Re: [Freesurfer] basic high res data question
When running this : recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT_HighRes mentionned on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I get these : mri_tessellate: max vertices 100 exceeded recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST 2014 Seems the issue has been raised before in this thread: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html So I have a similar request: would it be possible to provide another compiled version of mri_tessellate (centos6_x86_64-stable-pub-5.3.0) with the an increased max number of faces and vertices? Sorry to be so needy. Thanks in advance Remi Gau ___ 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] basic high res data question
Hi Remi I believe I upped that limit by an order of magnitude, which hopefully would be enough? If so, Zeke can get you a new version cheers Bruce On Thu, 10 Apr 2014, Remi Gau wrote: When running this : recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT_HighRes mentionned on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I get these : mri_tessellate: max vertices 100 exceeded recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST 2014 Seems the issue has been raised before in this thread: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html So I have a similar request: would it be possible to provide another compiled version of mri_tessellate (centos6_x86_64-stable-pub-5.3.0) with the an increased max number of faces and vertices? Sorry to be so needy. Thanks in advance Remi Gau ___ 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 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] basic high res data question
Good afternoon gurus- I’m new to FS and working with 0.7mm iso 7T MPRAGEs. After bias-correction with AFNI’s 3dUnifize, recon-all ran without hitch but downsampled everything to 1mm. Now I have basically the same sentiment and question as this thread from ~2 years ago (i’m linking to the middle for simplicity): http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg22852.html What’s the very latest on this? Thanks! -Salvatore (Sam) Torrisi Section on the Neurobiology of Fear and Anxiety National Institute of Mental Health ___ 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] basic high res data question
Hello all, I have a related question as I am also a freesurfer beginner and starting to use it on submilliter MP2RAGE 7T images. After having had a quick look at the videos, tutos and the archives, I found this: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon BTW on that page I guess that the line: recon-all -mprage -normalization -skulstrip -s $SUBJ should read recon-all -mprage -normalization *-skullstrip* -s $SUBJ For a test run and to familiarize mysef with freesurfer and the trouble shooting steps, I ran the basic recon-all on one of the native images which gave me results at a 1 mm res. My question is: is there any reason why these steps should work differently for a MP2RAGE compared to the MPRAGE described the HiResRecon page? For testing, I am currently running the steps in the page mentioned above on one image for practice before running more subjects. So far, so good but the following command: mri_nu_correct.mni --i $SUBJECTS_DIR/$SUBJ/mri/orig.mgz --o $SUBJECTS_DIR/$SUBJ/mri/nu.mgz --proto-iters 1000 --distance 15 --fwhm 0.15 --n 1 --uchar $SUBJECTS_DIR/$SUBJ/mri/transforms/talairach.xfm issued the following warning: Use of ?PATTERN? without explicit operator is deprecated at ~/Program/freesurfer/mni/bin/sharpen_volume line 153. Thanks *Remi Gau * On 09/04/14 21:57, Torrisi, Sam (NIH/NIMH) [F] wrote: Good afternoon gurus- I’m new to FS and working with 0.7mm iso 7T MPRAGEs. After bias-correction with AFNI’s 3dUnifize, recon-all ran without hitch but downsampled everything to 1mm. Now I have basically the same sentiment and question as this thread from ~2 years ago (i’m linking to the middle for simplicity): http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg22852.html What’s the very latest on this? Thanks! -Salvatore (Sam) Torrisi Section on the Neurobiology of Fear and Anxiety National Institute of Mental Health ___ 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.
