Freesurfer December 2012

freesurfer@nmr.mgh.harvard.edu

101 participants
161 discussions

(no subject)
by Hugh Pemberton 04 Dec '12

04 Dec '12

Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B______________/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B______________ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh

2 7

Re: [Freesurfer] functional ROI analysis
by Douglas Greve 04 Dec '12

04 Dec '12

Hi Susan, ok, I see what you are doing now. Let's do it this way: 1. First transfer your label to the volume: mri_label2vol --temp example_func.nii --reg anat2exf.register.dat --proj 0 1 .1 --hemi lh --label lh.your.label --o yourlabel.func.nii 2. Then run segstats: mri_segstats --i cope2.nii --seg yourlabel.func.nii --mask zstat1.nii --maskthresh 2 --masksign abs --o sum.dat The cope and the zstat are now volumes. doug On 11/26/12 8:26 PM, Susan Alice McLaughlin wrote: > Hi Doug, > > Thanks for the quick answer. Sorry to be dense, but does this need > somewhere to include registration matrix, anat2exf.register.dat, to > register to the subject's surface? > > And at this point in the analysis, the feat folder does not include > copes and zstats separated out by hemisphere, although there are > zstat[#].surf.lh.w and .rh.w files in the main feat folder. > > Again, sorry for my limited understanding of file structure. > > Susan > > > On Mon, 26 Nov 2012, Douglas N Greve wrote: > >> Hi Susan, you can't use func2roi-sess. You'll have to put together some >> commands, but it should not be too hard, something like >> >> mri_segstats --i lh.cope2.nii --slabel subjectname lh your.label --mask >> lh.zstat1.nii --maskthresh 2 --masksign abs --o sum.dat >> >> where zstat1 is your all/nothing contrast sampled onto the surface and >> cope2 is some other contrast sampled on the surface. >> You can do this for each subject, then run asegstats2table giving it >> paths to all of your sum.dat files >> >> doug >> >> >> >> >> On 11/26/2012 07:01 PM, Susan Alice McLaughlin wrote: >>> Hi, >>> >>> I am hoping do a surface-based functional ROI analysis on >>> subject-specific ROIs that are both defined structurally and are >>> masked by an all/nothing functional contrast. func2roi-sess seems >>> perfect for this except that my data are not in an FS-FAST >>> data/analysis structure, but are instead pre-processed and >>> preliminarily analyzed using FSL and mapped to the surface using >>> reg-feat2anat. >>> >>> Is there any way to pass my original analysis into func2roi-sess? I >>> tried using: >>> >>> func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis >>> 1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG >>> -maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz >>> -maskthreshold 2 -s 1012 -d >>> >>> but get "ERROR: cannot find any sessions." >>> >>> Or is there another tool more appropriate for what I am trying to >>> do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on >>> fsaverage in tksurfer and morphed to each subject using >>> label_2_label) are in .label format and are on the surface. >>> >>> Thanks in advance for and advice or suggestions. >>> >>> Susan McLaughlin >>> Doctoral Candidate >>> SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) >>> Dept. of Speech and Hearing Sciences >>> University of Washington >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> 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 >> 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 >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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 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. >> >> > > Susan McLaughlin > Doctoral Candidate > SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) > Dept. of Speech and Hearing Sciences > University of Washington > >

3 2

(no subject)
by José Ángel Pineda 04 Dec '12

04 Dec '12

Thanks Doug, I already downloaded the new script for mri_label2vol, but it seems it is just compiled for linux, as I cannot execute it in my Mac. If it is so, could you please upload another compiled for mac, or source. Thanks Jose > For the missing insula problem, try using a newer version of mri_label2vol > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol > > The 2nd problem is not so easy to fix. You might be better off using > aparc+aseg.mgz as input to mri_label2vol instead of the surface annotation. > doug > > > On 12/3/12 10:35 AM, Jos? ?ngel Pineda wrote: > > Dear experts, > > > > I am registering cortical labels from Talairach coordinates to my > > native T1. For doing this, I have run the next script lines: > > > > > > tkregister --targ brainmask.mgz --mov highres_brain.nii.gz --reg > > T1FS2Highres.dat --regheader --noedit > > > > mri_label2vol --annot rh.aparc.annot --temp highres_brain.nii.gz --reg > > T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject FS --proj > > frac 0 1 .1 --fillthresh .3 > > > > and the same for the left hemi. > > > > However I am finding two problems at the result. First Insula is > > missing for both hemispheres, and second the cortical ROIs have the > > shape of the figure attached, e.g. there are many voxels empty > > > > Im?genes integradas 1 > > > > I found in previous topics, that the mri_label2vol, was updated as it > > left last volume from the list out of the conversion. I tried to > > download it, but it is just compiled for linux, and since Im working > > with mac I am not able to run it. Could you please give me any > > comments to solve the problem with the missing voxels. > > About the problem with the insula, the other option is to just extract > > it with mri_annotation2label, but if I could get the mri_label2vol > > working correctly it would be better. > > > > Thanks a lot > > > > Jose > -- José Angel Pineda Pardo Center of Biomedical Technology (CTB) Parque Científico y Tecnológico de la UPM Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, ES

3 5

Exclusion of too much grey matter
by Kristina Nalbandian 04 Dec '12

04 Dec '12

Hello, I am having some problems editing the volume created after the -recon-all -all function in FreeSurfer. The brain that is being generated has too much grey matter excluded. I've searched the wiki for ways to include these grey matter regions during my editing, but have found nothing. I have attached a picture of the problem I am having. The orange arrow points to the part of the grey matter that I would like to be included in the boundary. Is there a way to do this? Thank you in advance, Kristina

3 2

whole brain volume, gap between wbv and ICV
by Hsu, Phillip 04 Dec '12

04 Dec '12

Hi all, I am looking for an accurate method of calculating whole brain volume (WBV) from a spreadsheet of FS MRI data. I had previously been using the following method: 1. Sum the following: CSF, lateral ventricles, 3,4,5 ventricles, and the choroid plexus 2. In a second column, sum the following: cortical wm, cerebellar white matter, brain stem, and total gray volume. 3. Whole Brain Volume = 2 - 1 However, this method gave WBV values greater than that of the intracranial volume (ICV) for some participants. Removing brain stem from the equation did not make a big impact. Is there a method to more accurately calculate WBV? Additionally, I am looking for a way to calculate the amount of space in the ICV that is not occupied by the brain (the "gap" volume). I have been using the equation gap = ICV-WBV. Is there, however, a more accurate way to calculate the value of gap, possibly using the sum of the spaces in the brain rather than the difference between ICV and WBV? Sincere thanks, Phil -- Phillip J. Hsu Washington University in St. Louis hsup(a)wustl.edu

1 0

flipping surface data
by kelsi 04 Dec '12

04 Dec '12

Hi Freesurfers, Is there a tool to flip the orientation of surface data to the opposite hemisphere? We are working with stroke patients, and I would like to do analysis of the contralesional hemisphere of all the patients. However, this requires putting them on the same hemisphere for ttests, etc. I saw an earlier thread online about a program for flipping in the works, I was just wondering if this is now possible? Thank you! Kelsi

3 3

Head, body and tail of hippocampus
by Antonella Kis 04 Dec '12

04 Dec '12

Dear FS team, I would like to know which subfield ( left_presubiculum, left_CA1, left_CA2-3, left_fimbria, left_subiculum, left_CA4-DG, left_hippocampal_fissure) contribute to the head, body and tail of left hippocampus. It also seems that the first column of nonPartialVolumeStatsLeft.txt file contains the total volume of the left hippoccampus but based on the numbers (I copied them below) the total volume is smaller than the volume of some of teh subfileds. How this is possible? volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissure C23 1681.2 2564.29 1405.07 3814.14 211.792 2983.06 2118.63 422.786 Thank you. Antonella

2 1

Longitudinal analysis of one timepoint
by Westeneng, H.J. 04 Dec '12

04 Dec '12

Hi Freesurfer experts, This week a read the article of Bernal-Rusiel et al. titled "Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models". In this article you described the submission of single time-point scans to the longitudinal pipeline of Freesurfer. I'm very interested in how to do this. Your help will be appreciated. Thanks in advance, Henk-Jan ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

2 1

Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 04 Dec '12

04 Dec '12

Hi Julia, I meant tksurfer-sess (not surf-sess) doug On 12/04/2012 05:39 AM, Julia Foecker wrote: > Hi Doug, > thanks for your reply. > > I got the following messages when running the > > > surf-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE > -retinotopy polar > > and there was also this kind of message: > > GL window already open: can't open second > % tksurfer: polar-views.tcl: save rgb's > saveviews.tcl: nosave setenv'd => nothing will be saved > invalid command name "dontsave_rgb_named"% surfer: dmin=0.2470, vno=45600, > > I am still not sure what I can do so that this issue will not occur. > Do you have another advice? > > Thanks! > > Julia > > > > > WARNING: No colortable found! > invalid command name "urfer/subjects]" > % invalid command name "WARNING:" > % invalid command name "WARNING:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name > "mrisReadTriangleFile(/Users/foecker/Documents/Data/FMRI/Freesurfer/subjects/VGP01/surf/lh.sphere.reg):" > % % invalid command name "mrisReadTriangleFile" > % % % % invalid command name "WARNING:" > % % e buffered window > surfer: tkoInitWindow(VGP01) > surfer: using interface > /Users/foecker/Documents/freesurfer4/lib/tcl/tksurfer.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_common.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_wrappers.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/fsgdfPlot.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > % > invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "surfer:" > % invalid command name "Reading" > % invalid command name "Reading" > % invalid command name "Reading" > % invalid command name "Reading" > % invalid command name "Successfully" > % invalid command name "reading" > % invalid command name "%" > % > % exit > [4157-JF-MACPRO1:FMRI/Freesurfer/subjects] foecker% tksurfer > usage: tksurfer subject hemisphere surface [options] > > subject : a subject directory in the SUBJECTS_DIR path > hemipshere : rh or lh > surface : a surface file name relative to the subject's surf directory > > Options > > -title title : set window title to title. Def is subject name. > -reassign : resample labels onto surface (set vnos=-1) > -sdir <path> : sets the subjects directory path > -orig <suffix> : sets the orig suffix string > -sphere <suffix>:sets the sphere.reg suffix string > > -patch <filename> : load a patch > > -tcl <filename> : run a script > > -annotation <filename> : load an annotation > -aparc : set annotation to aparc.annot and use outline mode > -colortable <filename> : load a color table file > -labels-under : display labels under any overlay > -label-outline : draw labels as outlines > > -curv : automatically load ?h.curv > -gray : automatically load ?h.curv and make it gray > > -overlay <filename> : load an overlay volume > -overlay-reg <filename> : use a file for the overlay registration > -overlay-reg-find : look in the data directory for a register.dat > : file > -overlay-reg-identity : calculate an identity transform for registration > -mni152reg : for use with average subject when overlay is mni152 > -zm : remove mean from overlays > -fslope <value> : set the overlay threshold slope value > -fmid <value> : set the overlay threshold midpoint value > -fthresh <value> : set the overlay threshold minimum value > -foffset <value> : set the overlay threshold offset value > -colscalebarflag <1|0> : display color scale bar > -colscaletext <1|0> : display text in color scale bar > -truncphaseflag <1|0> : truncate the overlay display > -revphaseflag <1|0> : reverse the overlay display > -invphaseflag <1|0> : invert the overlay display > > -timecourse <filename> : load an timecourse volume > -timecourse-reg <filename> : use a file for the timecourse > : registration > -timecourse-reg-find : look in the data directory for a > : register.dat file > -timecourse-reg-identity : calculate an identity transform for > : regisrtation > -timecourse-offset <filename> : load an timecourse offset volume > -timecourse-offset-reg-file <filename> : use a file for the timecourse offset > : registration > -timecourse-offset-reg-find : look in the data directory for a > : register.dat file > -timecourse-offset-reg-identity : calculate an identity transform for > : registration > > -delink : do not move tool window with image window > -scalebarflag <1|0> : display the scale bar > > [4157-JF-MACPRO1:FMRI/Freesurfer/subjects] foecker% tksurfer VGP01 lh > usage: tksurfer subject hemisphere surface [options] > > subject : a subject directory in the SUBJECTS_DIR path > hemipshere : rh or lh > surface : a surface file name relative to the subject's surf directory > > Options > > -title title : set window title to title. Def is subject name. > -reassign : resample labels onto surface (set vnos=-1) > -sdir <path> : sets the subjects directory path > -orig <suffix> : sets the orig suffix string > -sphere <suffix>:sets the sphere.reg suffix string > > -patch <filename> : load a patch > > -tcl <filename> : run a script > > -annotation <filename> : load an annotation > -aparc : set annotation to aparc.annot and use outline mode > -colortable <filename> : load a color table file > -labels-under : display labels under any overlay > -label-outline : draw labels as outlines > > -curv : automatically load ?h.curv > -gray : automatically load ?h.curv and make it gray > > -overlay <filename> : load an overlay volume > -overlay-reg <filename> : use a file for the overlay registration > -overlay-reg-find : look in the data directory for a register.dat > : file > -overlay-reg-identity : calculate an identity transform for registration > -mni152reg : for use with average subject when overlay is mni152 > -zm : remove mean from overlays > -fslope <value> : set the overlay threshold slope value > -fmid <value> : set the overlay threshold midpoint value > -fthresh <value> : set the overlay threshold minimum value > -foffset <value> : set the overlay threshold offset value > -colscalebarflag <1|0> : display color scale bar > -colscaletext <1|0> : display text in color scale bar > -truncphaseflag <1|0> : truncate the overlay display > -revphaseflag <1|0> : reverse the overlay display > -invphaseflag <1|0> : invert the overlay display > > -timecourse <filename> : load an timecourse volume > -timecourse-reg <filename> : use a file for the timecourse > : registration > -timecourse-reg-find : look in the data directory for a > : register.dat file > -timecourse-reg-identity : calculate an identity transform for > : regisrtation > -timecourse-offset <filename> : load an timecourse offset volume > -timecourse-offset-reg-file <filename> : use a file for the timecourse offset > : registration > -timecourse-offset-reg-find : look in the data directory for a > : register.dat file > -timecourse-offset-reg-identity : calculate an identity transform for > : registration > > -delink : do not move tool window with image window > -scalebarflag <1|0> : display the scale bar > > [4157-JF-MACPRO1:FMRI/Freesurfer/subjects] foecker% cd > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709 > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% source > example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% source > example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% source > example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% mkanalysis-sess.new > -analysis $ANALYSIS_PHASE -TR 3 -paradigm $PARADIGM_PHASE -designtype > retinotopy -fsd bold -runlistfile $RUNLIST_PHASE -tpef $TIMEEXCLUDEFILE > -funcstem fmcsm5 -ncycles 10 -motioncor -inorm -polyfit 2 -force > TIMEEXCLUDEFILE: Undefined variable. > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% source > example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% > source example_PhaseEncodedRetinotopy.csh > [4157-JF-MACPRO1:Freesurfer/sessions/ssRet_200709] foecker% surf-sess -s > $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE -retinotopy polar > grep: > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/session.info: > No such file or directory > ----------------------------------------------------------------- > surf-sess logfile is > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/log/surf-sess.AnalysisPhase.polar.log > ----------------------------------------------------------------- > ------------------------------------------------------ > ------------------------------------------------------ > Session: ssRet_200709 ---- > ------ lh hemisphere ------ > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/AnalysisPhase > ---------------------------------------------------------- > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/AnalysisPhase > tksurfer -ssRet lh inflated -tcl > /Users/foecker/Documents/freesurfer4/lib/tcl/polar-views.tcl > ---------------------------------------------------------- > > > WARNING: No colortable found! > > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_common.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_wrappers.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/fsgdfPlot.tcl > Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > tksurfer: polar-views.tcl: read and smooth complex Fourier comp > readenv.tcl: ==> read global setenv vars > readenv: set invphaseflag 0 > readenv: set fm fieldsign/fieldsignmask-lh > readenv: set angle_offset 0 > readenv: set dir > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/AnalysisPhase > readenv: set truncphaseflag 0 > readenv: set offset 0.4 > readenv: set fmid 0.8 > readenv: set fs fieldsign/fieldsign-lh > readenv: set lat > readenv: set fthresh 0.4 > readenv: set complexname -imag > readenv: set realname -real > readenv: set eccendir eccen > readenv: set floatstem map > readenv: set hemi lh > readenv: set rgbname map > readenv: set nosave 0 > readenv: set polardir polar > readenv: set noexit > readenv: set curv lh.curv > readenv: set fslope 1.3 > readenv: set colscale 0 > readenv: set smoothsteps 2 > readenv: set revpolarflag 0 > readenv.tcl: ==> read rgbname-specific setenv vars > % > tksurfer: polar-views.tcl: read curvature > surfer: current subjects dir: > /Users/foecker/Documents/Data/FMRI/Freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/AnalysisPhase > surfer: Reading header info from > /Users/foecker/Documents/Data/FMRI/Freesurfer/subjects/ssRet/mri/T1.mgz > surfer: vertices=164063, faces=328122 > surfer: single buffered window > surfer: tkoInitWindow(ssRet) > surfer: using interface > /Users/foecker/Documents/freesurfer4/lib/tcl/tksurfer.tcl > tksurfer: run tcl script: > /Users/foecker/Documents/freesurfer4/lib/tcl/polar-views.tcl > surfer: curvature read: min=-2.397066 max=4.657806 > % tksurfer: polar-views.tcl: read and smooth complex Fourier comp > surfer: smooth_val(2) > . > % tksurfer: polar-views.tcl: read and smooth real Fourier comp > surfer: smooth_val(2) > . > % tksurfer: polar-views.tcl: scale, position brain > surfer: ### GL window already open: can't open second > % tksurfer: polar-views.tcl: save rgb's > saveviews.tcl: nosave setenv'd => nothing will be saved > invalid command name "dontsave_rgb_named"% surfer: dmin=0.2470, vno=45600, > x=-9.9884, y=-67.7758, z=36.6844 > % surfer: curv=0.129080, fs=0.000000 > % surfer: val=0.085000, val2=0.865853 > % surfer: amp=0.870015, angle=84.393272 deg (0.234426) > % surfer: vertex 45600 marked (curv=0.129080, stat=0.000000) > x = (-10.0, -67.8, 36.7), n = (-0.7, -0.2, 0.6). > surfer: dmin=0.2022, vno=38559, x=-26.1600, y=-82.6320, z=-31.2516 > % surfer: curv=0.134054, fs=0.000000 > % surfer: val=1.473643, val2=1.667543 > % surfer: amp=2.225382, angle=48.532295 deg (0.134812) > % surfer: vertex 38559 marked (curv=0.134054, stat=0.000000) > x = (-26.2, -82.6, -31.3), n = (-0.9, -0.5, 0.2). > surfer: dmin=0.0986, vno=10616, x=-2.0371, y=-118.3332, z=-47.3615 > % surfer: curv=0.209849, fs=0.000000 > % surfer: val=-0.040989, val2=2.940233 > % surfer: amp=2.940519, angle=90.798691 deg (0.252219) > % > > > > On Mon, 03 Dec 2012 15:38:54 -0500 Douglas Greve <greve(a)nmr.mgh.harvard.edu> > wrote > >> Hi Julia, try using tksurfer-sess instead >> doug >> >> On 12/3/12 12:08 PM, Julia Foecker wrote: >>> Dear Doug, >>> I tried to run Freesurfer on polar angle mapping data (I do not have >>> anyeccentricity data). Therefore, I created fake runs (as it has been >>> suggested in the forum). When I try to run the following command to load >>> the maps on the surface, >>> >>> surf-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE >>> -retinotopy polar >>> >>> >>> I got the following error message: There seems to be an issue with the >>> colortables...I have seen a similar issue in the forum, but could not find >>> the answer to that question. Would you have any suggestions what I can do >>> in this case? Moreover, when the command was running I have also seen the >>> lines: > >>> >>> > MRISwriteValues(/Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/VGP01_ >>> 180112/bold/AnalysisPhase//eccen/map-imag-rh.w): val at vertex 30887 is not >>> finite > >>> >>> Not sure what this means. Would you have any advices? >>> Many thanks in advance! >>> >>> Julia >>> >>> >>> >>> >>> WARNING: No colortable found! >>> >>> Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_common.tcl >>> Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkm_wrappers.tcl >>> Reading /Users/foecker/Documents/freesurfer4/lib/tcl/fsgdfPlot.tcl >>> Reading /Users/foecker/Documents/freesurfer4/lib/tcl/tkUtils.tcl >>> Successfully parsed tksurfer.tcl >>> reading white matter vertex locations... >>> tksurfer: polar-views.tcl: read and smooth complex Fourier comp >>> readenv.tcl: ==> read global setenv vars >>> readenv: set invphaseflag 0 >>> readenv: set fm fieldsign/fieldsignmask-rh >>> readenv: set angle_offset 0 >>> readenv: set dir >>> >>> > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/VGP01_180112/bold/Anal >>> ysisPhase readenv: set truncphaseflag 0 >>> readenv: set offset 0.4 >>> readenv: set fmid 0.8 >>> readenv: set fs fieldsign/fieldsign-rh >>> readenv: set lat >>> readenv: set fthresh 0.4 >>> readenv: set complexname -imag >>> readenv: set realname -real >>> readenv: set eccendir eccen >>> readenv: set floatstem map >>> readenv: set hemi rh >>> readenv: set rgbname map >>> readenv: set nosave 0 >>> readenv: set polardir polar >>> readenv: set noexit >>> readenv: set curv rh.curv >>> readenv: set fslope 1.3 >>> readenv: set colscale 0 >>> readenv: set smoothsteps 2 >>> readenv: set revpolarflag 0 >>> readenv.tcl: ==> read rgbname-specific setenv vars >>> % >>> tksurfer: polar-views.tcl: read curvature >>> surfer: single buffered window >>> surfer: tkoInitWindow(VGP01) >>> surfer: using interface >>> /Users/foecker/Documents/freesurfer4/lib/tcl/tksurfer.tcl >>> tksurfer: run tcl script: >>> /Users/foecker/Documents/freesurfer4/lib/tcl/polar-views.tcl >>> surfer: curvature read: min=-2.640939 max=1.554826 >>> % tksurfer: polar-views.tcl: read and smooth complex Fourier comp >>> surfer: smooth_val(2) >>> . >>> % tksurfer: polar-views.tcl: read and smooth real Fourier comp >>> surfer: smooth_val(2) >>> . >>> % tksurfer: polar-views.tcl: scale, position brain >>> surfer: ### GL window already open: can't open second >>> % tksurfer: polar-views.tcl: save rgb's >>> saveviews.tcl: nosave setenv'd => nothing will be saved >>> invalid command name "dontsave_rgb_named"% >>> >>> >>> >> >> >> 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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files not in individual's folder
by Catherine Bois 04 Dec '12

04 Dec '12

I have noticed that when I reconstruct the brains (with edits) three files appear; fsaverage, lh/EC_average and rh.EC_average...I only recently noticed these and have before then been under the impression that all the useful data for analysis is in each individual's subject folder. Therefore I have not attempted to move these files when, for example, moving an individual to a new file etc. I What are these files/are they anything that I need for analysis? Thank you so, so much! Cathy

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Freesurfer December 2012