Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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.

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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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Extracting resting state time series from surface space using Lausanne 2008 parcellation
by Chris McNorgan 04 Dec '12

04 Dec '12

Hi all. I have a question regarding the use of freesurfer + fs-fast preprocessing to apply the Lausanne 2008 parcellation scheme to some structural data, and then extract from those ~1000 ROIs the average time series from a 4D resting state functional run. I'm posting what I have carried out so far, both to verify that I haven't missed anything important, but also because I have seen evidence within this and other mailing lists that others are interested in doing something similar. This thread may then answer their questions as well. Structural and functional data is in $SUBJECTS_DIR/sub00?/mri and $FUNC_DIR/sub00?/rest, respectively For each subject: * I carried out recon-all -autorecon1, -autorecon2, -autorecon 3, checking data quality in between * inspected ?h.aparc.annot, possibly made minor edits ( https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit) * used cmtk.Parcellate() with the Lausanne 2008 scheme ( https://groups.google.com/forum/#!topic/cmtk-users/k_o3s8Yy2jQ) <https://groups.google.com/forum/#%21topic/cmtk-users/k_o3s8Yy2jQ> * This created a number of .label files and some .annot files, notably ?h.myaparcP*.annot, which have sub-parcellations of the 1-16, 17-28 and 29-36 regions indicated in the ?h.aparc.annot files (I'm not entirely clear why they couldn't just go into a single .annot file) * Converted the .annot files to surface space using mri_aparc2aseg --subXX --annot myaparcPXXXXXX which generated myaparcPXXXXX+aseg.mgz (3 files total, as each of three sets of lh and rh annot files describe both hemispheres in a single file) * ran each of the functional runs through: preproc-sess -s subXX -fsd rest -surface self lhrh -mni305 -fwhm 0 That brings me to my question. I have my functional data: $FUNC_DIR/subXX/rest/001/fmcpr.siemens.sm0.mni305.2mm.nii.gz (I also have 2 fmcpr.siemens.sm0.self.?h.nii.gz files, but they didn't work either) I want to pull the average timeseries data for the functional data out of the ROIs defined in myaparcP1_17+aseg.mgz (and similarly for the other two myaparcP*.mgz files) I tried mri_segstats \ --seg $SUBJECTS_DIR/subXX/mri/myaparcP1_16+aseg.mgz \ --i $FUNCTIONALS_DIR/subXX/rest/001/fmcpr.siemens.sm0.mni305.2mm.nii.gz \ --annot subXX lh lh.myaparcP1_16.annot \ --sum lh_1_16.sum.txt \ --avgwf lh_1_16.wav.txt However, this gave me the following output: sysname Linux hostname Sage machine x86_64 user chris Loading /home/chris/resting/anat/subXX/mri/myaparcP1_16+aseg.mgz Loading /home/chris/resting/func/subXX/rest/001/fmcpr.siemens.sm0.mni305.2mm.nii.gz ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 256 256 256 I then tried resampling my resting state data with mri_vol2vol using my func data as the --mov parameter, and my myaparc files as the --targ parameter, and used tkregister2 on the resampled volume. mri_segstats just hung when I ran it on the resampled volume; by the next morning nothing had been written to either text output file. I can open my ?h surface files in tksurfer, and then load in the appropriate timecourse ($FUNCTIONALS_DIR/subXX/rest/001/fmcpr.siemens.sm0.self.?h.nii.gz) and when I do so, I can click on various vertices and see timecourse plots. And I can paint my surfaces with .annot files that define my ROIs. So it seems I should be able to get these timecourse data from ROIs in surface space without making a thousand individual ROIs in volumetric space (my guess is I'd use flsmaths on my myaparc files to do this). But I am not clear if mri_segstats can be used in this way, or if indeed it is the appropriate tool. Any assistance to get me through this last step would be appreciated. Thanks

2 1

wmparc 2 wmsurf
by Juranek, Jenifer 03 Dec '12

03 Dec '12

I'm running FSv5.1.0 on RHEL6. 1) My goal is to run a glm-fit on White Matter aparc regions for a "between group" surf-based analysis and evaluate spatial maps of significant differences. 2) I noticed that fsaverage does not have a wmparc.mgz file, so I'm currently working with bert as my subject. 3) I'd like to visualize each segid in the wmparc.mgz (volume-based) file on the white matter surface in the same subject (e.g. bert). 4) I have been able to breakdown bert's wmparc.mgz file into separate masks (e.g. *.mgz) and labels (e.g. *.label) based on segid using mri_cor2label and mri_vol2surf. To get the vertices written into the label file, I have loaded each label and re-saved each label in tksurfer. Q: Is there a better method for getting this (wmparc units moved from vol to surf) done (maybe using a matlab function?) Or is surf-based analysis of white matter not such a good idea. Many Thanks for any assistance you can provide. Cheers, Jenifer ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Jenifer Juranek, PhD University of Texas at Houston

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Reducing pial and main surfaces
by Jonathan Holt 03 Dec '12

03 Dec '12

I have not seen a lot of documentation on how to do this. I've attached two images of specific areas where I'd like to have the pial and main surfaces follow the actual surface of the brain. The aux volume OK in both of these cases. The empty space is segmented as white matter. In the past I have tried deleting the segmentation values and saving the segmentation, then running recon-all -autorecon2 -autorecon3 -s <subjid>. Unfortunately it just resegmented the same areas as white matter and the issue was never resolved. I know about freeview but I do not know how to manually edit surfaces... What should I be doing here? jon

2 1

Insula missing
by José Ángel Pineda 03 Dec '12

03 Dec '12

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 [image: Imágenes 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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hippocampal subfield segmentation
by Antonella Kis 03 Dec '12

03 Dec '12

Dear FS team, I would like to know if there is any options to get the hippocampal subfield segmentation so I can get the volume for each segmentation if I was running only recon-all for all my subjects or I need to re-run recon-all but with a hippocampal subfield segmentation option this time? Many thanks, Antonella

2 1

missing brain
by Catherine Bois 03 Dec '12

03 Dec '12

Hi, I am currently in the process of reconstructing my brains after edits. However, the brains keep being reconstructed with large portions of brain missing/cerebellum missing; ie they are much worse than before I edited them. However, I am sure that I have only put control points in white matter areas; ie not partial volume, so I am very confused as to why this is happening; in one brain for example I had not put any cotnrol points (only made a very small white matter edit). Has this happened to anyone else before? Am i somehow running the wrong command somewhere? Could the watershed be wrong in the script, ie accidentally changed? Grateful for help, Regards Cathy

2 1

aseg.stats
by charles laidi 03 Dec '12

03 Dec '12

Dear freesurfers. I'm using freesurfer for two weeks. I'm currently trying to make a script to get asegstats resultats for >100 patients. I did this script in tcsh : foreach filename (t1_????????) asegstats2table --subjects ${filename} \ --segno 12 18 14\ --tablefile asegstats.txt end The problem is that at each loop, the n+1 subject replace the n subject, so at the end I only have the asegstats for the last subject. When I am replacing t1_???????? (it's a wild card) by t1_63537193 t1_18394856 the result is fine so the question is : how to make a loop without over writing the n result by the n+1 result Thanks very much for you help Sincerely yours, Charles Laidi

2 1

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