Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message:
Command: mri_vol2surf --hemi lh --noreshape --o /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz --reg /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat --projfrac 0.500 --mov /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz Standard output: srcvol = /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz srcreg = /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run.
Thank you all in advance!
Yang
------ Qingyang Li
Balance and focus.
On Sun, Mar 18, 2012 at 8:28 AM, freesurfer-request@nmr.mgh.harvard.eduwrote:
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Can you run it outside of the pipeline to assure that it is not a pipeline issue? doug
On 03/18/2012 08:54 AM, Qingyang Li wrote:
Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message:
Command: mri_vol2surf --hemi lh --noreshape --o /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz --reg /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat --projfrac 0.500 --mov /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz Standard output: srcvol = /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz srcreg = /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run.Thank you all in advance!
Yang
Qingyang Li
Balance and focus.
On Sun, Mar 18, 2012 at 8:28 AM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Mailing list subscription confirmation notice for mailing list Freesurfer We have received a request from 67.244.70.75 for subscription of your email address, "congel@gmail.com <mailto:congel@gmail.com>", to the freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page: https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Or include the following line -- and only the following line -- in a message to freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu>: confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional "Re:" text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu>. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
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hi Qingyang,
you can simply copy and paste the command line into the shell.
cheers,
satra
On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Can you run it outside of the pipeline to assure that it is not a pipeline issue? doug
On 03/18/2012 08:54 AM, Qingyang Li wrote:
Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message:
Command: mri_vol2surf --hemi lh --noreshape --o/working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz
--reg/working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat
--projfrac 0.500 --mov/working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz
Standard output: srcvol =/working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz
srcreg =/working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat
srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run.Thank you all in advance!
Yang
Qingyang Li
Balance and focus.
On Sun, Mar 18, 2012 at 8:28 AM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Mailing list subscription confirmation notice for mailing list Freesurfer We have received a request from 67.244.70.75 for subscription of your email address, "congel@gmail.com <mailto:congel@gmail.com>", to the freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page:https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbcee...
Or include the following line -- and only the following line -- in a message to freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu>: confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional "Re:" text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu>. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
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Thank you Doug and Satra,
I ran the same pipeline on another machine after I post the question and it went through with no problem...
On the machine which the pipeline failed, I have freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. And on the machine that the pipeline went through, I have freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 on. This might be a version issue?
To rule out this possibility, we are testing the ver 5.0.0 of Freesurfer on the machine that failed this step... Will keep you posted when we finish testing ...
Also, we did tried to run the script outside the pipeline and received the same error...
Yang ------ Qingyang Li
Balance and focus.
On Mon, Mar 26, 2012 at 3:36 PM, Satrajit Ghosh satra@mit.edu wrote:
hi Qingyang,
you can simply copy and paste the command line into the shell.
cheers,
satra
On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Can you run it outside of the pipeline to assure that it is not a pipeline issue? doug
On 03/18/2012 08:54 AM, Qingyang Li wrote:
Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message:
Command: mri_vol2surf --hemi lh --noreshape --o/working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz
--reg/working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat
--projfrac 0.500 --mov/working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz
Standard output: srcvol =/working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz
srcreg =/working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat
srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run.Thank you all in advance!
Yang
Qingyang Li
Balance and focus.
On Sun, Mar 18, 2012 at 8:28 AM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
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right form (additional "Re:" text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu>. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Hi Yang
was this ever resolved?
Bruce On Sun, 18 Mar 2012, Qingyang Li wrote:
Hi all,I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message:
Command:mri_vol2surf --hemi lh --noreshape --o /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz --reg /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat --projfrac 0.500 --mov /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz Standard output: srcvol = /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz srcreg = /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run.
Thank you all in advance!
Yang
Qingyang Li
Balance and focus.
On Sun, Mar 18, 2012 at 8:28 AM, freesurfer-request@nmr.mgh.harvard.edu wrote: Mailing list subscription confirmation notice for mailing list Freesurfer
We have received a request from 67.244.70.75 for subscription of your email address, "congel@gmail.com", to the freesurfer@nmr.mgh.harvard.edu mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page: https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Or include the following line -- and only the following line -- in a message to freesurfer-request@nmr.mgh.harvard.edu: confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional "Re:" text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-owner@nmr.mgh.harvard.edu. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Qingyang Li -
Satrajit Ghosh