[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

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 probabili

[Freesurfer] tksurfer partial overlays?

le, but the tksurfer brain 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] 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

[Freesurfer] mni152reg error (file permission denied)

hanks! 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/ma

[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] dmri_trk2trk issue

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

[Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5

levant 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 ma

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

> >>> I would imagine that since FS 5.3 does not use GPU for analysis, this >>> is >>> mainly relevant for visualization (freeview etc) requiring 3D rendering >>> of >>> volumes, surfaces, and tractography results simultaneously. >>> >>&

[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

Re: [Freesurfer] preproc-sess registration problem

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 >> >> >> --- >> T

[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 sys

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

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

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

mi= lh 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 t

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

luster/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 >> a

[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

[Freesurfer] opseq2 efficiency vs VRF

ly reflect the balance for just the BOLD % signal 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

[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

[Freesurfer] func2sph-sess target brain setting

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 mailing list Freesurfer@nmr.mgh.harvard.edu https://

[Freesurfer] tksurfer hemodynamic waveforms for group analysis

arvard.edu/fswiki/FsTutorial_2fVisualization Is this function currently functional? If so, which file should I load? Details: group brain = fsaverage STUDY_DIR = /space/cognito/21/users/raij/avml_fmri_mctogether/ SUBJECTS_DIR = /space/cognito/5/users/raij/subjects_mri/ environment = nmr-std-env

Re: [Freesurfer] func2sph-sess target brain setting

gt;> at isxavg-fe-sess -s fegroup) >> >> >> *** 3 *** Or must/should I do both 1 and 2 of the above. >> >> >> I am using surf-sess/tksurfer to view the results and set -subject >> fsaverage even there. >> >> I get results that loo

[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

suggestions would be very much welcome. 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 ht

[Freesurfer] FS-FAST group analysis paint question

-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 mailing

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

am unsure how to do the corresponding paint job for the morphed group >>analysis data. Would the following command do what needs to be done? >> >>mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage --srcsurfval >>V-REST/sig-lh --src_type bfloat --hemi lh --trgsurfval ./V-REST

[Freesurfer] tksurfer time course script help

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.

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

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 mailing list Freesurfer@nmr.mgh.harvard

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

uot;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

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

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/subjects_mri setenv SUBJECT fsaverage Load the h-lh.bhdr

[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

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

[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] tksurfer - list overlay values inside a label

Ahh - that sounds exactly like what I need! So a script like this would do the trick (Kevin could you please have a quick look): tksurfer fsaverage lh inflated # tcl script sharts here # Load curvature set curv lh.curv read_binary_curv set curvflag 1 # Load my overlay (referring to the first

Re: [Freesurfer] tksurfer time course window

the time course 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

[Freesurfer] Q: masking statistical overlays

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] Q: masking statistical overlays

very 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., Ph.D. >> MGH/MIT/HMS Athinoula A. Martinos Center fo

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

ints 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

[Freesurfer] FS-FAST: missing time frame & time labeling of FIR analyses

by one frame or if the last frame is missing. So, which time frame is it that the cepct-lh.bhdr is missing - the 3rd or the 16th? 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] Number of voxels that intersect with inflated brain surface

voxel 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

[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

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

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

[Freesurfer] selxavg-sess error

rix 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 (/autof

Re: [Freesurfer] selxavg-sess error

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

[Freesurfer] fMRI raw data time course

uggestions would be much appreciated! Bests, Tommi on machine cuzco nmr-std-env (same problem with nmr-dev-env) cd /space/cuzco/1/users/raij/avml_fmri_mctogether/avml14_session_BRISI12/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJ

Re: [Freesurfer] EEG source localization?

es Imaging Center > 120 Chandlee Laboratory > The Pennsylvania State University > University Park, PA USA 16802 > Phone: 814-865-6774 > Email: ar...@psu.edu > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.n

[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

[Freesurfer] changing f.nii nframes

onvert can adjust 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 ma

[Freesurfer] CSF masks

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/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer

Re: [Freesurfer] CSF masks

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/MIT/HMS Athinoula A. Martinos Center for Biom

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

. Does this equal to using 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

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

Re: [Freesurfer] FS-FAST registration across sessions

DIR /space/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

[Freesurfer] Q: tkregister2 coronal/sagittal/horizontal discrepancy

eesurfer/nmr-std-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT avml07 cd /space/cognito/5/users/raij/subjects_mri tkregister2 --mgz --s avml07 --fstal ... and there you go, click away... Thanks for your advice in advance, Tommi --- Tommi Raij, M.D., Ph.D. MGH

[Freesurfer] Mean & SD over ROI in a FIR analysis (several timepoints)

load time course - except that in these programs the time courses are displayed for only a single voxel at a time). Any suggestions how this could be achieved? Example data/analysis can be found in /space/cognito/5/users/raij/avml_fmri/avml12_session_BRISI07_ISI1TR_BERT There are two

[Freesurfer] Problem with tkmedit Tools/fMRI/Select Contiguous Voxels by Threshold

the Threshold. Any suggested ways around this? Or am I just doing something plain wrong? 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 mai

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

d give the most accurate 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.

[Freesurfer] mris_pmake version issue

suggestions would be greatly 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

[Freesurfer] Older tksurfer and tkmedit (FS version 5.0.0) fail to launch: glut issue?

ther machine we tried had OpenGL version 4.6.0 NVIDIA 535.54.03 Thank you! Best regards, Tommi --- Tommi Raij, MD, PhD Director, TMS Clinical Research MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th st Charlestown, MA 02129 ___ F

[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