Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 05 Dec '12

05 Dec '12

It should automatically detect that this was a retinotopy analysis and then load the polar and eccen. Was this configured as a retinotopy analysis? Can you send me the $ANALYSIS_PHASE/analysis.info file? doug On 12/05/2012 04:12 PM, Julia Foecker wrote: > Hi Doug, > > I tried now several ways to get the maps on the surface: > > 1. When I am deleting -retinotopy flag and type in: > > >>> tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY >>> -analysis $ANALYSIS_PHASE > I got the message:no contrast has been specified > > (I do not have any contrasts in the analysis, just use polar angle maps) > > > 2. I tried to use the commands on the website you referred to, but I do not > have -surface in the preproc-sess (see attached) > The other commands depend on this preproc-sess command. > > > 3. I tried the following command > paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE > > > and I got the errors listed below... > > I am not sure how to procede. Would you have any further suggestions? > Many thanks, > Julia > > Thanks, > Julia

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recon-all -voxels numbers
by Sérgio Pereira 05 Dec '12

05 Dec '12

Hello, I want to run recon-all on my subjects, but my images are 256x256x176 and I would like to maintain the same resolution, but in the end I have 256x256x256. There is any way to keep the original resolution? Thank you, Sérgio Pereira

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Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 05 Dec '12

05 Dec '12

Don't use the -retinotopy flag. Look here http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis for more documentation on how to visualize the results doug On 12/05/2012 12:15 PM, Julia Foecker wrote: > sorry, there was a typo in the command line > > this is the correct version: > > > tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY -analysis > $ANALYSIS_PHASE -retinotopy polar > > Thanks, > Julia > > On Wed, 05 Dec 2012 11:01:43 -0500 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > wrote > >> Hi Julia, what is your command line when you give it the hemisphere? >> Also, when you run it, put "-debug" as the first argument and send me >> the terminal output. >> doug >> >> >> >> On 12/05/2012 10:55 AM, Julia Foecker wrote: >>> Hi Doug, >>> >>> I tried now several things to use the tksurfer command but it does not seem >>> to work. >>> >>> >>> tksurfer-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis >>> $ANALYSIS_PHASE -retinotopy polar >>> >>> >>> >>> when I run the command and just replace tksurfer, it is asking for the >>> hemisphere >>> >>> ERROR: no hemisphere specified >>> >>> >>> When I am specifying the hemisphere it does not find the command... >>> >>> I think the problem according to the colortables has been already posted in >>> the forum, but I cannot see any reply to that. It has been mentioned under >>> a different topic though (see link below). >>> >>> Thanks a lot for any advices, >>> Julia >>> >>> >>> >>> > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-April/007556.html >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On Tue, 04 Dec 2012 12:00:50 -0500 Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu> wrote >>> >>>> 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.i >>>>> nfo: 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/Anal >>>>> ysisPhase ---------------------------------------------------------- >>>>> >>>>> >>> > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/Anal >>>>> ysisPhase 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/Anal >>>>> ysisPhase 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/Anal >>>>> ysisPhase 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/ >>> >> -- >> 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/ -- 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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Re: [Freesurfer] Mssing Insula and mri_label2vol script
by José Ángel Pineda 05 Dec '12

05 Dec '12

Hi again, Sure I did set the permissions for execution, and also for this new one I am still having the same error. "*Exec format error. Binary file not executable*". I tried this on two macs (OSX Snow Leopard). I am still thinking that this is a compilation issue of the script, that is just compiled for linux. Thanks for your help > Try this one > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol… > > On 12/04/2012 12:13 PM, Sarosh, Cyrus wrote: > > Doug, > > > > I am unsure if Jose did this in his attempts to get it to work, but I > ran this command after downloading and receiving this error initially and > even after running this command I still receive the same error in the > Windows virtual machine version of FreeSurfer. Any other ideas? > > > > Thanks, > > > > Cyrus > > > > -----Original Message----- > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto: > freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > > Sent: Tuesday, December 04, 2012 11:58 AM > > To: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] (no subject) > > > > Hi Jose, did you set the permissions to be executable? > > chmod a+x mri_label2vol > > doug > > > > > > On 12/04/2012 11:34 AM, Sarosh, Cyrus wrote: > >> Doug, > >> > >> I am also curious about this mri_label2vol upgrade. Will this work on > >> the Windows virtual machine version of FreeSurfer? I downloaded and > >> placed it in the FREESURFER/bin directory, but when trying to run it I > >> receive an error that states: Exec format error. Binary file not > >> executable. Thanks for your help. > >> > >> Cyrus > >> > >> *From:*freesurfer-bounces@nmr.mgh.harvard.edu > >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Jos? > >> ?ngel Pineda > >> *Sent:* Tuesday, December 04, 2012 9:07 AM > >> *To:* freesurfer(a)nmr.mgh.harvard.edu > >> *Subject:* [Freesurfer] (no subject) > >> > >> 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_labe > >> l2vol > >> > >> 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 > >

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Re: [Freesurfer] Extracting resting state time series from surface space using Lausanne 2008 parcellation
by Chris McNorgan 05 Dec '12

05 Dec '12

Thanks, Doug That was quite helpful, and I have just extracted the mean timeseries from one of my parcellations. I just wanted to note a discrepancy between the mri_segstats output and what is indicated in the mri_segstats --help output. According to the program help: --avgwf textfile For each segmentation, compute an average waveform across all the voxels in the segmentation (excluding voxels masked out). The results are saved in an ascii text file with number of rows equal to the number of frames and number of columns equal to the number of segmentations reported plus 2. The first row is -1 -1 then all of the segid numbers. After that, the first two columns are: (1) 0-based frame number and (2) 0-based frame number times TR. However when I open the textfile, the average timeseries data appears to be there, but the column and row data indicating the segid and frame numbers and timings are missing. In other words, according to the --help description, there should be TR rows and SEGIDs+2 columns, but I instead have a TR x SEGID matrix (also, I would have thought that there should be TR+1 rows, to allow for the first row to contain the SEGIDs, followed by TR rows of signal data; is that a typo in the help information?). "-1 -1" doesn't appear anywhere in the output. I assume that the columns are written in ascending SEGID order, but I cannot be certain because the first row does not contain the SEGIDs. These problems don't seem insurmountable so long as I am clear as to which matrix entry corresponds to which SEGID at which timepoint. Any idea why the header row and two leftmost frame number and timing columns were omitted from the output? Thanks ================================================================================ Hi Chris, you're almost there. There are a few mods I'd make to your stream: 1. You can run preproc-sess -s subXX -fsd rest -surface self lhrh -fwhm 0 (without the -mni305 since you are working in the subject's anatomy) 2. mri_segstats \ --annot subXX lh myaparcPXXXXXX \ --i $FUNCTIONALS_DIR/subXX/rest/001/fmcpr.lh.self.nii.gz \ --sum lh_1_16.sum.txt \ --avgwf lh_1_16.wav.txt So you pass mri_segstats the surface data and the annotation doug

2 1

Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 05 Dec '12

05 Dec '12

Hi Julia, what is your command line when you give it the hemisphere? Also, when you run it, put "-debug" as the first argument and send me the terminal output. doug On 12/05/2012 10:55 AM, Julia Foecker wrote: > Hi Doug, > > I tried now several things to use the tksurfer command but it does not seem to > work. > > > tksurfer-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE > -retinotopy polar > > > > when I run the command and just replace tksurfer, it is asking for the > hemisphere > > ERROR: no hemisphere specified > > > When I am specifying the hemisphere it does not find the command... > > I think the problem according to the colortables has been already posted in the > forum, but I cannot see any reply to that. It has been mentioned under a > different topic though (see link below). > > Thanks a lot for any advices, > Julia > > > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-April/007556.html > > > > > > > > > > > > > > On Tue, 04 Dec 2012 12:00:50 -0500 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > wrote > >> 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.i >>> nfo: 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/Anal >>> ysisPhase ---------------------------------------------------------- >>> >>> > /Users/foecker/Documents/Data/FMRI/Freesurfer/sessions/ssRet_200709/bold/Anal >>> ysisPhase 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/Anal >>> ysisPhase 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/Anal >>> ysisPhase 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/ > > -- 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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Mindboggle-101 manually labeled brain data now available! {Disarmed}
by Arno Klein 05 Dec '12

05 Dec '12

We are happy to announce the release of the Mindboggle-101 dataset, the largest and most complete set of free, publicly accessible, manually labeled human brain images in the world: http://mindboggle.info/data/ This has special relevance to the FreeSurfer community, since we made use of FreeSurfer to extract and label surfaces, and to create surface templates and classifier atlases. We also adapted the Desikan-Killiany labeling protocol used by FreeSurfer. An article describing the data and labeling protocol has just been published: http://www.frontiersin.org/brain_imaging_methods/10.3389/fnins.2012.00171/f… An excerpt of the abstract reads: "To manually label the macroscopic anatomy in magnetic resonance images of 101 healthy participants, we created a new cortical labeling protocol that relies on robust anatomical landmarks and minimal manual edits after initialization with automated labels. The “Desikan–Killiany–Tourville” (DKT) protocol is intended to improve the ease, consistency, and accuracy of labeling human cortical areas. Given how difficult it is to label brains, the Mindboggle-101 dataset is intended to serve as brain atlases for use in labeling other brains, as a normative dataset to establish morphometric variation in a healthy population for comparison against clinical populations, and contribute to the development, training, testing, and evaluation of automated registration and labeling algorithms..." Cheers, @rno arno klein arno(a)binarybottle.com<https://mail.google.com/mail/?view=cm&fs=1&tf=1&to=arno@binarybottle.com> http://www.binarybottle.com -- research asst professor psychiatry & behavioral science stony brook university

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Error upon trying to load NIFTI image in freeview
by Tudor Popescu 05 Dec '12

05 Dec '12

Hi everyone, I tried opening a NIFTI (.nii.gz) image in freeview, but it gives me repeated "Failed to load <image name>" errors. That same image loads fine in FSLview, but even when trying with other NIFTI images, I get the same error. The default image (/home/virtualuser/freesurfer/subjects/bert/mri/brainmask.mgz) opens fine in freeview. I use FreeSurfer v5.1.0 on Xubuntu 9.10, running through VirtualBox on WinXP. Many thanks for any help! Tudor

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Re: [Freesurfer] recon-all unable to make pial and white surfaces
by Sebastian Moeller 04 Dec '12

04 Dec '12

Hi Negar, I guess this is where I have to leave the issue to Nick and Bruce as I am way out of my league here :). It would have been nice if switching to 64bit free surfer would have fixed the issue. One observation though, it looks like you are using the bert subject that was distributed with free surfer 4.5.0 (otherwise the first successful rte con in your log does not make any sense), maybe that is somewhere corrupted? Then you can try to copy bert from FS 5.1.0 into your $SUBJECTS_DIR and try again, on the remote chance that something with the bert data is off.. On that note: "setenv SUBJECTS_DIR /mnt/hgfs/LinuxShare/subjects4freesurfer" it seems you have your data sitting somewhere else (a network share perhaps from a windows host?) try to direct $SUBJECTS_DIR to "/usr/local/freesurfer/subjects" to a) use the bert data distributed with fs 5.1 and b) rule out any network/remote filesystem capabilities issues. But no guarantee :) Best Sebastian On Dec 4, 2012, at 16:10 , Negar Memarian wrote: > Hi Nick, Sebastian, > > Thank you for your replies. I am actually using the 64bit version. The info indicating 32bit in the header of the log file was old (from when I had tried an Ubuntu VM to do the same thing on this subjects and it never worked). So right now, I am indeed using a 64 bit Centos VM (freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20090807). I removed all my old files and started fresh with the bert subject as Nick had advised. . Unfortunately it crashes again at the same place. The new recon-all log (for bert) is attached. > > I really do not understand why this is happening. Why is it crashing despite running the 64bit version and 6GB of ram? Please note that I can view images (tkmedit), I can import images (recon-all -i), it just crashes during recon-all -all. This is really important for me and I greatly appreciate any suggestion/idea. > > Best regards, > Negar > > On Tue, Dec 4, 2012 at 3:30 PM, Sebastian Moeller <sebastian.moeller1(a)rwth-aachen.de> wrote: > Hi Nick, > > > On Dec 4, 2012, at 14:41 , Nick Schmansky wrote: > > > Negar, > > > > This appears to be a strange problem. From the recon-all.log file, the > > important error is this one: > > > > GCAread(/usr/local/freesurfer/average/RB_all_2008-03-26.gca): couldn't > > expand gcs to 1114693712 > > > > which means it failed to alloc the 1.2GB needed to load the atlas. but > > given that earlier in the log it says that there is 6974628 (6GB) free, > > it would seem that there is plenty of memory. > > well, but not for the 32bit freesurfer binaries, given a bit of memory fragmentation and a bit data already in memory before and getting 1.2 out of probably 2 can get quite challenging. So at this point I would bet that the 64bit distribution will fix his problem… > > best > Sebastian > > > > i would try two things: > > > > - first try running recon-all -s bert -all, where you can copy the > > subject 'bert' from freesurfer/subjects, to see if it fails as well. > > > > - then per sebastians suggestion, download and install the 64b centos > > freesurfer build. you can do that within your vm. your existing 32b > > should work so i am doubtful that 64b will work, but at the moment i'm > > at a loss as to the problem. > > > > nick > > > > > > > > On Tue, 2012-12-04 at 12:35 -0800, Sebastian Moeller wrote: > >> Hi Negar, > >> > >> > >> On Dec 4, 2012, at 12:19 , Negar Memarian wrote: > >> > >>> Hi Sebastian, > >>> > >>> Thank you for your reply. The virtual machine that I'm using was built by a friend who also uses FreeSurfer and I copied it entirely onto my computer (a huge folder, 263GB). Freesufer works just fine for him. So whatever version of Freesurfer he's using, it's working for him and I'm basically replicating exactly what he has on his computer and yet not able to complete the recon-all -all process. Any ideas? > >> > >> Sorry, no real idea. But can you have your friend run your subjects under his installation (I assume you are not trying to recon subjects that your friend already suddessfully reconned)? I assume that it will also fail, as the amount of memory required of some steps (not necessarily of the one that fails for you, I do not really know the free surfer code base well enough (read at all :) ) to judge). So if it also fails for the same subject for him, then I would really recommend to install the 64 bit free surfer version (can be installed in parallel so you can switch between the two) and these that. Testing the 64bit version seems like a no brainer to me, as your failure just takes around 3 minutes to materialize… But I am already at the end of my knowledge here… > >> > >> > >>> > >>> Thank you, > >>> Negar > >>> > >>> On Tue, Dec 4, 2012 at 10:57 AM, Sebastian Moeller <sebastian.moeller1(a)rwth-aachen.de> wrote: > >>> Hi Negar, > >>> > >>> from your log file: > >>> build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.1.0 > >>> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux > >>> > >>> So it looks like you are running the 32bit free surfer version which will be limited to >= 4GB addressable memory, most likely only 2GB. You might want to try again using: > >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux… > >>> That way your memory increase might actually have a chance affecting the free surfer processes :) > >>> > >>> > >>> Best > >>> Sebastian > >>> > >>> > >>> > >>> On Dec 4, 2012, at 09:41 , Negar Memarian wrote: > >>> > >>>> Hello, > >>>> In the VM setting, I increased the RAM to 8 GB (my computers' maximum) and increased number of working CPUs to 4. Unfortunately the crash still happens in the "EM Registration" stage with a similar error, i.e., > >>>> gcaAllocMax: node dims 64 64 64 > >>>> gcaAllocMax: prior dims 128 128 128 > >>>> gcaAllocMax: max_labels 0 > >>>> Cannot allocate memory > >>>> Linux VMprivate 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 EST 2012 x86_64 x86_64 x86_64 GNU/Linux > >>>> recon-all -s testimport exited with ERRORS at Mon Dec 3 16:38:39 PST 2012 > >>>> I have attached a screenshots of the result of "top" command, as well as the VM's system monitor graphs during the recon-all process before it crashed. I have also attached the recon-all.log file. > >>>> Would you kindly bring this question to the attention of Nick and PPJ? I really need to get this to work. > >>>> > >>>> Best regards, > >>>> Negar > >>>> > >>>> On Mon, Dec 3, 2012 at 5:42 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >>>> Hi Negar > >>>> > >>>> perhaps Nick or PPJ can comment on how much a virtual box needs? In any case, try increasing the ram and see what happens as the error message is pretty clear. Also, if you can run "top" or something similar (/usr/bin/free) to see how memory is actually available on the system that would help > >>>> > >>>> cheers > >>>> Bruce > >>>> > >>>> On Sat, 1 Dec 2012, Negar Memarian wrote: > >>>> > >>>> Thank you for your reply, Bruce. I'm running FreeSurfer using a VMWare > >>>> virtual machine on Windows 7. I've set the settings of the VM to use 2 CPUs > >>>> and 6GB ram. Here is the specifications of my computer hardware: > >>>> OS: Windows 7 professional > >>>> Processor: Intel Core i7-3770 CPU @ 3.40 GHz > >>>> RAM: 8 GB > >>>> System type: 64 bit > >>>> > >>>> Please let me know if you need any other info. Many thanks for your help. > >>>> -Negar > >>>> > >>>> > >>>> On Sat, Dec 1, 2012 at 11:52 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >>>> wrote: > >>>> can you check to see how much you actually have free? You are > >>>> definitely running out of memory, so something else is using it. > >>>> What is your hardware/software environment? > >>>> > >>>> On Sat, 1 Dec 2012, Negar Memarian wrote: > >>>> > >>>> No, I tried running just one recon and I only have > >>>> one xterm window open. > >>>> Anything I can do to fix this? > >>>> > >>>> > >>>> > >>>> On Sat, Dec 1, 2012 at 11:11 AM, Bruce Fischl > >>>> <fischl(a)nmr.mgh.harvard.edu> > >>>> wrote: > >>>> 6G should be plenty. Do you have anything else > >>>> running? Maybe > >>>> another recon at the same time? > >>>> On Fri, 30 Nov 2012, Negar Memarian wrote: > >>>> > >>>> Hi Bruce, > >>>> I have 8 GB ram and have assigned 6GB of > >>>> it to > >>>> FreeSurfer. Shall I increase > >>>> it to 8? Would that be enough or still > >>>> too low? > >>>> > >>>> Thank you, > >>>> Negar > >>>> > >>>> > >>>> On Fri, Nov 30, 2012 at 7:31 PM, Bruce > >>>> Fischl > >>>> <fischl(a)nmr.mgh.harvard.edu> > >>>> wrote: > >>>> Look like it is running out of > >>>> memory. How > >>>> much ram do you have > >>>> on that machine? > >>>> Bruce > >>>> > >>>> > >>>> > >>>> On Nov 30, 2012, at 9:29 PM, Negar > >>>> Memarian > >>>> <negar.memarian(a)utoronto.ca> > >>>> wrote: > >>>> > >>>>> Hello, > >>>>> > >>>>> I ran recon-all -all on my > >>>> subject. The > >>>> process ended after > >>>> several minutes with this message > >>>> at the end: > >>>>> recon-all -s 350_FS exited with > >>>> ERRORS at > >>>> Fri Nov 30 17:57:59 > >>>> PST 2012 > >>>>> > >>>>> I tried loading the pial and > >>>> white surfaces > >>>> for editing using > >>>> this command: > >>>>> tkmedit 350_FS brainmask.mgz > >>>> rh.white > >>>> -aux-surface lh.white > >>>>> > >>>>> but looks like these surfaces do > >>>> not exist > >>>> (since the > >>>> recon-all exited prematurely). > >>>> When I check > >>>> the recon-all.log > >>>> file I do not see any errors > >>>> except a few > >>>> MCSRCH errors. So I > >>>> cannot understand what exactly > >>>> went wrong in > >>>> the recon-all. I've > >>>> attached the recon-all log file. > >>>> Can someone > >>>> please tell me what > >>>> the problem is and how I can fix > >>>> it? > >>>>> > >>>>> Many thanks, > >>>>> Negar > >>>>> p.s. I tried on more than one > >>>> subject and I > >>>> still face the > >>>> same issue. > >>>>> > >>>>> > >>>>> Negar Memarian, MASc, PhD > >>>>> NSERC Postdoctoral Fellow > >>>>> Department of Neurology > >>>>> David Geffen School of Medicine > >>>> at UCLA > >>>>> > >>>>> <recon-all.log> > >>>>> > >>>> > >>>> _______________________________________________ > >>>>> 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. > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> <screeshot-top.JPG><recon-all.log>_______________________________________________ > >>>> 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. > >>> > >>> -- > >>> Sebastian Moeller > >>> > >>> telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 > >>> fax: 626-395-8826 > >>> German GSM: +49 - 15 77 - 1 90 31 41 > >>> mobile: +1-626-325-8598 > >>> +1-626-807-5242 > >>> US CDMA: +1-626-807-5242 > >>> moeller(a)caltech.edu > >>> > >>> Division of Biology > >>> MC 114-96 > >>> California Institute of Technology > >>> 1200 East California Boulevard > >>> CA 91125, Pasadena > >>> USA > >>> > >>> > >>> _______________________________________________ > >>> 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. > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Sebastian Moeller > > telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 > fax: 626-395-8826 > German GSM: +49 - 15 77 - 1 90 31 41 > mobile: +1-626-325-8598 > +1-626-807-5242 > US CDMA: +1-626-807-5242 > moeller(a)caltech.edu > > Division of Biology > MC 114-96 > California Institute of Technology > 1200 East California Boulevard > CA 91125, Pasadena > USA > > > <recon-all.log> -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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recon-all unable to make pial and white surfaces
by Negar Memarian 04 Dec '12

04 Dec '12

Hello, I ran recon-all -all on my subject. The process ended after several minutes with this message at the end: recon-all -s 350_FS exited with ERRORS at Fri Nov 30 17:57:59 PST 2012 I tried loading the pial and white surfaces for editing using this command: tkmedit 350_FS brainmask.mgz rh.white -aux-surface lh.white but looks like these surfaces do not exist (since the recon-all exited prematurely). When I check the recon-all.log file I do not see any errors except a few MCSRCH errors. So I cannot understand what exactly went wrong in the recon-all. I've attached the recon-all log file. Can someone please tell me what the problem is and how I can fix it? Many thanks, Negar p.s. I tried on more than one subject and I still face the same issue. Negar Memarian, MASc, PhD NSERC Postdoctoral Fellow Department of Neurology David Geffen School of Medicine at UCLA

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