[Freesurfer] recon-all error

Hi, We're getting the following error from recon-all: command line: pbsubmit -m etanski -c 'recon-all -s DODASD012 -all -i /cluster/archive/300/siemens/TrioTim-35006-20120718-151622-227000/391000-15-01.dcm -mail etan...@nmr.mgh.harvard.edu' output: ... ... mri_binarize --i ./tmp.

[Freesurfer] Freesurfer Command in Matlab

Hi, I'm trying to run the following command in through matlab: system(['mri_surf2surf --srcsubject average7 --trgsubject average7 --srcsurfval /space/schnook/1/users/yigal/projects/dti/data/old_recons/results/control_vs_sch_rh_average7_2mm_ttest.mgz --trgsurfval /space/schnook/1/users/yigal/

[Freesurfer] Output of selxavg3

Hi, Of all the files that selxavg3 generates inside the contrast folder, only three are described in the wiki: ces.nii, cesvar.nii, and sig.nii. Does anyone know the other files below represent? Also, which files are used for subsequent group analyses? cesmag.nii fsig.nii minsig.nii cesmagpc

[Freesurfer] tksurfer ftimepoint variable

Hi, I'm trying to use a TCL script that runs through every time point in a surface. I'm using the following commands: set gaLinkedVars(ftimepoint) 0 (or 1, 2, etc) SendLinkedVarGroup overlay But tksurfer is always showing point 0 (doesn't advance in time). Similar TCL commands for fthresh an

[Freesurfer] mri_vol2surf - MNI subject

Hi, If I have volume data in MNI subject space (produced using --tal option in mri_vol2vol), how do I project it onto the surface in the same subject space? There does not seem to be an equivalent tal option in mri_vol2surf. Thanks, Yigal ___ Frees

[Freesurfer] Problem running tksurfer

tksurfer fsaverage lh inflated surfer: current subjects dir: /autofs/space/ventzl_001/users/SUBJECTS_DIR surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/schnook_001/users/yigal/projects/functional surfer: Readin

[Freesurfer] Cortical thickness conversion

Hi, I'm trying to convert corical thickness maps into a common space and getting this error. Any ideas? mri_surf2surf --srcsubject mano002_new --trgsubject fsaverage --hemi lh --srcsurfval lh.thickness --trgsurfval /space/schnook/1/users/yigal/projects/dti/data/new_recons/mano002_new/surf/l

[Freesurfer] mri_surfcluster

Hi, When I run mri_surfcluster on a surface with 12 timepoints, how do I know when each of the reported clusters occurred? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

[Freesurfer] mris_fwhm problem

Hi, I'm getting an NAN value for some surfaces but not for others. Any ideas? Both surfaces below were generated using an identical process. [yi...@schnook sph_sm20]$ pwd /autofs/space/ventzl_001/users/SUBJECTS_DIR/mano010/bold/EMexec3/sph_sm20 [yi...@schnook sph_sm20]$ mris_fwhm --i e001-rh.b

[Freesurfer] mni152.register.dat

Hi, Does mni152.register.dat map from fsaverage to mni152 or vice versa? Specifically, I'm using an fsaverage surface that I want to project onto mni152 volume using surf2vol. Should I invert the matrix? Thanks, Yigal ___ Freesurfer mailing list Fre

Re: [Freesurfer] mni152.register.dat

How about when viewing an mni152 volume in tkmedit - what should I use as overlay-reg? Douglas N Greve wrote: you don't need to invert it, just use as is. doug Yigal Agam wrote: Hi, Does mni152.register.dat map from fsaverage to mni152 or vice versa? Specifically, I'm using an

[Freesurfer] [Fwd: fsaverage to average7]

Hi all, Is there a way to convert results that I have on fsaverage to average7? I need to do that to be compatible with some average7 results that go into the same paper. When I use mri_surf2surf, activation is displaced. Any advice would be appreciated. This is what I've done: mri_surf2surf

[Freesurfer] fsaverage to mni152

Hi, What's the best way to convert an fsaverage volume into an MNI152 volume that can be viewed on top of a standard brain (MNI152_T1_2mm_brain.nii.gz) in fslview? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

Re: [Freesurfer] fsaverage to mni152

Thanks, Doug. Also, how can this be done from an individual brain to mni152? Do I need to use fsaverage as an intermediate? Yigal Douglas N Greve wrote: > Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with > --inv > > Yigal Agam wrote: >> Hi, >> &

[Freesurfer] Circle around vertex

Hi, In surface-based analysis, is it possible to create an ROI label that is a circle of a certain radius around a given vertex? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/

[Freesurfer] Comments in paradigm files

Hi, Can you add comments to a paradigm file? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fsaverage to mni152

d use? Thanks, Yigal Douglas N Greve wrote: > Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with > --inv > > Yigal Agam wrote: >> Hi, >> >> What's the best way to convert an fsaverage volume into an MNI152 >> volume

[Freesurfer] w file conversion

Hi, Is it possible to convert a .w file to another format? Thanks, Yigal ___ 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 pe

[Freesurfer] Tutorial Files

Hi, We're having problems untarring the tutorial data. Are the uncompressed data available anywhere? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] Getting Talairach Coordinates

Hi, Is there a way to get the Tal and MNI coordinates of a given fsaverage vertex through matlab or the unix command line, without opening tksurfer? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e

[Freesurfer] MNI305 to MNI152

How do I convert between the two coordinate systems? Yigal ___ 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

[Freesurfer] aparc.a2005s.annot errors?

Hi, There are some "holes" in fsaverage lh cingulate labels in the a2005s annotation. For example, vertex 16631, between the cingulate gyrus and sulcus is part of the superior frontal gyrus label. Same with vertices 20390 and 141081. Is that an error? This is a problem for us because it create

[Freesurfer] MNI152

Hi, Is it possible to export a functional volume from individual brain space to mni152, so it can be overlaid on the standard mni152 brain in fslview? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard

[Freesurfer] FDR in gray matter

Hi, Is it possible to restrict FDR correction to gray matter in tkmedit? Thanks ___ 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

[Freesurfer] mni coordinates to volume index

Hi, Is it possible in matlab to get the volume index coordinates corresponding to specific MNI coordiates? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The infor