[Freesurfer] Pial surfaces include cerebellum - unable to fix with manual edits

greatly appreciated! Also happy to send a link to the original T1 and recon-all results if you would like. Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th st Charlestown, MA 02129 ___ Fre

[Freesurfer] mris_pmake version issue

appreciated. Btw the command line documentation (mris_pmake --help) does not seem to be quite match the version distributed with FS v6.0.0, at least when it comes to the option names for surface and curve, and if there are separate definitions for 0 and 1. Thank you! Best reg

Re: [Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5

simultaneously. In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here. Thanks! Tommi --- Tommi Raij, MD, PhD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5

for visualization (freeview etc) requiring 3D rendering of volumes, surfaces, and tractography results simultaneously. In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here. Thanks! Tommi --- Tommi Raij, MD, PhD ___ Freesurfer mailing list

[Freesurfer] dmri_trk2trk issue

if you would like to replicate the error. Thanks! Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] CVS registration questions

Thanks Lilla! Which MNI152 version was used as template when doing nonlinear CVS-registering from cvs_avg35 into MNI152 space? For example, was this MNI152 ICBM 2009a 1mm Nonlinear Asymmetric? Bests, Tommi Hi Tommi, I am preparing to CVS register 30+ subjects to improve FSL probabilistic

[Freesurfer] CVS registration questions

--- Tommi Raij, MD, PhD TM Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

[Freesurfer] tksurfer partial overlays?

surface window still shows an overlay with a value of 0 in these vertices. Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer

[Freesurfer] FS 5.1 MNI305 aparc+aseg registration with FSL MNI152

? Thanks! Tommi Details: On machine ernie nmr-std-env (5.1.0 stable) $FSLDIR = /usr/pubsw/packages/fsl/current/ $FREESURFER_HOME = /usr/local/freesurfer/stable5_1_0/ --- Tommi Raij, MD, PhD TMS Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown

[Freesurfer] mni152reg error (file permission denied)

! Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

[Freesurfer] Averaging overlays/labels across subjects

in advance! (In case it matters, the overlays are E-field estimates, with a numerical value given for each vertex point. Also each overlay has only one time point.) Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown

Re: [Freesurfer] mri_surfcluster .w input from MEG/EEG data

trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /cluster/scratch/monday/raij/MRIs/Wyss_000/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to test.lh.mgz

Re: [Freesurfer] mri_surfcluster .w input from MEG/EEG data

/scratch/monday/raij/MEEG/test-lh.mgz ls: /autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz: No such file or directory r...@nmr.mgh.harvard.edu wrote: Hi Doug, I am still receiving a similar error. mri_surf2surf inputes the w file and writes out a mgz file and exits apparently ok. However

[Freesurfer] mri_surfcluster .w input from MEG/EEG data

and observe that it looks fine (which makes me think that the problem originates at the mri_surfcluster side rather than at mne_analyze; however, see below for evidence suggesting the opposite). on machine adapt nmr-std-env (=FreeSurfer 5.1) mne_setup cd /cluster/scratch/monday/raij/MEEG setenv

[Freesurfer] Coordinate transformations from orig/001.mgz to T1.mgz

Hi, We (Aapo Nummenmaa and I) are developing cross-platform software that would allow translating third-party coordinates back and forth with Freesurfer segmentations. Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic, 192 sagittal slices, T1 weighting). Our third-party

Re: [Freesurfer] preproc-sess registration problem

Total of 3 runs per analysis (each with different number of TRs) Total of categories in mkanalysis-sess = 18 (9 main plus 9 rare target) FIR analysis Thank you for the advice in advance! Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging

[Freesurfer] preproc-sess registration problem

--- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] CSF masks

these from aseg.mgz or how should we go about this? Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] CSF masks

/30 -PD if needed). We are interested in two CSF compartments: - superficial CSF outside grey matter and inside inner skull - deep CSF inside ventricles Is there a way to simply extract these from aseg.mgz or how should we go about this? Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH

[Freesurfer] changing f.nii nframes

many other things but not this one it seems). Any suggestions? Bests, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list

[Freesurfer] Version conflict in FS-FAST or unpacksdcmdir?

(even today), whereas if I re-unpack the exact same raw data the preprocessing fails. Details: cd /space/avml/3/users/bletham/ADA_fMRI/AD003/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT AD003_FSvs4.5 nmr-std-env # this takes us to version 5.0 of course so we also

Re: [Freesurfer] EEG source localization?

University University Park, PA USA 16802 Phone: 814-865-6774 Email: ar...@psu.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Tommi Raij, M.D., Ph.D. TMS Core Director MGH

[Freesurfer] opseq2 efficiency vs VRF

change? The ultimate goal is to make sure that changes in BOLD % signal change amplitude are not due to the different number of stimuli across runs. Thanks! Best regards, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St

[Freesurfer] RA position at the Martinos Center

/martinos/opportunities/employment.php#rs032609 Tommi Raij r...@nmr.mgh.harvard.edu --- Tommi Raij, M.D., Ph.D. TMS Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer

Re: [Freesurfer] selxavg-sess error

-- func2sph-sess logfile is /autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/log/func2sph-sess.log

[Freesurfer] selxavg-sess error

dimensions must agree. Error in == fast_selxavg at 439 extreg = extreg - repmat(mean(extreg), [ntrs 1]); ??? Undefined function or variable 'r'. quiting matlab -- ERROR: fast_selxavg() failed\n ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether

Re: [Freesurfer] Freesurfer error: Load Time Course causes abort

/space/cuzco/2/users/raij/avml_fmri_mctogether/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT fsaverage tksurfer fsaverage lh inflated -overlay avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr -timecourse

[Freesurfer] Freesurfer error: Load Time Course causes abort

Hi guys, On machine inv (more or less the same error on machine ai) nmr-dev-env (same error on nmr-std-env) cd /space/cuzco/2/users/raij/avml_fmri_mctogether/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT fsaverage tksurfer fsaverage lh inflated -overlay

[Freesurfer] Number of voxels that intersect with inflated brain surface

space by very densely spaced vertex points on the surface). For this purpose, the voxel size was 3.125 x 3.125 x 4.4 mm, the FOV covered the entire brain, and the anatomical brain is fsaverage. Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical

Re: [Freesurfer] Q: masking statistical overlays

with our custom script to generate the mask (e.g., mark all masked vertex points as 0 in the overlay), but it seems that in a stats map every vertex point needs to have an overlay value (i.e., we cannot just skip the vertex points we want to omit - right?). Thanks! -Tommi --- Tommi Raij, M.D

Correction: Re: [Freesurfer] Q: masking statistical overlays

., we cannot just skip the vertex points we want to omit - right?). Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer

[Freesurfer] Q: masking statistical overlays

an overlay value (i.e., we cannot just skip the vertex points we want to omit - right?). Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A

Re: [Freesurfer] tksurfer time course window

window in tksurfer? Thanks in advance, Elaine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center

[Freesurfer] tksurfer - list overlay values inside a label

Hi Doug Kevin, I am trying to save a text list from tksurfer that contains all the overlay values (one value per each vertex point) inside in a functionally defined label. The labels were originally defined from a different data set than the overlays where I need the values. The overlay where I

Re: [Freesurfer] Color threshold in freesurfer

What is the corresponding tcl variable called (i.e. the one that selects between the three options Linear/Linear Opaque/Piecewise)? Thanks, Tommi Kevin has now implemented this in tkmedit in dev. doug Doug Greve wrote: Kevin has just made a change to the default way that the DEV

[Freesurfer] FS-FAST: problem with extracting BOLD time courses with a tksurfer tcl script

appreciated! Also if anyone needs the full script I am happy to send you a copy - however notice that currently one of the command lines only works in the developmental environment (nmr-dev-env). Cheers, Tommi Specs: on machine ai nmr-dev-env cd /space/cuzco/12/users/raij/avml_fmri_mctogether

[Freesurfer] FS-FAST: FIR analysis baseline corrected BOLD % signal change values?

values (when plotted using the tcl script) are baseline corrected. Thanks!!! -Tommi Details: On machine cuzco nmr-dev-env (or nmr-std-env, does not seem to make a difference in this case) cd /space/cuzco/7/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij

[Freesurfer] func2sph-sess registration question - where should individual subject's register.dat files be?

of the sessid file would list all my $SESSION_DIRs (i.e., different subjects). Question: Where does func2sph-sess look for the individual level register.dat files? I assume it will automatically find them at $STUDY_DIR/$SESSION_DIR/bold/register.dat Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH

[Freesurfer] tksurfer BOLD time course display: show multiple overlays?

waveforms from new overlays (with the possibility of still selecting which waveforms will be visible). We are trying to do this within tksurfer. Any suggestions are much appreciated! Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149

Re: [Freesurfer] tksurfer BOLD time course display: show multiple overlays?

Ok Doug, I guess I should have talked about time courses instead of overlays. Let me clarify: on machine stim (via remote VNC): nmr-dev-env cd /space/cuzco/7/user/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage Launch tksurfer

[Freesurfer] Percent signal change: what stats to read

with matlab and would need to use % signal change as the input values for those analyses. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A

[Freesurfer] Rendering results of custom fMRI analyses on FreeSurfer surface

of the matlab analysis look like so that rendering it onto a FreeSurfer surface will work? Is there any documentation related to this? Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED] ___ Freesurfer

[Freesurfer] tksurfer time course script help

in many subjects - just edit the list of ROIs/labels and time courses to be loaded, and let the computer do the rest! Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED

Re: [Freesurfer] FS-FAST group analysis paint question

-REST/sig-lh --src_type bfloat --hemi lh --trgsurfval ./V-REST-lh.w --trg_type paint Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED

[Freesurfer] FS-FAST group analysis paint question

-lh.w --trg_type paint Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] FS-FAST: mkcontrast-sess -setwdelay

just set in the analysis script, for example, mkcontrast-sess -analysis XXX -setwdelay 0 0 0 0 1 1 1 0 0 0 0 0 -sumdelays -contrast A-REST -a 1 -c 0 Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129

[Freesurfer] viewing group analysis results in tkmedit (3D) while using spherical space intersubject morphing

. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] func2sph-sess target brain setting

. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

Re: [Freesurfer] func2sph-sess target brain setting

either way. I just wonder what is the difference between the methods, and if either method is unambiguously correct. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A

[Freesurfer] FS-FAST seq.info with multiple ntrs

selxavg-sess to look for a custom filename instead of seq.info? This might make things more flexible. Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED

Re: [Freesurfer] FS-FAST registration across sessions

/cognito/5/users/raij/subjects_mri setenv SUBJECT avml19 cd /space/cognito/21/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT # MOTION CORRECT mc-sess -sf sessid -df sesspar # SPATIAL SMOOTHING AND INORM, OUTSTEM = ifmcsm6 spatialsmooth-sess -sf sessid -df sesspar -fwhm 6 -i fmc -o

[Freesurfer] Question: FS-FAST mc-sess -perrun

the mc-sess -rlf runlistfile flag, and changing the contents of the runlistfile to match each of the run numbers, one at a time? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL

Re: [Freesurfer] Question: FS-FAST mc-sess -perrun

mc-sess with -perrun failed with the output: targstem: Undefined variable. *** Bug report: *** on machine ai source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri cd /space/cognito/5/users/raij/avml_fmri_mcseparately

[Freesurfer] FS-FAST spatialsmooth-sess error

Hi Doug, spatialsmooth-sess failed on the second run (out of 6 runs) with the output: ... ERROR: failure writing /tmp/ipfsl_19705/fmc.img as volume type 16 /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold mri_convert 005/fmc.bhdr /tmp/ipfsl_19705

[Freesurfer] FS-FAST Registration Question: registration across sessions within subjects

result? And what kind of tools currently exist? Thanks, Tommi --- Tommi Raij MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu