-base triggers creation of the base subject, and requires the usual additional flags to run the entire stream. -all is the what is recommended here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing but you could also run the stages separately. On Mon, 2010-01-25 at 15:05 -0600, Guang Zeng wrote: > Hi, there, > > Does the -base step of the FreeSurfer longitudinal stream also > contains three step, > and can be called through recon-all as recon-all -base ...... > -autorecon1, > > recon-all -base ...... -autorecon2, > recon-all > -base...... -autorecon3 > > Thanks! > > > > ______________________________________________________________________ > From: freesurfer...@hotmail.com > To: ni...@nmr.mgh.harvard.edu > Date: Mon, 25 Jan 2010 13:57:58 -0600 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] images with poor resolution > > Hi, there, > > Does the -base step of FreeSurfer also contains three step, and can be > called through recon-all as recon-all...... -autorecon1, > recon-all ...... -autorecon2, recon-all ...... -autorecon3 > > Thanks! > > > From: ni...@nmr.mgh.harvard.edu > > To: freesurfer...@hotmail.com > > Date: Mon, 25 Jan 2010 12:34:47 -0500 > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] images with poor resolution > > > > also the base step > > > > On Mon, 2010-01-25 at 10:41 -0600, Guang Zeng wrote: > > > Hello, Nick, > > > > > > I am using the latest 4.5.0. > > > So I only need add those -seg-wlo -segwhi flags at the "-long" > step, > > > not the "-base" step, right? > > > > > > Thank! > > > Guang > > > > > > > Subject: RE: [Freesurfer] images with poor resolution > > > > From: ni...@nmr.mgh.harvard.edu > > > > To: freesurfer...@hotmail.com > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > Date: Mon, 25 Jan 2010 11:18:07 -0500 > > > > > > > > the longitudinal stream will take any controls points added to > the > > > > cross-sectional stream, but will not take any expert options or > > > special > > > > -seg-wlo -segwhi flags, so you would have to add those yourself > to > > > the > > > > longitudinal stream. > > > > > > > > On Sat, 2010-01-23 at 22:02 -0600, Guang Zeng wrote: > > > > > Hello, Nick, > > > > > > > > > > I read your answer to this thread posted few months ago. > > > > > Currently, I met the same kind of problem, and I used the > method > > > you > > > > > recommended below, it works pretty well on my cases. > > > > > My question is: > > > > > > > > > > The results of my data have been improved in FS > cross-sectional > > > > > stream, if I want to send them to the FS longitudinal stream, > > > > > Could I just need follow the general FS longitudinal stream or > I > > > still > > > > > need the -expert <path_to>/xopts.txt and -seg-wlo wlo -seg-ghi > ghi > > > > > options > > > > > somewhere in the longitudinal stream? > > > > > > > > > > Thanks! > > > > > Guang > > > > > > > > > > > > > > > > > > > > > From: ni...@nmr.mgh.harvard.edu > > > > > > To: dwm2...@med.cornell.edu; freesurfer@nmr.mgh.harvard.edu > > > > > > Date: Mon, 5 Oct 2009 19:11:15 -0400 > > > > > > Subject: Re: [Freesurfer] images with poor resolution > > > > > > > > > > > > Dana, > > > > > > > > > > > > First I would run: > > > > > > > > > > > > recon-all -s subid -clean > > > > > > > > > > > > to remove any prior control points and edits. > > > > > > > > > > > > Then I would open nu.mgz: > > > > > > > > > > > > tkmedit subjid nu.mgz > > > > > > > > > > > > and *sparingly* put control points well into white matter > areas > > > on a > > > > > few > > > > > > different slices. you only need a half dozen or so. to add > > > control > > > > > > points, see: > > > > > > > > > > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints > > > > > > > > > > > > except you will add them to nu.mgz, to make sure that T1.mgz > > > gets > > > > > > created properly. > > > > > > > > > > > > Then create a file name xopts.txt containing these lines: > > > > > > > > > > > > mri_normalize -gentle > > > > > > > > > > > > Then run: > > > > > > > > > > > > recon-all -s subjid -autorecon1 -expert <path_to>/xopts.txt > > > > > > > > > > > > and when done, open brainmask.mgz > > > > > > > > > > > > tkmedit subjid brainmask.mgz > > > > > > > > > > > > and check again to get a sense of the low value for white > matter > > > and > > > > > > high value for gray matter, then run: > > > > > > > > > > > > recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi > > > > > > > > > > > > replacing wlo and ghi with those values. > > > > > > > > > > > > if the surfaces still look bad, you can add a line to the > > > xopts.txt > > > > > > file : > > > > > > > > > > > > mris_make_surfaces -max_gray val -min_gray_at_white_border > val > > > > > > > > > > > > replacing the two 'val's with something you find > appropriate, > > > then > > > > > run: > > > > > > > > > > > > recon-all -s subjid -autorecon2-pial -autorecon3 \ > > > > > > -expert <path_to>/xopts.txt > > > > > > > > > > > > good luck! > > > > > > > > > > > > Nick > > > > > > > > > > > > > > > > > > On Mon, 2009-10-05 at 16:56 -0400, Dana W. Moore wrote: > > > > > > > Hi Nick, > > > > > > > > > > > > > > Below is Bruce's response to a problem I'm having with the > > > > > gray/white > > > > > > > segmentation. (Pasted below, you can see the brainmask.mgz > > > volume > > > > > and > > > > > > > surfaces--the entire brain is labeled as white matter). I > > > could > > > > > use > > > > > > > some guidance in carrying out his advice. He says to > adjust > > > the > > > > > > > intensity normalization using control points and then use > > > expert > > > > > opts > > > > > > > for mri_segment and mris_make_surfaces. > > > > > > > > > > > > > > When I look at the brain.mgz volume, the white matter > tends to > > > > > have an > > > > > > > intensity of 110, as it should, but the gray matter at > times > > > goes > > > > > as > > > > > > > high as 115. I was thinking, I could set ghi to 115 and > wlo to > > > > > 110. > > > > > > > Then, I am not sure how to actually run the corrections > and > > > what > > > > > > > language to use to implement the control points and > > > mri_segment > > > > > > > adjustments. I will save control points and then run: > > > recon-all > > > > > > > -autorecon2-cp -autorecon3 -subjed <subject>. Can I > somehow > > > > > include > > > > > > > the mri_segment adjustments into this command, or do I > have to > > > run > > > > > > > that separately? > > > > > > > > > > > > > > I am also not sure how options for mris_make_surfaces > might > > > help. > > > > > > > > > > > > > > I appreciate your help with this! > > > > > > > > > > > > > > Thanks, > > > > > > > dana > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > [] > > > > > > > > > > > > > > At 04:40 PM 10/2/2009, Bruce Fischl wrote: > > > > > > > > Hi Dana, > > > > > > > > > > > > > > > > it looks like the gray/white density estimation failed. > Try > > > > > setting > > > > > > > > them with the expert opts for mri_segment and > > > mris_make_surfaces > > > > > > > > (Nick can point you in the right direction if you can't > > > figure > > > > > it > > > > > > > > out). Things like max gm at white border and such. > > > > > > > > > > > > > > > > cheers, > > > > > > > > Bruce > > > > > > > > > > > > > > > > > > > > > p.s. it also looks like the intensity normalization went > too > > > far > > > > > due > > > > > > > to the low contrast. You'll probably need to add some > control > > > > > points > > > > > > > and run it with the -gentle option > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Fri, 2 Oct 2009, Dana W. Moore wrote: > > > > > > > > > > > > > > > > > Hi everyone, > > > > > > > > > > > > > > > > > > I am trying to salvage some images that were done with > > > poor > > > > > > > > > gray/white boundary contrasts. First, FreeSurfer > includes > > > an > > > > > area > > > > > > > > > of dura in the skull strip. I tried adjusting the > > > watershed > > > > > but > > > > > > > > > it made no differences. FreeSurfer is subsequently > unable > > > to > > > > > > > > > detect the gray/white boundary and labels the dura as > > > cortex: > > > > > > > > > > > > > > > > > > [] > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Looking at the raw images, the gray/white boundaries > are > > > faint > > > > > but > > > > > > > > > visible. Is there anything I can adjust to try to make > > > this > > > > > work > > > > > > > > > with FreeSurfer? > > > > > > > > > > > > > > > > > > Thanks, > > > > > > > > > Dana > > > > > > > > > > > > > > > > > > > > > > > > > > > Dana W. Moore, Ph.D. > > > > > > > > > Neuropsychology Fellow > > > > > > > > > Cornell Neuropsychology Service > > > > > > > > > Weill Medical College of Cornell University > > > > > > > > > New York Presbyterian Hospital > > > > > > > > > Department of Neurology & Neuroscience > > > > > > > > > 428 East 72nd Street, Suite 500 > > > > > > > > > New York, NY 10021 > > > > > > > > > Phone: 212-746-2823 > > > > > > > > > Fax: 212-746-5584 > > > > > > > > > Email: dwm2...@med.cornell.edu > > > > > > > > > > > > > > Dana W. Moore, Ph.D. > > > > > > > Neuropsychology Fellow > > > > > > > Cornell Neuropsychology Service > > > > > > > Weill Medical College of Cornell University > > > > > > > New York Presbyterian Hospital > > > > > > > Department of Neurology & Neuroscience > > > > > > > 428 East 72nd Street, Suite 500 > > > > > > > New York, NY 10021 > > > > > > > Phone: 212-746-2823 > > > > > > > Fax: 212-746-5584 > > > > > > > Email: dwm2...@med.cornell.edu > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > ______________________________________________________________________ > > > > > Hotmail: Free, trusted and rich email service. Get it now. > > > > > > > > > > > > > > ______________________________________________________________________ > > > Hotmail: Powerful Free email with security by Microsoft. Get it > now. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ______________________________________________________________________ > Hotmail: Free, trusted and rich email service. Get it now. > > ______________________________________________________________________ > Hotmail: Free, trusted and rich email service. Get it now. > _______________________________________________ > 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
