Re: [Freesurfer] mri_watershed Error: indices out of bounds
Hello Bruce, I just wanted to touch base regarding the Indices_oob.nii subject I had sent to MGH. Were you by any chance able to detect the issue with running recon-all on this subject. Thanks in advance for taking a look at this. Best regards, Edgar Busovaca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mri_watershed Error: indices out of bounds
Hello Bruce, I took a look at the file with freeview and I can't identify anything peculiar about the data. The file is named Indices_oob.nii and has been uploaded to /transfer/incoming on the FTP file exchange server. Thank you for your swift reply and in advance for your time. Best regards, Edgar Busovaca On Tue, Mar 24, 2015 at 5:34 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Edgar the LINE SEARCH thing is not a real problem. I've never seen indices out of bounds before though. Is there anything strange about your dataset? Does freeview display it properly (that is, are what freeview thinks the RAS dirs the correct anatomical ones)? If you upload the dataset we'll see if we can replicate and fix the problem cheers Bruce On Tue, 24 Mar 2015, Edgar Busovaca wrote: Dear Freesurfer users, I have attempted to process a subject (.nii type input) through recon-all -all, but for some reason the processing gambit is terminated early ( during the skullstrip). During skullstripping the following warning appears twice: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO=3 POSSIBLE CAUSES FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof WuasiNewtonEMA: 007: -log(p) = 10341.8 tol 0.10 following the skullstrip step in ***WATERSHED the following appears: mri_watershed Error: indices out of bounds Oddly, this particular subject failed where the rest of the data set successfully completed recon-all -all. As a reference I am running freesurfer 5.1 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.11.2.e16.x86_64 x86_64 Is there a flag to push this subject through recon-all? Thanks in advance for your time. Best, Edgar Busovaca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] mri_watershed Error: indices out of bounds
Dear Freesurfer users, I have attempted to process a subject (.nii type input) through recon-all -all, but for some reason the processing gambit is terminated early ( during the skullstrip). During skullstripping the following warning appears twice: IFLAG= -1 LINE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] mri_watershed Error: indices out of bounds
Dear Freesurfer users, I have attempted to process a subject (.nii type input) through recon-all -all, but for some reason the processing gambit is terminated early ( during the skullstrip). During skullstripping the following warning appears twice: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO=3 POSSIBLE CAUSES FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof WuasiNewtonEMA: 007: -log(p) = 10341.8 tol 0.10 following the skullstrip step in ***WATERSHED the following appears: mri_watershed Error: indices out of bounds Oddly, this particular subject failed where the rest of the data set successfully completed recon-all -all. As a reference I am running freesurfer 5.1 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.11.2.e16.x86_64 x86_64 Is there a flag to push this subject through recon-all? Thanks in advance for your time. Best, Edgar Busovaca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
