Re: [Freesurfer] Intermediate stages of cortical inflation

sorry, it shouldn't say "patch", but "file". We will fix that. I wouldn't run it with -n. Without it, it will run until it asymptotes. I would try: mris_sphere -w 20 lh.inflated lh.sphere cheers Bruce cheers Bruce On Fri, 11 Apr 2014, Xuelong Zhao wrote: > Thanks for pointing this binary

Re: [Freesurfer] Intermediate stages of cortical inflation

Thanks for pointing this binary out- I didn't realize the user could access it outside of recon-all. I've had a look at the fswiki for mris_sphere and it doesn't seem to be complete. I used it in the following format but not sure if this is correct: mris_sphere -n 160 -w 20 -scale 1 lh.orig lh

Re: [Freesurfer] caudate and putamen to surface

Hi Prof. Greve, Thanks for your reply. Sorry, perhaps I have made some mistake in my data analysis. I just want to show tractography results of basal ganglia in surface space using FSL. Could transform fit_paths.nii.gz to surface be a brief way? In order to do mdi_vol2surf (trans

Re: [Freesurfer] longitudinal template generation with manual registration

Hi Andreas, It is extremely different to get good registrations manually (as you have to work in 3D and you only see 2D planes), and you'll most certainly not be able to achieve the accuracy of an automated method (especially not of robust_register/robust_template, which are pretty damn accur

[Freesurfer] Vertexwise surface area value?

Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surf

Re: [Freesurfer] Large areas of white matter ignored, even with control points

Hi Andrea, Take a look at the ?h.orig.nofix surfaces. Does it look like the wm edits were picked up in those initial surfaces? Also, just check that the edits to the wm.mgz were 255 and that there are no major disconnects anywhere. -Louis On Fri, 4 Apr 2014, Andrea Grant wrote: I was able

[Freesurfer] Post-doctoral Research Position at Columbia University

Post-doctoral Research Position at Columbia University A postdoctoral research position is currently available at Columbia University and the New York State Psychiatric Institute. Candidates must have completed a PhD in clinical, developmental, or cognitive neuroscience, or a related field. Resear

Re: [Freesurfer] select_talairach_point function?

Hi I just find out how to launch the command, it is in the terminal where tksurfer is running, after the % sign. (I didn't understand what the tcl window was meaning) Best Celine > Hi > I am sorry if my question is really basic, but I am choosing the seeds for > fsfast resting state connectivity a

[Freesurfer] Easy automated workflow for separating non-contiguous labels

Hi Freesurfers, Some of the Freesurfer annotations (specifically the Yeo atlases) have multiple disconnected regions with the same label. What's the best way to separate these annotations (or the labels produced by mri_annotation2label) so that I can get multiple label files where each label has

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

no, I was in subjects_dir. Updated the command to this and it works now. thanks. mri_aparc2aseg --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o FGH_09112013/mri/wmdivided.mgz --annot aparc.split On Thu, Apr 10, 2014 at 11:24 AM, Douglas N Greve wrote: > > Are you in the fo

Re: [Freesurfer] caudate and putamen to surface

The caudate and putamen are not on the cortical surface. I'm confused as to what you are trying to do. On 04/10/2014 08:52 AM, gong jinnan wrote: > Dear all, > I want to use caudate and putamen as seed in surface to do PROBTRACK > in FSL. > For doing that, I acquired target surface which in the

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

Re: [Freesurfer] Intermediate stages of cortical inflation

yes, many of our binaries take the -w flag to write out a snapshot of the minimization every nth step, including mris_sphere cheers Bruce On Thu, 10 Apr 2014, Xuelong Zhao wrote: > Is it also possible to track the inflation all the way to the sphere? I was > hoping that > I could take snapsh

Re: [Freesurfer] mri_vol2surf --projopt

I don't understand what the question is. If you need to interpolate, then use --interp trilinear doug On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote: > Allright! The only point I would like to emphasize is: > > Regardless if option trilin or nearest is used I need to interpolate the > functio

Re: [Freesurfer] how to convert fsaverage space mask into other subject original space

Please send the terminal output for mri_label2label On 04/10/2014 02:16 AM, Rujing Zha wrote: > > Hi Bruce and others, > I completed the mri_annotation2label and mri_label2label(which used > mask created from the mri_binarize), but the result is the same as > that without mask.Here are my code

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

Are you in the folder just above the mri folder? On 04/10/2014 11:20 AM, Corinna Bauer wrote: > Hi Doug, > Following the example in recon-all.log, I tried this: mri_aparc2aseg > --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o > mri/wmdivided.mgz --annot aparc.split > > and r

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

Hi Doug, Following the example in recon-all.log, I tried this: mri_aparc2aseg --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmdivided.mgz --annot aparc.split and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1): could not open file On Thu, Apr 10, 2014 at

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

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log file for an example command line that generates wmparc.mgz doug On 04/10/2014 09:52 AM, Corinna Bauer wrote: > For creating corresponding wm segmentations to the rois derived from > mris_divide_parcellation, should mri_apar

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

For creating corresponding wm segmentations to the rois derived from mris_divide_parcellation, should mri_aparc2wmseg be used or should I follow the steps outlined in this posting https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html? Thanks Corinna On Wed, Apr 9, 201

[Freesurfer] caudate and putamen to surface

Dear all, I want to use caudate and putamen as seed in surface to do PROBTRACK in FSL. For doing that, I acquired target surface which in the cortex seed using kris_convert and label2surf script. But I met some problems in extracting caudate and putamen in the surface.

Re: [Freesurfer] Intermediate stages of cortical inflation

Is it also possible to track the inflation all the way to the sphere? I was hoping that I could take snapshots of equi-area intermediate forms as the cortex is unfolded onto the sphere instead of stopping at the inflated cortex. Thanks. > Date: Wed, 9 Apr 2014 08:31:46 -0400 > From: fis..

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 BS

Re: [Freesurfer] mri_vol2surf --projopt

Allright! The only point I would like to emphasize is: Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function "build_sample_array" in the "mri_vol2surf" source code. In this

Re: [Freesurfer] Mac OSX installations incomplete? What to do?

Thank you Zeke, that seems to work all fine! Best, Markus 2014-04-08 21:17 GMT+02:00 Z K : > Markus, > > Thanks for pointing that out. I have added those files to the ftp link. > > -Zeke > > > On 04/04/2014 04:16 PM, Markus Gschwind wrote: > >> Thank you Zeke, >> >> What about these? >> >> /usr/