Hi Rachel
all processing is done in the subject's native space. If you want to downsample probably the easiest thing to do is map to one of the lower res fsaverage subjects (e.g. fsaverage3 or fsaverage4) using mri_surf2surf/mri_label2label and the like after running recon-all.
cheers Bruce
On Wed, 7 Aug 2019, Rachel S wrote:
External Email - Use Caution
Hello freesurfer developers, I am trying to get the user defined segmentation for a subject generated in here (https://github.com/mattcieslak/easy_lausanne) . After recon-all, I have the pial surface with ~250k vertices. My first question is about the recon-all space. I thought the output of recon-all is already registered with the fsaverage space since it uses bucker40 as the template for segmentation. But some mentioned it is in the individual native space. Which one is true?
My second question is about the procedure to generate the segmentation for downsampled surface. I have the .annot file and .label file for that subject and also for fsaverage. Reading the .annot file can give me the region mapping for ~250k matrix. I want to map the subject to fsaverage5 space and also downsample the vertices for the cortical surface to ~20k. And I want to get the region mapping for this ~20k vertices from the ~250k vertice .annot file. I looked into the documentation and email archive, here is a few things I tried.
I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
- Try to map to fsaverage in the recon-all step by using
recon-all -i 0000.dcm -s p6_fs5 -all -qcache -target fsaverage5 And here is the error:
#@# 1/1 p6_fs5 Wed 07 Aug 2019 04:49:09 AM EDT --------------
mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness --sfmt curv --noreshape --cortex MRISread(/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaver age5.sphere.reg): could not open file Source registration surface changed to fsaverage5.sphere.reg Target registration surface changed to sphere.reg
$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
setenv SUBJECTS_DIR /home/rachelsun/Software/freesurfer/subjects cd /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness --sfmt curv --noreshape --cortex
sysname Linux hostname rachel-pc machine x86_64 user rachelsun srcsubject = p6_fs5 srcval = /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness srctype = curv trgsubject = fsaverage5 trgval = ./tmp.mris_preproc.7614/p6_fs5.1.mgh trgtype = srcsurfreg = fsaverage5.sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphe re.reg No such file or directory mri_surf2surf: could not read surface/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphe re.reg No such file or directory Linux rachel-pc 4.19.62-1-MANJARO #1 SMP PREEMPT Sun Jul 28 09:14:58 UTC 2019 x86_64 GNU/Linux
- Use the basic recon-all step recon-all -i 0000.dcm -s p6 -all, and run
mri_surf2surf --srcsubject p6 --sval-xyz pial --trgsubject fsaverage5 --tval-xyz --tval lh.pial.p6 --hemi lh And I can get the surface mapped to fsaverage space, but I am not sure how to get the region segmentation for this new surface. From what I learned, mri_surf2surf is to map .annot between subjects.
Sorry for the long email and thank you for your time. I would really appreciate it your input.
Best regards, Rachel