Freesurfer

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30132 discussions

Re: [Freesurfer] multiple overlay - tksurfer
by Douglas Greve 13 Dec '11

13 Dec '11

Is your register.dat correct? On 12/13/11 10:33 PM, vin . wrote: > Thanx Doug, > > atleast I see, now something. (see attached "seg.mgh -annot > seg.annot.tiff) > > tksurfer Sub_ID lh inflated -annot seg.annot -ov lh.seg.mgh -fthresh > 0.01 -fmid 0.3 -fslope 1 > > just to check, I also summed, all binary files. (attached sum_binarymap) > >tksurfer Sub_ID lh inflated -ov sum_binmap.nii -overlay-reg > register.dat -fthresh 0.01 -fmid 0.3 -fslope 1 > > also find colortable. > > Greetings! > > On Wed, Dec 14, 2011 at 4:18 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Try tksurfer Sub_ID lh inflated -annot seg.annot > doug > > > On 12/13/11 9:39 PM, vin . wrote: >> no, in tksurfer, just inflated lh appears (no overlay). so, I >> viewed lh.seg.mgh in freeview and converted it to .nii and >> viewed in fslview. >> >> On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> wrote: >> >> oh, so you mean you see a line on the surface? >> >> On Wed, 14 Dec 2011, vin . wrote: >> >> Thanx Bruce for quick reply. >> >> you are right, it's surface based file after >> mri_vol2surf. yeah, tried with >> following command. >> >> >tksurfer Sub_ID lh inflated -annot lh.seg.annot -ov >> lh.seg.mgh -fthresh >> 0.01 -fmid 0.3 -fslope 1 >> >> >> On Wed, Dec 14, 2011 at 3:33 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu >> <mailto:fischl@nmr.mgh.harvard.edu>> >> wrote: >> Hi Vin >> >> it looks like your lh.seg.mgh is a surface-based >> .mgz not a >> volume one. Did you try loading it into tksurfer? >> >> cheers >> Bruce >> >> On Wed, 14 Dec 2011, vin . wrote: >> >> Thank you Doug, >> >> >tkregister2 --mov $d/T1.nii.gz --targ >> $d/mri/brain.mgz \ >> --regheader --reg $d/register.dat --noedit >> >> after creating register.dat, I followed the >> explained procedure, >> Which resulted in "lh.seg.mgh". can't view this >> file. ( appears a line ) >> >> >mri_info lh.seg.mgh >> Volume information for lh.seg.mgh >> type: MGH >> dimensions: 163842 x 1 x 1 x 17 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> type: FLOAT (3) >> fov: 163842.000 >> >> >mri_info 3b.nii >> Volume information for 3b.nii >> type: nii >> dimensions: 182 x 218 x 182 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> >> #binary maps looks okay >> >> may be I am doing mistake in registration or >> mri_vol2surf ? >> >mri_vol2surf --reg register.dat --mov Nb.nii >> --interp nearest --hemi lh --o >> lh.Nb.mgh >> >> Greetings! >> >> On Tue, Dec 13, 2011 at 5:56 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> wrote: >> It's a little involved but possible. >> 1. Binarize Nth cluster to have a binary >> value >> of N >> mri_binarize --i N.nii --min 0.5 >> --binval N >> --o Nb.nii >> 2. Sample Nth cluster to the surface >> mri_vol2surf --reg register.dat --mov >> Nb.nii --interp >> nearest --hemi lh lh.Nb.mgh >> After doing that will all clusters, combine >> them together with >> mri_concat lh.1b.mgh lh.2b.mgh ... --vote >> --o lh.seg.mgh >> Now create a surface annotation >> mris_seg2annot --seg lh.seg.mgh --hemi >> lh --s >> subject --o >> lh.seg.annot --ctab yourctab >> yourctab is a color table like >> $FREESURFER_HOME/ FreeSurferColorLUT.txt. >> You >> >> list your regions >> and give them the colors you want. >> >> doug >> >> vin . wrote: >> Hi Doug, >> sorry for confusing names. >> >> - 1.nii is name of the cluster, >> which I >> want to >> overlay. it's a coritical region, >> resulted from >> fsl-probtrackx. >> I want to have few color codes in RGB >> R G B >> 1. 255 0 255 >> 2. 116 0 116 >> 3. 0 0 255 >> ... >> >> in this way, I would like to overlay 20 >> cortical >> regions in different colours on >> inflated >> brain. >> >> -fthresh 0.3 here >> (1/(10^0.3) == 50.12 % >> in freesurfer email archieve, I found >> this. hope >> it's correct. >> >> Thank you >> >> >> >> >> On Mon, Dec 12, 2011 at 11:11 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard. edu >> <mailto:greve@nmr.mgh.harvard.edu>>> >> wrote: >> >> Hi Vin, why do you say it's a 50% >> threshold? What >> is the >> 1.nii >> data? What colors do you want? >> doug >> >> vin . wrote: >> >> Dear FreeSurfer list, >> Greetings! >> >> a newbie to freesurfer. >> -- would like to overlay tracking group >> results (Sum from >> all >> subjects)-(from FSL ) in the inflated lh & >> rh. -- >> >> - it works with one region (hope it's >> correct), with >> following command, where, -fthresh ?? means >> it shows 50 % >> threshold based on intensity / only voxels >> which are >> overlaid >> by atleast half of the subjects ?? >> >> >tksurfer #Sub_ID lh inflated -annot >> aparc.annot -ov >> 1.nii >> -ovreg register.dat -fthresh 0.3 >> -fmid 0.3 >> -fslope 1 >> >> - How I can overlay multiple regions, in >> specific >> colours, >> with 50% thr. ? , >> Thank you :) >> Vin >> ----------------------------- - >> ------------------------------ >> ------------ >> >> _____________________________ _ >> _________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard. edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh. harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard. >> edu/mailman/listinfo/ >> freesurfer >> >> <https://mail.nmr.mgh. harvard.edu/mailman/listinfo/ >> freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard. edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 >> <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: >> 617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/ >> <http://surfer.nmr.mgh.harvard.edu/> >> fswiki/BugReporting >> >> <http://surfer.nmr.mgh. harvard.edu/fswiki/ BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> FileDrop: www.nmr.mgh.harvard.edu/ >> <http://www.nmr.mgh.harvard.edu/> >> facility/filedrop/index.html >> >> <http://www.nmr.mgh.harvard. edu/facility/filedrop/index. >> html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> >> >> >> The information in this e-mail is intended only >> for the >> person to >> whom it is >> addressed. If you believe this e-mail was >> sent to >> you in >> error and >> the e-mail >> contains patient information, please >> contact the >> Partners >> Compliance HelpLine at >> http://www.partners.org/ complianceline >> <http://www.partners.org/ complianceline >> <http://www.partners.org/complianceline>> . If the >> >> e-mail was >> sent >> to you in error >> but does not contain patient information, >> please >> contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/ >> fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> www.nmr.mgh.harvard.edu/ facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> >> >> >

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Re: [Freesurfer] multiple overlay - tksurfer
by Douglas N Greve 13 Dec '11

13 Dec '11

It's a little involved but possible. 1. Binarize Nth cluster to have a binary value of N mri_binarize --i N.nii --min 0.5 --binval N --o Nb.nii 2. Sample Nth cluster to the surface mri_vol2surf --reg register.dat --mov Nb.nii --interp nearest --hemi lh lh.Nb.mgh After doing that will all clusters, combine them together with mri_concat lh.1b.mgh lh.2b.mgh ... --vote --o lh.seg.mgh Now create a surface annotation mris_seg2annot --seg lh.seg.mgh --hemi lh --s subject --o lh.seg.annot --ctab yourctab yourctab is a color table like $FREESURFER_HOME/FreeSurferColorLUT.txt. You list your regions and give them the colors you want. doug vin . wrote: > Hi Doug, > sorry for confusing names. > > - 1.nii is name of the cluster, which I want to overlay. it's a > coritical region, resulted from fsl-probtrackx. > I want to have few color codes in RGB > R G B > 1. 255 0 255 > 2. 116 0 116 > 3. 0 0 255 > ... > > in this way, I would like to overlay 20 cortical regions in different > colours on inflated brain. > > -fthresh 0.3 > here > (1/(10^0.3) == 50.12 % > in freesurfer email archieve, I found this. hope it's correct. > > Thank you > > > > > On Mon, Dec 12, 2011 at 11:11 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Vin, why do you say it's a 50% threshold? What is the 1.nii > data? What colors do you want? > doug > > vin . wrote: > > Dear FreeSurfer list, > Greetings! > > a newbie to freesurfer. > -- would like to overlay tracking group results (Sum from all > subjects)-(from FSL ) in the inflated lh & rh. -- > > - it works with one region (hope it's correct), with > following command, where, -fthresh ?? means it shows 50 % > threshold based on intensity / only voxels which are overlaid > by atleast half of the subjects ?? > > >tksurfer #Sub_ID lh inflated -annot aparc.annot -ov 1.nii > -ovreg register.dat -fthresh 0.3 -fmid 0.3 -fslope 1 > > - How I can overlay multiple regions, in specific colours, > with 50% thr. ? , > Thank you :) > Vin > ------------------------------ ------------------------------ > ------------ > > ______________________________ _________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/ facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/ complianceline > <http://www.partners.org/complianceline> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Freesurfer Digest, Vol 94, Issue 13
by Maryam Vaziri Pashkam 13 Dec '11

13 Dec '11

Hi Doug, following up on my problem with preprocessing, here is the line that we ran: preproc-sess -sf sessid3 -df sessdir -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh -force the part that is failing is: mc-afni2 --i 004/f.nii.gz --t 004/template.nii.gz --o 004/fmcpr.nii.gz --mcdat 004/fmcpr.mcdat that line calls 3dvolreg.afni, which is the part that is really failing: 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.24802/tempvol.nii.gz -prefix 004/tmp.mc-afni2.24802/outvol.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz we tried running it without the .afni extenstion, so using the actual afni 3dvolreg and got no error message: 3dvolreg -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.24802/tempvol.nii.gz -prefix 004/tmp.mc-afni2.24802/outvol.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz This is the output for mc-afni2: mc-afni2 --i 004/f.nii.gz --t 004/template.nii.gz --o 004/fmcpr.nii.gz --mcdat 004/fmcpr.mcdat /ncf/vcn/Maryam/mri-space/studies/SM_PDM/unpackdata/111206_xu_SM_PDM_05/bold mri_info --nframes --o /tmp/mriinfo.24802 004/template.nii.gz log file is 004/fmcpr.nii.gz.mclog mcdat file is 004/fmcpr.mcdat tmp dir is 004/tmp.mc-afni2.24802 #@# -------------------------------- /ncf/vcn/Maryam/mri-space/studies/SM_PDM/unpackdata/111206_xu_SM_PDM_05/bold mri_convert 004/template.nii.gz 004/tmp.mc-afni2.24802/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 004/template.nii.gz 004/tmp.mc-afni2.24802/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 004/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997352, 0.0123936, -0.0716608) j_ras = (-0.0197242, -0.994536, 0.102512) k_ras = (-0.0699987, 0.103654, 0.992147) changing data type from short to float (noscale = 0)... writing to 004/tmp.mc-afni2.24802/tempvol.nii.gz... #@# -------------------------------- /ncf/vcn/Maryam/mri-space/studies/SM_PDM/unpackdata/111206_xu_SM_PDM_05/bold mri_convert 004/f.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz -odt float mri_convert 004/f.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 004/f.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997352, 0.0123936, -0.0716608) j_ras = (-0.0197242, -0.994536, 0.102512) k_ras = (-0.0699987, 0.103654, 0.992147) changing data type from short to float (noscale = 0)... writing to 004/tmp.mc-afni2.24802/invol.nii.gz... #@# -------------------------------- /ncf/vcn/Maryam/mri-space/studies/SM_PDM/unpackdata/111206_xu_SM_PDM_05/bold 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.24802/tempvol.nii.gz -prefix 004/tmp.mc-afni2.24802/outvol.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 004/tmp.mc-afni2.24802/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:004/tmp.mc-afni2.24802/tempvol.nii.gz is 7.185125 degrees from plumb. ++ Reading in base dataset 004/tmp.mc-afni2.24802/tempvol.nii.gz ++ Oblique dataset:004/tmp.mc-afni2.24802/invol.nii.gz is 7.185125 degrees from plumb. ++ Reading input dataset 004/tmp.mc-afni2.24802/invol.nii.gz ++ Edging: x=4 y=4 z=2 ++ Creating mask for -maxdisp + Automask has 37793 voxels + 5984 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 192 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191.. ++ CPU time for realignment=12.2 s [=0.0634 s/sub-brick] ++ Min : roll=-0.043 pitch=-0.422 yaw=-0.218 dS=-0.084 dL=-0.077 dP=-0.160 ++ Mean: roll=+0.044 pitch=+0.020 yaw=-0.018 dS=-0.014 dL=-0.020 dP=+0.024 ++ Max : roll=+0.151 pitch=+0.373 yaw=+0.107 dS=+0.130 dL=+0.037 dP=+0.166 ++ Max displacements (mm) for each sub-brick: 0.72 0.79 0.72 0.79 0.72 0.71 0.71 0.71 0.72 0.66 0.72 0.67 0.72 0.66 0.70 0.68 0.65 0.70 0.62 0.69 0.63 0.67 0.60 0.68 0.58 0.64 0.58 0.60 0.55 0.58 0.51 0.61 0.51 0.54 0.49 0.57 0.46 0.55 0.44 0.46 0.41 0.46 0.41 0.40 0.41 0.42 0.41 0.37 0.40 0.36 0.32 0.23 0.20 0.18 0.17 0.17 0.15 0.16 0.18 0.20 0.19 0.17 0.22 0.17 0.15 0.18 0.11 0.12 0.15 0.10 0.21 0.38 0.23 0.20 0.19 0.18 0.15 0.14 0.20 0.13 0.17 0.13 0.11 0.06 0.09 0.04 0.10 0.12 0.13 0.04 0.11 0.03 0.05 0.06 0.05 0.04 0.00 0.03 0.04 0.10 0.09 0.10 0.07 0.12 0.11 0.12 0.19 0.10 0.21 0.16 0.31 0.24 0.28 0.26 0.39 0.26 0.42 0.32 0.40 0.29 0.34 0.32 0.26 0.35 0.32 0.36 0.36 0.31 0.35 0.36 0.39 0.48 0.40 0.55 0.41 0.50 0.41 0.47 0.40 0.49 0.47 0.37 0.56 0.45 0.49 0.50 0.47 0.33 0.60 0.48 0.43 0.35 0.51 0.46 0.45 0.32 0.46 0.39 0.46 0.32 0.49 0.39 0.46 0.36 0.49 0.41 0.46 0.51 0.45 0.47 0.42 0.44 0.47 0.42 0.52 0.47 0.49 0.57 0.52 0.59 0.64 0.62 0.54 0.64 0.62 0.57 0.66 0.57 0.64 0.63 0.53 0.65 ++ Max displacement in automask = 0.79 (mm) at sub-brick 3 Can't connect? tcp_connect[connect]: Connection timed out ++ Wrote dataset to disk in 004/tmp.mc-afni2.24802/outvol.nii.gz ** Warning: overwriting file 004/fmcpr.mcdat Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out goes on forever......but did create an output vol: -rw-r--r-- 1 mvpashkam vcn 111254803 Dec 13 12:47 outvol.nii.gz output from afni's 3dvolreg: 3dvolreg -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.24802/tempvol.nii.gz -prefix 004/tmp.mc-afni2.24802/outvol.nii.gz 004/tmp.mc-afni2.24802/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_05_26_1457 (Aug 17 2011) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 004/tmp.mc-afni2.24802/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:004/tmp.mc-afni2.24802/tempvol.nii.gz is 7.185125 degrees from plumb. ++ Reading in base dataset 004/tmp.mc-afni2.24802/tempvol.nii.gz ++ Oblique dataset:004/tmp.mc-afni2.24802/invol.nii.gz is 7.185125 degrees from plumb. ++ Reading input dataset 004/tmp.mc-afni2.24802/invol.nii.gz ++ Edging: x=4 y=4 z=2 ++ Creating mask for -maxdisp + Automask has 37791 voxels + 5976 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 192 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191.. ++ CPU time for realignment=0 s [=0 s/sub-brick] ++ Min : roll=-0.043 pitch=-0.422 yaw=-0.218 dS=-0.084 dL=-0.077 dP=-0.160 ++ Mean: roll=+0.044 pitch=+0.020 yaw=-0.018 dS=-0.014 dL=-0.020 dP=+0.024 ++ Max : roll=+0.151 pitch=+0.373 yaw=+0.107 dS=+0.130 dL=+0.037 dP=+0.166 ++ Max displacements (mm) for each sub-brick: 0.72 0.79 0.72 0.79 0.72 0.71 0.71 0.71 0.72 0.66 0.72 0.67 0.72 0.66 0.70 0.68 0.65 0.70 0.62 0.69 0.63 0.67 0.60 0.68 0.58 0.64 0.58 0.60 0.55 0.58 0.51 0.61 0.51 0.54 0.49 0.57 0.46 0.55 0.44 0.46 0.41 0.46 0.41 0.40 0.41 0.42 0.41 0.37 0.40 0.36 0.32 0.23 0.21 0.18 0.17 0.17 0.15 0.16 0.18 0.20 0.19 0.17 0.22 0.17 0.15 0.18 0.11 0.12 0.15 0.10 0.21 0.38 0.23 0.20 0.19 0.18 0.15 0.14 0.20 0.13 0.17 0.13 0.11 0.06 0.09 0.04 0.10 0.12 0.13 0.04 0.11 0.03 0.05 0.06 0.05 0.04 0.00 0.03 0.04 0.10 0.09 0.10 0.07 0.12 0.11 0.12 0.19 0.10 0.21 0.16 0.31 0.24 0.28 0.26 0.39 0.26 0.42 0.32 0.40 0.29 0.34 0.32 0.26 0.35 0.32 0.36 0.36 0.31 0.35 0.36 0.39 0.48 0.40 0.55 0.41 0.50 0.41 0.47 0.40 0.49 0.47 0.37 0.56 0.45 0.49 0.50 0.47 0.33 0.60 0.48 0.43 0.35 0.51 0.46 0.45 0.32 0.46 0.39 0.46 0.32 0.49 0.39 0.46 0.36 0.49 0.41 0.46 0.51 0.45 0.47 0.42 0.44 0.47 0.42 0.52 0.47 0.49 0.57 0.52 0.59 0.64 0.62 0.54 0.64 0.62 0.57 0.66 0.57 0.64 0.63 0.53 0.65 ++ Max displacement in automask = 0.79 (mm) at sub-brick 3 ++ Wrote dataset to disk in 004/tmp.mc-afni2.24802/outvol.nii.gz ** Warning: overwriting file 004/fmcpr.mcdat created an output vol: -rw-r--r-- 1 mvpashkam vcn 111260685 Dec 13 13:01 outvol.nii.gz Any idea where the problem might be? Thanks, Maryam On Mon, Dec 12, 2011 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. preprocessing error (Maryam Vaziri Pashkam) > 2. Re: preprocessing error (Douglas Greve) > 3. convert surface label on to functional image (Zhangyuanchao) > 4. References/materials for interaction analysis in freesurfer > (Bhavani Shankara Bagepally) > 5. Re: dt_recon error (Yuko Yotsumoto) > 6. Re: dt_recon error (Yuko Yotsumoto) > 7. Re: run preproc-sess with -nomc (Thunell Evelina) > 8. Re: mri_ca_register from virtual box (Lorenzo Busti) > 9. Re: mri_ca_register from virtual box (Lorenzo Busti) > 10. Converting thickness maps to vtk (Navid Shiee) > 11. Re: tracula and snow leopard: can't allocate region / memory > error (Anastasia Yendiki) > 12. tracula failed to find header file for -t (Scott Hayes) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 11 Dec 2011 14:34:05 -0500 > From: Maryam Vaziri Pashkam <mvaziri.p(a)gmail.com> > Subject: [Freesurfer] preprocessing error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAEEXA4cePaYDO8EPMpma7ThADfnd1qcYfg2HnnHz+7sVrVBTjw(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am running preprocessing on my data using freesurfer 5.1, fsl 4.1.7, and > matlab R2009a (I also tried it with matlab 2007a) on Harvard cluster and I > am receiving an error. I connect to the cluster using terminal and SSH > connection in mac. > > the preprocessing is stalled in the middle with this error: > > ++ Max displacement in automask = 0.79 (mm) at sub-brick 3 > Can't connect? tcp_connect[connect]: Connection timed out > ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz > ** Warning: overwriting file 004/fmcpr.mcdat > Can't connect? tcp_connect[connect]: Connection timed out > Can't connect? tcp_connect[connect]: Connection timed out > Can't connect? tcp_connect[connect]: Connection timed out > > > It does not stop running and output an error. But rather keeps printing the > last line and does not move forward. Any idea where the problem might be? > > > Thanks, > Maryam >

2 1

rtview: ERROR cannot find eccen/real.nii
by Michelle Umali 13 Dec '11

13 Dec '11

Dear All, I am still having trouble generating polar and eccen maps with rtview. I did this: cd $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh rtview.sh --s sj07 --lh --eccen \ --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii The subjectname file is in $SUBJECTS_DIR/retinotopy/sj07 and I've tried when a copy of rtview is in $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh or in $SUBJECTS_DIR/retinotopy The error I got : ERROR: cannot find eccen/real.nii even though all the appropriate images exist in the directories and can be seen through tksurfer-sess. Where am I going wrong? Thanks. Michelle

2 4

Re: [Freesurfer] convert surface label on to functional image
by Douglas N Greve 13 Dec '11

13 Dec '11

The easiest thing is to use mri_label2vol, something like mri_label2vol --label yourlabel.label --temp functemplate.nii --reg register.dat --proj frac 0 1 .1 --hemi lh --subject subject --o yourlabel.nii doug Zhangyuanchao wrote: > Thanks for your response! > > In fact, the label that I want to convert to functional space was > obtained by between-group comparisons, so it does not belong to any > existing parcellation template. > > What should I do in this case? > > Thanks! > > Best, > > --- *11年12月13日，周二, Douglas N Greve > /<greve(a)nmr.mgh.harvard.edu>/* 写道： > > > 发件人: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > 主题: Re: [Freesurfer] convert surface label on to functional image > 收件人: "Zhangyuanchao" <woshizhangyc(a)yahoo.cn> > 抄送: freesurfer(a)nmr.mgh.harvard.edu > 日期: 2011年12月13日,周二,上午5:48 > > Hi Yuanchao, I would recommend that you use the aparc+aseg.mgz > file for this. This file has cortical labels already in the > volume, you just need to map them to your functional space, > something like > > mri_label2vol --aparc+aseg --temp functemplate.nii --reg > register.dat --o aparc+aseg.fmri.nii > > doug > > Zhangyuanchao wrote: > > hi, expert, > > > > By mapping a surface label to a functional template, I want to > extract the corresponding cortical gray matter region in the > functional space. I know I should use the mri_label2vol command. > > In the help page of mri_label2vol, I see some examples of this > command. > > > > 2. Convert a surface label into a binary mask in the functional > space. > > Fill in all the cortical gray matter. Require that a functional > voxel > > be filled at least 30% by the label: > > > > mri_label2vol --label lh-avg_central_sulcus.label --temp > f.nii --reg register.dat --fillthresh .3 --proj frac 0 1 > .1 --subject bert --hemi lh > > --o cent-lh.nii > > > > 3. Convert a surface label into a binary mask in the functional > space. > > Sample a 1mm ribbon 2mm below the gray/white surface. Do not > require a fill threshold: > > > > mri_label2vol --label lh-avg_central_sulcus.label --temp > f.nii --reg register.dat --proj abs -3 -2 .1 --subject bert > --hemi lh > > --o cent-lh.nii > > > > I want to extract the cortical gray matter on the functional > images corresponding to the surface label. I do not know which of > the above commands could obtain the result I want and which > parameters I should use to obtain what I want. > > > > For example 3, I do not quite catch what "Sample a 1mm ribbon > 2mm below the gray/white surface. " this sentence means. > > Thanks for your help! > > > > > > Best > > > > Yuanchao > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > </mc/compose?to=Freesurfer(a)nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu </mc/compose?to=greve(a)nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

Cluster-wise correction for multiple comparisons: customized Zstats data
by Xinian Zuo 13 Dec '11

13 Dec '11

Hi List, I have a question on how to write out the matlab vector containing the Z-statistics and perform subsequent multiple corrections. I already read some functions and know how to write it to a mgh surface file. Here, my question is 'is there any specific things on the header of the surface file, which allows me to do cluster-wise correction (see corrected p-value < 0.025) if there is such a command for that?'. Thanks! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) Google Scholar Citations: http://scholar.google.com/citations?user=a3-gVGMAAAAJ&hl=en

2 3

thickness or volume?
by Lindsay Ercole 13 Dec '11

13 Dec '11

What is the current opinion on using cortical volumes rather than reporting on thickness? Sincerest thanks, Lindsay

3 2

problem using an older environment...
by Joe Andreano 12 Dec '11

12 Dec '11

Hello folks, I'm trying to reanalyze some old data that was originially analyzed in freesurfer version 4. Because the code I was using was from 4.0, I set the environment to 4 before starting, then made a new analysis and a few new contrasts. When I tried to run selxavg3-sess with the following command: selxavg3-sess -analysis nmdm_ALL42_V_fix -sf SESSID_ALL_FINAL -df . I got the following error message: /autofs/space/albus_003/users/nmdm_2/nmdm_004 ---------------------------------------- $id:fastselxavg3.m, v 1.88.2.5 2010/11/11 16:55:08 greve Exp $ /usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/stable5_0_0/matlab/MRIread.m --------------------------------------- outtop = /autofs/space/albus/3/users/nmdm_2 Extension format = nii.gz ??? Reference to non-existent field 'mcstem' Error in ==> fast_ldanaflac at 171 if(isempty(flac.mcstem)) Error in ==> fast_selxavg3 at 55 flac0=fast_ldanaflac(analysis); >>-------------------------------------- ERROR: fast_selxavg3() failed\n Note that I have confirmed that I am indeed running version 4, but the commands called in the error ("/usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_selxavg3.m", etc.) are referencing version 5. Note also that the code being used here is adapted directly from an earlier analysis which was run in version 4 and which I know worked without errors. Anybody have any idea what's happening here? Even some information on what 'mcstem', or ldanaflac do would be helpful. (I have attached my analysis.info file) Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Research Fellow Interdisciplinary Affective Science Lab Massachusetts General Hospital _________________________________

2 1

multiple overlay - tksurfer
by vin . 12 Dec '11

12 Dec '11

Dear FreeSurfer list, Greetings! a newbie to freesurfer. -- would like to overlay tracking group results (Sum from all subjects)-(from FSL ) in the inflated lh & rh. -- - it works with one region (hope it's correct), with following command, where, -fthresh ?? means it shows 50 % threshold based on intensity / only voxels which are overlaid by atleast half of the subjects ?? >tksurfer #Sub_ID lh inflated -annot aparc.annot -ov 1.nii -ovreg register.dat -fthresh 0.3 -fmid 0.3 -fslope 1 - How I can overlay multiple regions, in specific colours, with 50% thr. ? , Thank you :) Vin

2 1

convert surface label on to functional image
by Zhangyuanchao 12 Dec '11

12 Dec '11

hi, expert, By mapping a surface label to a functional template, I want to extract the corresponding cortical gray matter region in the functional space. I know I should use the mri_label2vol command. In the help page of mri_label2vol, I see some examples of this command. 2. Convert a surface label into a binary mask in the functional space.Fill in all the cortical gray matter. Require that a functional voxelbe filled at least 30% by the label: mri_label2vol --label lh-avg_central_sulcus.label --temp f.nii --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject bert --hemi lh --o cent-lh.nii 3. Convert a surface label into a binary mask in the functional space.Sample a 1mm ribbon 2mm below the gray/white surface. Do not require a fill threshold: mri_label2vol --label lh-avg_central_sulcus.label --temp f.nii --reg register.dat --proj abs -3 -2 .1 --subject bert --hemi lh --o cent-lh.nii I want to extract the cortical gray matter on the functional images corresponding to the surface label. I do not know which of the above commands could obtain the result I want and which parameters I should use to obtain what I want. For example 3, I do not quite catch what "Sample a 1mm ribbon 2mm below the gray/white surface. " this sentence means. Thanks for your help! Best Yuanchao

2 1

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