.7.0: Thu Jan 23 06:52:12 PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 > x86_64 > > # > > #@# Hippocampal Subfields processing (T1 only) left Tue Mar 24 15:09:44 > EDT 2020 > > \n /Applications/freesurfer/bin/segmentSF_T1.sh > /Applications/freesurfer/MCRv80 /Applications/freesurfer Sub_42 > /Applications/freesurfer/BAP/3003 left \n > > See log file: > /Applications/freesurfer/BAP/3003/Sub_42/scripts/hippocampal-subfields-T1.log > > -- > > Setting up environment variables > > --- > > DYLD_LIBRARY_PATH is > .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: > > Warning: application is running on a locale different from the original > platform locale. > > JavaVM: Failed to load JVM: > /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib > > JavaVM FATAL: Failed to load the jvm library. > > 2020-03-24 15:09:45.262 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.263 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not
Re: [Freesurfer] Hippocampal Subfield Segmentation Error
2020-03-31
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Hello Eugenio, No I wasn't! When I first tried to run the subfields I wasn't pointed to downloading a version of Java. I do have Java on the MAC I'm using, but the error "unable to start JVM because of a bad java option" still appears. Any other ideas on how to fix this? Thanks, Alex On Mon, Mar 30, 2020 at 10:12 AM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > HI Alex, > > Were you pointed to downloading a version of Java when you first tried to > run > > the subfields? If so, did you follow the instructions? > > Cheers, > > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list > *Date: *Saturday, March 28, 2020 at 02:07 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Hippocampal Subfield Segmentation Error > > > > *External Email - Use Caution* > > Dear Freesurfer experts, > > > > Hope everyone is well! I'm unfortunately continuing to have errors running > the hippocampal subfield segmentation. Apparently it's being caused by > issues with the java.opts files. I tried removing it (as recommended by a > link someone set me from the Matlab help website), but it made no > difference. Please find my code and error message below: > > > > > > > > CCASPH-A1900447:3003 ajobsaid$ recon-all -s Sub_42 > -hippocampal-subfields-T1 > > Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > INFO: SUBJECTS_DIR is /Applications/freesurfer/BAP/3003 > > Actual FREESURFER_HOME /Applications/freesurfer > > -rw-rw-r-- 1 ajobsaid wheel 859204 Mar 24 12:59 > /Applications/freesurfer/BAP/3003/Sub_42/scripts/recon-all.log > > Darwin CCASPH-A1900447.cloud.ccas.gwu.edu 18.7.0 Darwin Kernel Version > 18.7.0: Thu Jan 23 06:52:12 PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 > x86_64 > > # > > #@# Hippocampal Subfields processing (T1 only) left Tue Mar 24 15:09:44 > EDT 2020 > > \n /Applications/freesurfer/bin/segmentSF_T1.sh > /Applications/freesurfer/MCRv80 /Applications/freesurfer Sub_42 > /Applications/freesurfer/BAP/3003 left \n > > See log file: > /Applications/freesurfer/BAP/3003/Sub_42/scripts/hippocampal-subfields-T1.log > > -- > > Setting up environment variables > > --- > > DYLD_LIBRARY_PATH is > .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: > > Warning: application is running on a locale different from the original > platform locale. > > JavaVM: Failed to load JVM: > /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib > > JavaVM FATAL: Failed to load the jvm library. > > 2020-03-24 15:09:45.262 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.263 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.263 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.264 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.264 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.264 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator privileges. This is not supported. > > 2020-03-24 15:09:45.265 > segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is > attempting to exclude an item from Time Machine by path without > administrator pr
Re: [Freesurfer] Hippocampal Subfield Segmentation Error
2020-03-28
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2020-03-24 15:09:46.334 segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2020-03-24 15:09:46.334 segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2020-03-24 15:09:46.334 segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2020-03-24 15:09:46.335 segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2020-03-24 15:09:46.335 segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2020-03-24 15:09:46.336 segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2020-03-24 15:09:46.336 segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2020-03-24 15:09:46.336 segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Started at Tue Mar 24 15:09:43 EDT 2020 Ended at Tue Mar 24 15:09:46 EDT 2020 #@#%# recon-all-run-time-hours 0.001 recon-all -s Sub_42 finished without error at Tue Mar 24 15:09:46 EDT 2020 Hopefully someone has an idea of what could be done next. Thanks! All the best, Alex On Sun, Mar 22, 2020 at 10:57 AM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Alex, > > Can you please try this? > > > https://uk.mathworks.com/matlabcentral/answers/196961-why-do-i-receive-fatal-error-on-startup-unable-to-start-the-jvm-because-of-a-bad-java-option-or-un > > Cheers, > > /E > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list > *Date: *Saturday, March 21, 2020 at 23:33 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Hippocampal Subfield Segmentation Error > > > > *External Email - Use Caution* > > Dear Freesurfer experts, > > > > I am having a problem with hippocampal subfield segmentation. The issue > appears to be related to JavaVM - after I run the code: recon-all -s > (subject ID) -hippocampal-subfields-T1 > > This is the error: > > > > JavaVM: Failed to load JVM: > /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib > > JavaVM FATAL: Failed to load the jvm library. > > Fatal Error on startup: Unable to start the JVM because of a bad Java > option or unknown error. > > Please check your java.opts file. > > Any suggestions? > > > > Thank you, > > Alex > ___ > 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] Hippocampal Subfield Segmentation Error
2020-03-21
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I am having a problem with hippocampal subfield segmentation. The issue appears to be related to JavaVM - after I run the code: recon-all -s (subject ID) -hippocampal-subfields-T1 This is the error: JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file. Any suggestions? Thank you, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Issue with MATLAB 2012 runtime download
2020-03-20
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution It worked! Thank you! On Wed, Mar 18, 2020 at 10:07 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Please try: > > sudo curl " > https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2014bMAC.tar.gz; > -o "runtime.tar.gz" > > Cheers, > > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list > *Date: *Wednesday, March 18, 2020 at 19:40 > *To: *"freesurfer@nmr.mgh.harvard.edu" > *Subject: *[Freesurfer] Issue with MATLAB 2012 runtime download > > > > *External Email - Use Caution* > > Dear Freesurfer experts, > > > > I'm having an issue while attempting to download Matlab 2012 runtime for > its use in the hippocampal subfield segmentation. The error is: "Warning: > Failed to create the file runtime.tar.gz: Permission denied". > > See details below: > > curl " > https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2014bMAC.tar.gz; > -o "runtime.tar.gz" > > % Total% Received % Xferd Average Speed TimeTime Time > Current > > Dload Upload Total SpentLeft > Speed > > 0 00 00 0 0 0 --:--:-- --:--:-- --:--:-- > 0Warning: Failed to create the file runtime.tar.gz: Permission denied > > 0 656M0 77710 0 15040 0 12:43:08 --:--:-- 12:43:08 > 15060 > > curl: (23) Failed writing body (0 != 7771) > > > > Any ideas why this is happening? > > > > Thank you, > > Alex > > > ___ > 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] Issue with MATLAB 2012 runtime download
2020-03-18
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, I'm having an issue while attempting to download Matlab 2012 runtime for its use in the hippocampal subfield segmentation. The error is: "Warning: Failed to create the file runtime.tar.gz: Permission denied". See details below: curl " https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2014bMAC.tar.gz; -o "runtime.tar.gz" % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 0 00 00 0 0 0 --:--:-- --:--:-- --:--:-- 0Warning: Failed to create the file runtime.tar.gz: Permission denied 0 656M0 77710 0 15040 0 12:43:08 --:--:-- 12:43:08 15060 curl: (23) Failed writing body (0 != 7771) Any ideas why this is happening? Thank you, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec not running ("image not found" error message)
2020-02-25
Thread
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
External Email - Use Caution Dear Freesurfer experts, Please help me with this simple error for running Qdec: - First I try to open qdec: qdec & - Then this occurs: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reason: image not found Abort Any ideas on how I could fix this? Thanks! All the best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
