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.
Re: [Freesurfer] basic high res data question
Hi Sam have you tried running the post-hoc surface deformation on the 0.7mm data? Jon Polimeni (ccd) has experience with this and might be able to help you out (or Matt Glasser for that matter) cheers Bruce On Wed, 9 Apr 2014, 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 ___ 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
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
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.
[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.
