[Freesurfer] ?????? ?????? ?????? Recon-all run error
External Email - Use Caution Dear Bruce, I am sorry to let you wait so long, I have some troubles in transferring the data set, but it has been solved. Now I have sent the data set to ftp. I hope you can take the time to help us deal with the data set. We have already Running this data set for a long time but did not get results, the name of the data set is data_Yujunjie.zip,. The run command and the expert file are in the attachment. Express your heartfelt thanks again?? yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??18??(??) 11:15 ??: "Freesurfer support list"; ????: Re: [Freesurfer] ?????? ?? Recon-all run error Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Sun, 18 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I am very sorry to bother you. We are currently experimenting with > freesurfer, but I have > encountered a lot of problems during the experiment. We have three > resolutions of data, the skull of > medium-resolution data can't be removed (neck can't be removed), and with > high-resolution data, it > will report memory transfer errors. You said before that we can submit data > sets to you, how should > we provide you with data sets? > > Thanks in advance > yours yujunjie > > -- -- > ??: "Bruce Fischl"; > ????: 2018??11??7??(??????) ????2:42 > ??: "Freesurfer support list"; > : Re: [Freesurfer] ?? Recon-all run error > > does it occur if you run it outside of recon-all? Do you have enough free > ram? If so, you can filedrop us the dataset and we can try to replicate and > fit ix. > > On Tue, 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I found the error location in the recon-all.log folder. Here is the place > > where it went wrong??I > > don't think it's the reason for insufficient memory.. > > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == > > 0' failed.'' > > This data is ok when we run with versions prior to freesurfer 6.0. But > > after we run the 6.0 > > version and set the expert file, this error will occur.Do I need to step > > through the instructions > to > > see the problem? How should this error be solved? > > > > Thanks in advance > > > > yours yujunjie > > > > -- -- > > ??: "Bruce Fischl"; > > : 2018??11??6??(??) 9:40 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] Recon-all run error > > > > that certainly looks like something is running out of ram. Can you run > > the command that failed directly on the command line and see if it works? > > Was anything else running on the machine at the time? We do report total > > and free memory at the start of the recon in the recon-all.log file > > > > cheers > > Bruce > > On Tue, > > 6 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped > > > appears when the > > mri_convert > > > command is executed. The specific errors are as follows: > > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 > > > Aborted (core dumped) > > > mri_convert.bin "$@" > > > ERROR: converting to minc > > > We want to know if our high resolution image is too large for freesurfer > > > to handle, or our > > computer > > > memory (64GB running memory) is limited. > > > > > > Thanks a lot in advance! > > > yours sincerely, > > > yu junjie > > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer expert.opts Description: Binary data recon-all.txt Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? ?????? ?????? Recon-all run error
External Email - Use Caution Dear Bruce, Thank you very much for your reply, I will submit our data set as soon as possible. yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??18??(??) 11:15 ??: "Freesurfer support list"; ????: Re: [Freesurfer] ?????? ?? Recon-all run error Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Sun, 18 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I am very sorry to bother you. We are currently experimenting with > freesurfer, but I have > encountered a lot of problems during the experiment. We have three > resolutions of data, the skull of > medium-resolution data can't be removed (neck can't be removed), and with > high-resolution data, it > will report memory transfer errors. You said before that we can submit data > sets to you, how should > we provide you with data sets? > > Thanks in advance > yours yujunjie > > -- -- > ??: "Bruce Fischl"; > ????: 2018??11??7??(??????) ????2:42 > ??: "Freesurfer support list"; > : Re: [Freesurfer] ?? Recon-all run error > > does it occur if you run it outside of recon-all? Do you have enough free > ram? If so, you can filedrop us the dataset and we can try to replicate and > fit ix. > > On Tue, 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I found the error location in the recon-all.log folder. Here is the place > > where it went wrong??I > > don't think it's the reason for insufficient memory.. > > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == > > 0' failed.'' > > This data is ok when we run with versions prior to freesurfer 6.0. But > > after we run the 6.0 > > version and set the expert file, this error will occur.Do I need to step > > through the instructions > to > > see the problem? How should this error be solved? > > > > Thanks in advance > > > > yours yujunjie > > > > -- -- > > ??: "Bruce Fischl"; > > : 2018??11??6??(??) 9:40 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] Recon-all run error > > > > that certainly looks like something is running out of ram. Can you run > > the command that failed directly on the command line and see if it works? > > Was anything else running on the machine at the time? We do report total > > and free memory at the start of the recon in the recon-all.log file > > > > cheers > > Bruce > > On Tue, > > 6 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped > > > appears when the > > mri_convert > > > command is executed. The specific errors are as follows: > > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 > > > Aborted (core dumped) > > > mri_convert.bin "$@" > > > ERROR: converting to minc > > > We want to know if our high resolution image is too large for freesurfer > > > to handle, or our > > computer > > > memory (64GB running memory) is limited. > > > > > > Thanks a lot in advance! > > > yours sincerely, > > > yu junjie > > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ?????? ?????? Recon-all run error
Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Sun, 18 Nov 2018, 1013364183 wrote: External Email - Use Caution Dear Bruce, I am very sorry to bother you. We are currently experimenting with freesurfer, but I have encountered a lot of problems during the experiment. We have three resolutions of data, the skull of medium-resolution data can't be removed (neck can't be removed), and with high-resolution data, it will report memory transfer errors. You said before that we can submit data sets to you, how should we provide you with data sets? Thanks in advance yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??7??(??) 2:42 ??: "Freesurfer support list"; ????: Re: [Freesurfer] ?? Recon-all run error does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place where it went wrong??I > don't think it's the reason for insufficient memory.. > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' > This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 > version and set the expert file, this error will occur.Do I need to step through the instructions to > see the problem? How should this error be solved? > > Thanks in advance > > yours yujunjie > > -- -- > ??: "Bruce Fischl"; > ????: 2018??11??6??(??????) ????9:40 > ??: "Freesurfer support list"; > : Re: [Freesurfer] Recon-all run error > > that certainly looks like something is running out of ram. Can you run > the command that failed directly on the command line and see if it works? > Was anything else running on the machine at the time? We do report total > and free memory at the start of the recon in the recon-all.log file > > cheers > Bruce > On Tue, > 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the > mri_convert > > command is executed. The specific errors are as follows: > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > > mri_convert.bin "$@" > > ERROR: converting to minc > > We want to know if our high resolution image is too large for freesurfer to handle, or our > computer > > memory (64GB running memory) is limited. > > > > Thanks a lot in advance! > > yours sincerely, > > yu junjie > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? ?????? Recon-all run error
External Email - Use Caution Dear Bruce, I am very sorry to bother you. We are currently experimenting with freesurfer, but I have encountered a lot of problems during the experiment. We have three resolutions of data, the skull of medium-resolution data can't be removed (neck can't be removed), and with high-resolution data, it will report memory transfer errors. You said before that we can submit data sets to you, how should we provide you with data sets? Thanks in advance yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??7??(??) 2:42 ??: "Freesurfer support list"; ????: Re: [Freesurfer] ?? Recon-all run error does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place > where it went wrong??I > don't think it's the reason for insufficient memory.. > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' > failed.'' > This data is ok when we run with versions prior to freesurfer 6.0. But > after we run the 6.0 > version and set the expert file, this error will occur.Do I need to step > through the instructions to > see the problem? How should this error be solved? > > Thanks in advance > > yours yujunjie > > -- -- > ??: "Bruce Fischl"; > ????: 2018??11??6??(??) 9:40 > ??: "Freesurfer support list"; > : Re: [Freesurfer] Recon-all run error > > that certainly looks like something is running out of ram. Can you run > the command that failed directly on the command line and see if it works? > Was anything else running on the machine at the time? We do report total > and free memory at the start of the recon in the recon-all.log file > > cheers > Bruce > On Tue, > 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped > > appears when the > mri_convert > > command is executed. The specific errors are as follows: > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 > > Aborted (core dumped) > > mri_convert.bin "$@" > > ERROR: converting to minc > > We want to know if our high resolution image is too large for freesurfer to > > handle, or our > computer > > memory (64GB running memory) is limited. > > > > Thanks a lot in advance! > > yours sincerely, > > yu junjie > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? ?????? ?????? Recon-all run error
External Email - Use Caution Dear Greve, Thank you very much for your reply.Where is the tutorial for checking for and fixing defects? Is it the link below? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFixV6.0 yours yujunjie -- -- ??: "Greve, Douglas N.,Ph.D."; : 2018??11??15??(??) 5:12 ??: "freesurfer@nmr.mgh.harvard.edu"; ????: Re: [Freesurfer]?????? ?? Recon-all run error It looks like you might have a very big defect. Probably there is a bit of skull or cerebellum still attached. Follow the tutorial for checking for and fixing defects. On 11/14/2018 02:59 AM, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce Fischl, > I am very sorry that I have not reply to you last week. > Our data has been running for a few weeks, but the computer did not > react. There is a log file in the attachment. We want to ask that > could you help us run the data? We will send you a set of data > firstly(We still have two sets of data). If you can help us run our > high resolution data, we will be very grateful. And can we write your > name in the acknowledgments section? Our tutor is now at Boston > Children's Hospital (BCH). If possible, she would like to consult you > in person. > The download link is: > https://drive.google.com/file/d/1_5tYKHipNOTFe96p4BOMc1kbNPK1O93W/view?usp=drive_web > https://drive.google.com/file/d/12TZ0_J_njiZju9PDyvwxnHIiDe8D5SOA/view?usp=drive_web > > Looking forward to your reply. > Thanks in advance > > yours yujunjie > -- -- > *??:* "Bruce Fischl"; > *:* 2018??11??7??(??) 2:42 > *??:* "Freesurfer support list"; > *:* Re: [Freesurfer] ?? Recon-all run error > > does it occur if you run it outside of recon-all? Do you have enough free > ram? If so, you can filedrop us the dataset and we can try to > replicate and > fit ix. > > On Tue, 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I found the error location in the recon-all.log folder. Here is > the place where it went wrong??I > > don't think it's the reason for insufficient memory.. > > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % > 4 == 0' failed.'' > > This data is ok when we run with versions prior to freesurfer 6.0. > But after we run the 6.0 > > version and set the expert file, this error will occur.Do I need to > step through the instructions to > > see the problem? How should this error be solved? > > > > Thanks in advance > > > > yours yujunjie > > > > -- -- > > ??: "Bruce Fischl"; > > : 2018??11??6??(??) 9:40 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] Recon-all run error > > > > that certainly looks like something is running out of ram. Can you run > > the command that failed directly on the command line and see if it > works? > > Was anything else running on the machine at the time? We do report total > > and free memory at the start of the recon in the recon-all.log file > > > > cheers > > Bruce > > On Tue, > > 6 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > When we run ??recon-all?? with a 5GB high-resolution image, core > dumped appears when the > > mri_convert > > > command is executed. The specific errors are as follows: > > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: > 29235 Aborted (core dumped) > > > mri_convert.bin "$@" > > > ERROR: converting to minc > > > We want to know if our high resolution image is too large for > freesurfer to handle, or our > > computer > > > memory (64GB running memory) is limited. > > > > > > Thanks a lot in advance! > > > yours sincerely, > > > yu junjie > > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer 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] ?????? ?????? Recon-all run error
It looks like you might have a very big defect. Probably there is a bit of skull or cerebellum still attached. Follow the tutorial for checking for and fixing defects. On 11/14/2018 02:59 AM, 1013364183 wrote: > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > Dear Bruce Fischl, > I am very sorry that I have not reply to you last week. > Our data has been running for a few weeks, but the computer did not > react. There is a log file in the attachment. We want to ask that > could you help us run the data? We will send you a set of data > firstly(We still have two sets of data). If you can help us run our > high resolution data, we will be very grateful. And can we write your > name in the acknowledgments section? Our tutor is now at Boston > Children's Hospital (BCH). If possible, she would like to consult you > in person. > The download link is: > https://drive.google.com/file/d/1_5tYKHipNOTFe96p4BOMc1kbNPK1O93W/view?usp=drive_web > https://drive.google.com/file/d/12TZ0_J_njiZju9PDyvwxnHIiDe8D5SOA/view?usp=drive_web > > Looking forward to your reply. > Thanks in advance > > yours yujunjie > --?0?2?0?2-- > *??:*?0?2"Bruce Fischl"; > *:*?0?22018??11??7??(??) 2:42 > *??????:*?0?2"Freesurfer support list"; > *:*?0?2Re: [Freesurfer] ?? Recon-all run error > > does it occur if you run it outside of recon-all? Do you have enough free > ram? If so, you can filedrop us the dataset and we can try to > replicate and > fit ix. > > On Tue, 6 Nov 2018, 1013364183 wrote: > > > > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > > > Dear?0?2Bruce, > > ?0?2 I found the error location in the recon-all.log folder. Here is > the place where it went wrong??I > > don't think it's the reason for insufficient memory.. > > ?0?2 ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % > 4 == 0' failed.'' > > ?0?2 This data is ok when we run with versions prior to freesurfer 6.0. > But after we run the 6.0 > > version and set the expert file, this error will occur.Do I need to > step through the instructions to > > see the problem? How should this error be solved? > > > > Thanks in advance > > > > yours yujunjie > > > > --?0?2?0?2-- > > ??:?0?2"Bruce Fischl"; > > :?0?22018??11??6??(??) 9:40 > > ??:?0?2"Freesurfer support list"; > > :?0?2Re: [Freesurfer] Recon-all run error > > > > that certainly looks like something is running out of ram. Can you run > > the command that failed directly on the command line and see if it > works? > > Was anything else running on the machine at the time? We do report total > > and free memory at the start of the recon in the recon-all.log file > > > > cheers > > Bruce > > On Tue, > > 6 Nov 2018, 1013364183 wrote: > > > > > > > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > > > > > Dear FS, > > > When we run ??recon-all?? with a 5GB high-resolution image, core > dumped appears when the > > mri_convert > > > command is executed. The specific errors are as follows: > > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: > 29235 Aborted (core dumped) > > > mri_convert.bin "$@" > > > ERROR: converting to minc > > > We want to know if our high resolution image is too large for > freesurfer to handle, or our > > computer > > > memory (64GB running memory) is limited. > > > > > > Thanks a lot in advance! > > > yours sincerely, > > > yu junjie > > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ?????? Recon-all run error
does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: External Email - Use Caution Dear Bruce, I found the error location in the recon-all.log folder. Here is the place where it went wrong??I don't think it's the reason for insufficient memory.. ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 version and set the expert file, this error will occur.Do I need to step through the instructions to see the problem? How should this error be solved? Thanks in advance yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??6??(??) 9:40 ??: "Freesurfer support list"; ????: Re: [Freesurfer] Recon-all run error that certainly looks like something is running out of ram. Can you run the command that failed directly on the command line and see if it works? Was anything else running on the machine at the time? We do report total and free memory at the start of the recon in the recon-all.log file cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS, > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the mri_convert > command is executed. The specific errors are as follows: > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > mri_convert.bin "$@" > ERROR: converting to minc > We want to know if our high resolution image is too large for freesurfer to handle, or our computer > memory (64GB running memory) is limited. > > Thanks a lot in advance! > yours sincerely, > yu junjie > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? Recon-all run error
External Email - Use Caution Dear Bruce, I found the error location in the recon-all.log folder. Here is the place where it went wrong??I don't think it's the reason for insufficient memory.. ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 version and set the expert file, this error will occur.Do I need to step through the instructions to see the problem? How should this error be solved? Thanks in advance yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??6??(??) 9:40 ??: "Freesurfer support list"; ????: Re: [Freesurfer] Recon-all run error that certainly looks like something is running out of ram. Can you run the command that failed directly on the command line and see if it works? Was anything else running on the machine at the time? We do report total and free memory at the start of the recon in the recon-all.log file cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS, > When we run ??recon-all?? with a 5GB high-resolution image, core dumped > appears when the mri_convert > command is executed. The specific errors are as follows: > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 > Aborted (core dumped) > mri_convert.bin "$@" > ERROR: converting to minc > We want to know if our high resolution image is too large for freesurfer to > handle, or our computer > memory (64GB running memory) is limited. > > Thanks a lot in advance! > yours sincerely, > yu junjie > > > ___ 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] Recon-all run error
that certainly looks like something is running out of ram. Can you run the command that failed directly on the command line and see if it works? Was anything else running on the machine at the time? We do report total and free memory at the start of the recon in the recon-all.log file cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote: External Email - Use Caution Dear FS, When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the mri_convert command is executed. The specific errors are as follows: /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) mri_convert.bin "$@" ERROR: converting to minc We want to know if our high resolution image is too large for freesurfer to handle, or our computer memory (64GB running memory) is limited. Thanks a lot in advance! yours sincerely, yu junjie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Recon-all run error
External Email - Use Caution Dear FS, When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the mri_convert command is executed. The specific errors are as follows: /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) mri_convert.bin "$@" ERROR: converting to minc We want to know if our high resolution image is too large for freesurfer to handle, or our computer memory (64GB running memory) is limited. Thanks a lot in advance! yours sincerely, yu junjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
