Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

cortical thickness maps and some cortical thickness comparison analysis
by Renat Yakupov 01 Jul '05

01 Jul '05

Hello, everybody. In 2004 FreeSurfer course lecture slides by D Salat, B Fischl and D Greve there are a couple of slides I am curious about. These are slides # 65 and #66 named correspondingly "Thickness maps" and "Thinning from young to old age". Have those images been produced by FreeSurfer or some other tool? If it is images from FreeSurfer, how do I get them? Is there a way to do some group comparison or averaging with *.thickness surface files? And displaying it afterwards? Thank you. Regards, Renat.

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RE: [Freesurfer] mri_vol2surf
by Fornito, Alexander 01 Jul '05

01 Jul '05

Hi Doug, I tried the tkmedit command and it loaded the volume with the mask, although I got a message saying: Error: Parsing command line options Option -reg not recognized This option was not recognized and ignored. Not sure why this occurred, as I loaded it from scratch through the GUI (File > Load Overlay Data, with the mask as the volume and register.dat as the registration file) and it produced the same with no error. In any case, I can see from tkmedit that the mask is not where it should be (It's in the neck, where it should be in the cingulate, above the corpus callosum). However, I tried running tkregister as you suggested to me, and although the GUI pops up, I'm unable to see the movable volume (ie., the mask). This has happened to me before when i tried something else in tkregister, and am not sure if I'm doing anything wrong. The output is below. Thanks for your help, Alex. tkregister2 --s ./1000186 --mov ./186_corconv_mask.img --reg ./register.dat --regheader INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./186_corconv_mask.img reg file ./register.dat LoadVol 1 $Id: tkregister2.c,v 1.22 2003/11/05 21:30:50 greve Exp $ Diagnostic Level -1 INFO: analyzeRead(): found 1 files for ./186_corconv_mask.img ----------------------------------------------------------------- INFO: could not find ./186_corconv_mask.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ./186_corconv_mask.mat file ----------------------------------------------------------------- INFO: loading target /data/flanders/work/alex/freesurfer/subjects/./1000186/mri/orig INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ./186_corconv_mask.img INFO: analyzeRead(): found 1 files for ./186_corconv_mask.img ----------------------------------------------------------------- INFO: could not find ./186_corconv_mask.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ./186_corconv_mask.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 1 INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 -0.000; 0.000 -1.000 0.000 0.000; 0.000 0.000 0.000 1.000; --------------------------------------- subject = ./1000186 Zoom Factor = 2 ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 -0.000; 0.000 -1.000 0.000 0.000; 0.000 0.000 0.000 1.000; Opening window ./1000186 Setting scale tkregister2: interface: /usr/local/freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro} -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Fri 7/1/2005 12:47 PM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mri_vol2surf The first thing that you should do is load your mask as an overlay in tkmedit to make sure that it is actually falling where you think it is: tkmedit yoursubject orig -overlay ./mask.img -reg ./register.dat \ -fthresh 0.5 The fthresh is set assuming your mask is 0 or 1. You can even load the surface to see if it actually inersects. If this fails, then you need a new registration file. You can create this with: tkregiser2 --s yoursubject --mov mask.img --reg reg.dat --regheader tkregiser2 allows you to interactively change the registration. Note that you only use --regheader the first time you run it (ie, before you have a reg.dat). doug On Fri, 1 Jul 2005, Fornito, Alexander wrote: > Sorry, I forgot to mention, I have the mask in analyze format (I traced it in another program). I ran mri_vol2surf using the register.dat file format that Doug provided, and got the output below. Although it creates a .w file, nothing happens when I load it in tksurfer, I'm gessing because the vertex values are zero (?). Have I done something wrong? > > mri_vol2surf --src 186_corconv_mask --src_type analyze --srcreg register.dat --hemi lh --out ./186_mask_surf.w --out_type paint > INFO: output format is paint > srcvol = 186_corconv_mask > srctype = analyze > srcreg = register.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > interp = nearest > float2int = round > INFO: float2int code = 0 > INFO: analyzeRead(): found 1 files for /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask > ----------------------------------------------------------------- > INFO: could not find /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask.mat file for direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). > INFO: if not valid, please provide the information in /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask.mat file > ----------------------------------------------------------------- > INFO: analyzeRead(): min = 0, max = 1 > INFO: chaning type to float > Done loading volume > Reading surface /data/flanders/work/alex/freesurfer/subjects/1000186/surf/lh.white > Done reading source surface > Mapping Source Volume onto Source Subject Surface > vol2surf_linear: nhits = 152789/152789 > Done mapping volume to surface > Number of source voxels hit = 96553 > Warning: all vertex values are zero > > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Fri 7/1/2005 11:06 AM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_vol2surf > Hi Alex, > > I think you can just load the label into tksurfer (file->label->load) and > it will sample it onto the surface, assuming that it was drawn on one of > the volumes that the surface was created from (or a coregistered one). > The 1st time you do this it may take a bit, but if you save it again it > will save the vertex #s. > > cheers, > Bruce > > > On Fri, 1 Jul 2005, Fornito, Alexander wrote: > >> Hi, >> I'm trying apply ROI masks that I've manually traced in volume space to the same image's surface using mri_vol2surf. mri_vol2surf seems to requires a register.dat file, and I'm unsure what needs to be registered, since the volume that I traced the masks on is exactly the same as the one that I began with to create the surface (so presumably they are in the same space?) . Any hints would be appreciated. >> Thanks, >> Alex >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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RE: [Freesurfer] mri_vol2surf
by Fornito, Alexander 30 Jun '05

30 Jun '05

Sorry, I forgot to mention, I have the mask in analyze format (I traced it in another program). I ran mri_vol2surf using the register.dat file format that Doug provided, and got the output below. Although it creates a .w file, nothing happens when I load it in tksurfer, I'm gessing because the vertex values are zero (?). Have I done something wrong? mri_vol2surf --src 186_corconv_mask --src_type analyze --srcreg register.dat --hemi lh --out ./186_mask_surf.w --out_type paint INFO: output format is paint srcvol = 186_corconv_mask srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask ----------------------------------------------------------------- INFO: could not find /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /data/flanders/work/alex/freesurfer/subjects/186_corconv_mask.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 1 INFO: chaning type to float Done loading volume Reading surface /data/flanders/work/alex/freesurfer/subjects/1000186/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 152789/152789 Done mapping volume to surface Number of source voxels hit = 96553 Warning: all vertex values are zero -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 7/1/2005 11:06 AM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Hi Alex, I think you can just load the label into tksurfer (file->label->load) and it will sample it onto the surface, assuming that it was drawn on one of the volumes that the surface was created from (or a coregistered one). The 1st time you do this it may take a bit, but if you save it again it will save the vertex #s. cheers, Bruce On Fri, 1 Jul 2005, Fornito, Alexander wrote: > Hi, > I'm trying apply ROI masks that I've manually traced in volume space to the same image's surface using mri_vol2surf. mri_vol2surf seems to requires a register.dat file, and I'm unsure what needs to be registered, since the volume that I traced the masks on is exactly the same as the one that I began with to create the surface (so presumably they are in the same space?) . Any hints would be appreciated. > Thanks, > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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mri_vol2surf
by Fornito, Alexander 30 Jun '05

30 Jun '05

Hi, I'm trying apply ROI masks that I've manually traced in volume space to the same image's surface using mri_vol2surf. mri_vol2surf seems to requires a register.dat file, and I'm unsure what needs to be registered, since the volume that I traced the masks on is exactly the same as the one that I began with to create the surface (so presumably they are in the same space?) . Any hints would be appreciated. Thanks, Alex

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generate label files
by Kirk, Gregory 30 Jun '05

30 Jun '05

A while ago Dr. Fischl sent me - use mris_anotomical_stats -l <label file> to get stats for a region. I have not found how to create these label files. Can somebody give me a starting hint. Thankx Greg.

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Freesurfer Conversion Difficulties
by David Soscia 30 Jun '05

30 Jun '05

Hey guys, After some help from Andy Bell, I was able to get one of my images converted from .dcm format, up and running with the program. For some reason now, I keep getting the same error message when trying to convert some other files (in a different location to COR format). It keeps saying "unknown file type for file 00000001.dcm" which is completely odd because I successfully converted a set of dicom images just 2 days ago. Here is what I type in... "mri_convert --out_type cor 00000001.dcm /home/amc/dave/ND167FU-4/mri/orig" ...... where 00000001.dcm is the first file name in the set, and /home/amd/dave/DN167FU-4/mri/orig is the output directory. I also made sure I changed the directory to the location of the files before conversion. If anyone has seen this before, or knows what to do, let me know please. Thanks. Dave Soscia

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MRInormalize failure
by Toshihiko Aso 30 Jun '05

30 Jun '05

Hi, I encounter the error in processing one of my MPRAGE brain image. MRInormalize: could not find any valid peaks I found the previous post suggesting to add the -no1d option, but it doesn't work, the same error message. I use the 2004 snapshot version on Fedora Core 3, getting successful results on other images but this one. Another suggestion was to check the talairach.xfm. Should I use the MNI tools for this problem? I figured I can live without the tools, especially after having no luck with installing them... Are there any workaround for this, and which part of the documents should I read to understand the nature of this "valid peak" problem? Best regards, Toshihiko Aso Human Brain Research Center Kyoto University School of Medicine

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reconstruction problem
by Michele Perry 29 Jun '05

29 Jun '05

I am trying to recon a sagittal T1 series from a functional scan, originally in AFNI format. I converted it to COR using mri_convert -it brik /path/to/<file>.BRIK $SUBJECTS_DIR/subjid/mri/orig The first run of recon-all -stage1 (-nomotioncor) exited with errors (mri_fill exited with non-zero status). It said that the cerebellum may be attached and then had messages related to rh and lh wm seed points so I ran recon-all with -cc-xyz, -rh-xyz, -lh-xyz and -pons-xyz. That finished without errors. When I tried csurf after that, the wm was mainly in the cerebellum, not a whole lot anywhere else. I was advised to check the T1 to make sure the T1 wm intensities were close to 110. Those intensities are close to 110. Any idea what might be wrong with this data or with my processing? Thank you for your help, Michele

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RE: [Freesurfer] mris_glm
by Fornito, Alexander 28 Jun '05

28 Jun '05

Hi again, I've been playing around with the other segmentation fault I was getting (stage 1 recon-all with the 3T images). I've noticed that my 1.5T images (with which I have no problems) are coronally acquired, 256 x 256 x 123 (x, y, z) , voxel size 0.9 x 0.9 x 1.5, 16 bit. My 3Ts are 512 x 512 x 124, coronally acquired, voxel size 0.6 x 0.6 x 1.7, 16 bit. It seems the FOV is too big, since mri_convert ends up producing a COR image with 330 slices instead of 256. I registered and resmapled the 3T to one of my 1.5Ts using a 6 parameter rigid body registration in AIR so that the 3T took on the properties of the 1.5T (ie., it became 256 x 256 x 123, 0.9 x 0.9 x 1.5). recon-all -stage1 only worked if I converted the resampled image to 8 bit. If I tried to run it on the 16bit image, the intensity normalization failed. The relevant output is below. Do images need to be in a certain format before mri_convert can convert them to COR format successfully? Thanks again for all your help, Alex Intensity Normalization Tue Jun 28 14:40:54 EST 2005 /data/flanders/work/alex/freesurfer/subjects/mw_3T_2_186/mri mri_normalize orig T1 reading from orig... normalizing image... talairach transform 1.051 0.565 0.381 -29.026; -0.317 1.126 -0.797 -10.790; -0.719 0.586 1.113 -42.660; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory ERROR: mri_normalize exited with non-zero status ------------------------------------------ Filesystem 1k-blocks Used Available Use% Mounted on /dev/hda9 130282400 12379432 111284996 11% /data/flanders ------------------------------------------ recon-all exited with errors at Tue Jun 28 14:41:03 EST 2005 -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 6/29/2005 2:26 AM To: Fornito, Alexander Cc: Itamar Kahn; Freesurfer Mailing List Subject: RE: [Freesurfer] mris_glm Alex, I'm trying to track down the source of the segmentation fault. In the meantime, can you re-run the script with the parameter --echo just after 'make_average_surface' (and before the --subjects)? This will give me a better idea on where its faulting. I don't think the subject naming is the problem, but I am wondering about the two warnings about not being able to open the .avg_curv files. Thanks, Itamar, for pointing out the problem with the script. I'm not sure how the file got converted to DOS format (as we use Linux), maybe a mail system, but I hadn't seen that error before. I've posted a gzip'd make_average_surface on the ftp site (same as sent prior), in case others want the script. At: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/make_average_surface.gz Copy it to $FREESURFER_HOME/bin, and remember to make it executable by typing 'chmod 755 make_average_surface' after gunzip'ing it. Nick On Tue, 2005-06-28 at 13:11 +1000, Fornito, Alexander wrote: > Thanks - that got it working! > > I tried running it on a small sample of 8 subjects, and got a segmentation fault (below). I've noticed that make_average_surface requires subject names to start with a letter. My subjects were coded as numbers, so I just added an 's' to the beginning to get it going. I'm not sure if this has anything to do with the problem. > Any help is appreciated. > Alex > > make_average_surface --subjects s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 > ==================== > make_average_surface > ==================== > input subjects: s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 > output subject: average > mris_average_curvature... > processing subject s1000186... > processing subject s1000187... > processing subject s1000188... > processing subject s1000189... > processing subject s1000190... > processing subject s1000191... > processing subject s1000192... > processing subject s1000194... > MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc > No such file or directory > mris_average_curvature... > processing subject s1000186... > processing subject s1000187... > processing subject s1000188... > processing subject s1000189... > processing subject s1000190... > processing subject s1000191... > processing subject s1000192... > processing subject s1000194... > MRISwriteCurvature: could not open ../average/surf/lh.avg_curv > No such file or directory > mris_make_average_surface... > reading vertex positions from orig... > processing subject s1000186... > The following must be revisited********************************** > Segmentation fault > > > > -----Original Message----- > From: Itamar Kahn [mailto:kahn@MIT.EDU] > Sent: Tue 6/28/2005 9:51 AM > To: Fornito, Alexander > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] mris_glm > The 'make_average_surface' script is in Dos format. You can use the > 'dos2unix' application to remove the offending characters from it > (dos2unix comes with all linux dist and you can use fink to download > it for mac os x). > > Cheers, > Itamar > > ------------------------- > [kahn@###### kahn]$ dos2unix --help > dos2unix Copyright (c) 1994-1995 Benjamin Lin > Copyright (c) 1998 Bernd Johannes Wuebben (Version 3.0) > Copyright (c) 1998 Christian Wurll (Version 3.1) > Usage: dos2unix [-hkqV] [-c convmode] [-o file ...] [-n infile > outfile ...] > -h --help give this help > -k --keepdate keep output file date > -q --quiet quiet mode, suppress all warnings > always on in stdin->stdout mode > -V --version display version number > -c --convmode conversion mode > convmode ASCII, 7bit, ISO, Mac, default to ASCII > -l --newline add additional newline in all but Mac convmode > -o --oldfile write to old file > file ... files to convert in old file mode > -n --newfile write to new file > infile original file in new file mode > outfile output file in new file mode > > > On Jun 27, 2005, at 4:39 PM, Fornito, Alexander wrote: > > > Hi Nick, > > I copied the script into > > the bin dir, but when I type make_average_surface, I get the > > following: > > > > make_average_surface > > 'nknown option: `- > > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. > > > > Is this normal? > > Thanks, > > Alex > > > > > > -----Original Message----- > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > Sent: Tue 6/21/2005 11:00 PM > > To: Fornito, Alexander > > Cc: Freesurfer Mailing List; Bruce Fischl > > Subject: RE: [Freesurfer] mris_glm > > Alex, > > > > Attached is the make_average_surface script. Copy it to the > > freesurfer/bin directory, and be sure to make it executable (run > > 'chmod > > 755 make_average_surface' in the freesurfer/bin directory). > > > > Type 'make_average_surface' to get help. Basically, just the subject > > names are required. By default, a 'subject' named 'average' will be > > created from your set of subjects (a name instead of 'average' can be > > specified on the command line). > > > > Nick > > > > ps. I am working on the mris_surface seg-fault problem using the > > rh.orig > > file that you sent. > > > > > > On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote: > > > >> Hi Alex, > >> > >> you're better off using the make_average_surfaces.csh script to > >> make an > >> average of your subjects. Nick: can you send Alex a copy? > >> > >> thanks, > >> Bruce > >> On Tue, 21 Jun > >> 2005, Fornito, Alexander wrote: > >> > >> > >>> Def. sounds worth doing then! I'll give it a try. > >>> My other question is, where can I get my hands on the average7? It's > >>> used as the target in the mris_glm examples, but I haven't been > >>> able to > >>> find the actual average7 surface in any of the freesurfer > >>> directories. > >>> Am I missing something? > >>> Thanks again, > >>> Alex > >>> > >>> -----Original Message----- > >>> From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > >>> Sent: Tuesday, June 21, 2005 4:11 PM > >>> To: Fornito, Alexander > >>> Cc: freesurfer(a)nmr.mgh.harvard.edu > >>> Subject: Re: [Freesurfer] mris_glm > >>> > >>> > >>> You can run with just the design matrix, but you won't be able to > >>> use > >>> the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a > >>> way to > >>> specify how to build the des mtx. The fsgdf keeps track of what the > >>> regressors mean (eg, Age, Class, IQ, etc). When you save the > >>> preprocessed data with --y, you'll see that there will be an fsgdf > >>> file saved with it. Load this in tksurfer, click on a point, and you > >>> will be able to make a scatter plot of, say, thickness vs age, with > >>> each class (eg, Male, Female) having a different color dot in the > >>> scatter plot. When you mouse-over the dot, it tells you the subject > >>> name. Click on a new point and you'll see the scatter plot for that > >>> point. If you use --xmat, you can save the design matrix (in > >>> matlab-4 > >>> format). > >>> > >>> doug > >>> > >>> > >>> On Tue, 21 Jun 2005, Fornito, Alexander wrote: > >>> > >>> > >>>> Hi, > >>>> > >>>> I was seeking some clarification re: the relationship between the > >>>> > >>> fsgdf > >>> > >>>> and design matrix file for use with mris_glm. It seems to me > >>>> that the > >>>> two contain very similar info, the examples in the -help don't > >>>> use the > >>>> fsdf at all. Is it necessary to create one, or can you just run an > >>>> analysis with the desmtx? > >>>> > >>>> Thanks, > >>>> > >>>> Alex > >>>> > >>>> > >>>> > >>>> Alexander Fornito > >>>> > >>>> M.psych (Clin. Neuro.)/PhD candidate > >>>> > >>>> Melbourne Neuropsychiatry Centre and Department of Psychology > >>>> > >>>> The University of Melbourne > >>>> > >>>> alexander.fornito(a)wh.org.au > >>>> > >>>> > >>>> > >>>> > >>>> > >>> > >>> > >>> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _________________________________________________ > Itamar Kahn > Department of Psychology > Stanford University > Jordan Hall, Bldg 420 > Mail Code 2130 > Stanford, CA 94305 > office: 650-724-9515 fax: 650-725-5699 > url: http://web.mit.edu/kahn/www > _________________________________________________ > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RE: [Freesurfer] mris_glm
by Fornito, Alexander 28 Jun '05

28 Jun '05

Hi Nick, Here's the output with the echo command. Thanks for your help. make_average_surface --echo --subjects 1000186 1000187 1000188 1000189 1000190 1000191 1000192 1000194 if ( 0 ) then breaksw end while ( 9 != 0 ) set flag = --subjects if ( ! 0 ) then shift endif switch ( --subjects ) if ( 8 == 0 ) goto arg1moreerr set SUBJECTS = 1000186 shift set getting_subjects = 1 breaksw end while ( 7 != 0 ) set flag = 1000187 if ( ! 1 ) then switch ( 1000187 ) if ( 1 ) then set SUBJECTS = 1000186 1000187 shift set getting_subjects = 1 else breaksw end while ( 6 != 0 ) set flag = 1000188 if ( ! 1 ) then switch ( 1000188 ) if ( 1 ) then set SUBJECTS = 1000186 1000187 1000188 shift set getting_subjects = 1 else breaksw end while ( 5 != 0 ) set flag = 1000189 if ( ! 1 ) then switch ( 1000189 ) if ( 1 ) then set SUBJECTS = 1000186 1000187 1000188 1000189 shift set getting_subjects = 1 else breaksw end while ( 4 != 0 ) set flag = 1000190 if ( ! 1 ) then switch ( 1000190 ) if ( 1 ) then set SUBJECTS = 1000186 1000187 1000188 1000189 1000190 shift set getting_subjects = 1 else breaksw end while ( 3 != 0 ) set flag = 1000191 if ( ! 1 ) then switch ( 1000191 ) if ( 1 ) then set SUBJECTS = 1000186 1000187 1000188 1000189 1000190 1000191 shift set getting_subjects = 1 else breaksw end while ( 2 != 0 ) set flag = 1000192 if ( ! 1 ) then switch ( 1000192 ) if ( 1 ) then set SUBJECTS = 1000186 1000187 1000188 1000189 1000190 1000191 1000192 shift set getting_subjects = 1 else breaksw end while ( 1 != 0 ) set flag = 1000194 if ( ! 1 ) then switch ( 1000194 ) if ( 1 ) then set SUBJECTS = 1000186 1000187 1000188 1000189 1000190 1000191 1000192 1000194 shift set getting_subjects = 1 else breaksw end while ( 0 != 0 ) goto parse_args_return goto check_params if ( ! 1 ) then if ( ! 1 ) then if ( ! -e /data/flanders/work/alex/freesurfer/subjects ) then if ( ! 1 ) then if ( ! -e /usr/local/freesurfer ) then goto check_params_return echo ==================== ==================== echo make_average_surface make_average_surface echo ==================== ==================== echo input subjects: 1000186 1000187 1000188 1000189 1000190 1000191 1000192 1000194 input subjects: 1000186 1000187 1000188 1000189 1000190 1000191 1000192 1000194 echo output subject: average output subject: average mkdir -p /data/flanders/work/alex/freesurfer/subjects/average /data/flanders/work/alex/freesurfer/subjects/average/surf /data/flanders/work/alex/freesurfer/subjects/average/mri /data/flanders/work/alex/freesurfer/subjects/average/mri/transforms /data/flanders/work/alex/freesurfer/subjects/average/mri/T1 /data/flanders/work/alex/freesurfer/subjects/average/mri/orig /data/flanders/work/alex/freesurfer/subjects/average/mri/label if ( -e /data/flanders/work/alex/freesurfer/subjects/average == 0 ) then mkdir -p /data/flanders/work/alex/freesurfer/subjects/average/surf endif set tmp_subjects = ( 1000186 1000187 1000188 1000189 1000190 1000191 1000192 1000194 ) cp /data/flanders/work/alex/freesurfer/subjects/1000186/mri/T1/COR-.info /data/flanders/work/alex/freesurfer/subjects/average/mri/T1 cp /data/flanders/work/alex/freesurfer/subjects/1000186/mri/orig/COR-.info /data/flanders/work/alex/freesurfer/subjects/average/mri/orig foreach hemi ( lh rh ) foreach c ( sulc curv ) echo mris_average_curvature... mris_average_curvature... mris_average_curvature sulc lh sphere.reg 1000186 1000187 1000188 1000189 1000190 1000191 1000192 1000194 ../average/surf/lh.avg_sulc processing subject 1000186... processing subject 1000187... processing subject 1000188... processing subject 1000189... processing subject 1000190... processing subject 1000191... processing subject 1000192... processing subject 1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory end echo mris_average_curvature... mris_average_curvature... mris_average_curvature sulc lh sphere.reg 1000186 1000187 1000188 1000189 1000190 1000191 1000192 1000194 ../average/surf/lh.avg_curv processing subject 1000186... processing subject 1000187... processing subject 1000188... processing subject 1000189... processing subject 1000190... processing subject 1000191... processing subject 1000192... processing subject 1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_curv No such file or directory end foreach s ( orig white pial inflated ) echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface -i 7 -o orig lh orig_avg sphere.reg average 1000186 1000187 1000188 1000189 1000190 1000191 1000192 1000194 reading vertex positions from orig... processing subject 1000186... The following must be revisited********************************** Segmentation fault -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 6/29/2005 2:26 AM To: Fornito, Alexander Cc: Itamar Kahn; Freesurfer Mailing List Subject: RE: [Freesurfer] mris_glm Alex, I'm trying to track down the source of the segmentation fault. In the meantime, can you re-run the script with the parameter --echo just after 'make_average_surface' (and before the --subjects)? This will give me a better idea on where its faulting. I don't think the subject naming is the problem, but I am wondering about the two warnings about not being able to open the .avg_curv files. Thanks, Itamar, for pointing out the problem with the script. I'm not sure how the file got converted to DOS format (as we use Linux), maybe a mail system, but I hadn't seen that error before. I've posted a gzip'd make_average_surface on the ftp site (same as sent prior), in case others want the script. At: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/make_average_surface.gz Copy it to $FREESURFER_HOME/bin, and remember to make it executable by typing 'chmod 755 make_average_surface' after gunzip'ing it. Nick On Tue, 2005-06-28 at 13:11 +1000, Fornito, Alexander wrote: > Thanks - that got it working! > > I tried running it on a small sample of 8 subjects, and got a segmentation fault (below). I've noticed that make_average_surface requires subject names to start with a letter. My subjects were coded as numbers, so I just added an 's' to the beginning to get it going. I'm not sure if this has anything to do with the problem. > Any help is appreciated. > Alex > > make_average_surface --subjects s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 > ==================== > make_average_surface > ==================== > input subjects: s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 > output subject: average > mris_average_curvature... > processing subject s1000186... > processing subject s1000187... > processing subject s1000188... > processing subject s1000189... > processing subject s1000190... > processing subject s1000191... > processing subject s1000192... > processing subject s1000194... > MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc > No such file or directory > mris_average_curvature... > processing subject s1000186... > processing subject s1000187... > processing subject s1000188... > processing subject s1000189... > processing subject s1000190... > processing subject s1000191... > processing subject s1000192... > processing subject s1000194... > MRISwriteCurvature: could not open ../average/surf/lh.avg_curv > No such file or directory > mris_make_average_surface... > reading vertex positions from orig... > processing subject s1000186... > The following must be revisited********************************** > Segmentation fault > > > > -----Original Message----- > From: Itamar Kahn [mailto:kahn@MIT.EDU] > Sent: Tue 6/28/2005 9:51 AM > To: Fornito, Alexander > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] mris_glm > The 'make_average_surface' script is in Dos format. You can use the > 'dos2unix' application to remove the offending characters from it > (dos2unix comes with all linux dist and you can use fink to download > it for mac os x). > > Cheers, > Itamar > > ------------------------- > [kahn@###### kahn]$ dos2unix --help > dos2unix Copyright (c) 1994-1995 Benjamin Lin > Copyright (c) 1998 Bernd Johannes Wuebben (Version 3.0) > Copyright (c) 1998 Christian Wurll (Version 3.1) > Usage: dos2unix [-hkqV] [-c convmode] [-o file ...] [-n infile > outfile ...] > -h --help give this help > -k --keepdate keep output file date > -q --quiet quiet mode, suppress all warnings > always on in stdin->stdout mode > -V --version display version number > -c --convmode conversion mode > convmode ASCII, 7bit, ISO, Mac, default to ASCII > -l --newline add additional newline in all but Mac convmode > -o --oldfile write to old file > file ... files to convert in old file mode > -n --newfile write to new file > infile original file in new file mode > outfile output file in new file mode > > > On Jun 27, 2005, at 4:39 PM, Fornito, Alexander wrote: > > > Hi Nick, > > I copied the script into > > the bin dir, but when I type make_average_surface, I get the > > following: > > > > make_average_surface > > 'nknown option: `- > > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. > > > > Is this normal? > > Thanks, > > Alex > > > > > > -----Original Message----- > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > Sent: Tue 6/21/2005 11:00 PM > > To: Fornito, Alexander > > Cc: Freesurfer Mailing List; Bruce Fischl > > Subject: RE: [Freesurfer] mris_glm > > Alex, > > > > Attached is the make_average_surface script. Copy it to the > > freesurfer/bin directory, and be sure to make it executable (run > > 'chmod > > 755 make_average_surface' in the freesurfer/bin directory). > > > > Type 'make_average_surface' to get help. Basically, just the subject > > names are required. By default, a 'subject' named 'average' will be > > created from your set of subjects (a name instead of 'average' can be > > specified on the command line). > > > > Nick > > > > ps. I am working on the mris_surface seg-fault problem using the > > rh.orig > > file that you sent. > > > > > > On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote: > > > >> Hi Alex, > >> > >> you're better off using the make_average_surfaces.csh script to > >> make an > >> average of your subjects. Nick: can you send Alex a copy? > >> > >> thanks, > >> Bruce > >> On Tue, 21 Jun > >> 2005, Fornito, Alexander wrote: > >> > >> > >>> Def. sounds worth doing then! I'll give it a try. > >>> My other question is, where can I get my hands on the average7? It's > >>> used as the target in the mris_glm examples, but I haven't been > >>> able to > >>> find the actual average7 surface in any of the freesurfer > >>> directories. > >>> Am I missing something? > >>> Thanks again, > >>> Alex > >>> > >>> -----Original Message----- > >>> From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > >>> Sent: Tuesday, June 21, 2005 4:11 PM > >>> To: Fornito, Alexander > >>> Cc: freesurfer(a)nmr.mgh.harvard.edu > >>> Subject: Re: [Freesurfer] mris_glm > >>> > >>> > >>> You can run with just the design matrix, but you won't be able to > >>> use > >>> the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a > >>> way to > >>> specify how to build the des mtx. The fsgdf keeps track of what the > >>> regressors mean (eg, Age, Class, IQ, etc). When you save the > >>> preprocessed data with --y, you'll see that there will be an fsgdf > >>> file saved with it. Load this in tksurfer, click on a point, and you > >>> will be able to make a scatter plot of, say, thickness vs age, with > >>> each class (eg, Male, Female) having a different color dot in the > >>> scatter plot. When you mouse-over the dot, it tells you the subject > >>> name. Click on a new point and you'll see the scatter plot for that > >>> point. If you use --xmat, you can save the design matrix (in > >>> matlab-4 > >>> format). > >>> > >>> doug > >>> > >>> > >>> On Tue, 21 Jun 2005, Fornito, Alexander wrote: > >>> > >>> > >>>> Hi, > >>>> > >>>> I was seeking some clarification re: the relationship between the > >>>> > >>> fsgdf > >>> > >>>> and design matrix file for use with mris_glm. It seems to me > >>>> that the > >>>> two contain very similar info, the examples in the -help don't > >>>> use the > >>>> fsdf at all. Is it necessary to create one, or can you just run an > >>>> analysis with the desmtx? > >>>> > >>>> Thanks, > >>>> > >>>> Alex > >>>> > >>>> > >>>> > >>>> Alexander Fornito > >>>> > >>>> M.psych (Clin. Neuro.)/PhD candidate > >>>> > >>>> Melbourne Neuropsychiatry Centre and Department of Psychology > >>>> > >>>> The University of Melbourne > >>>> > >>>> alexander.fornito(a)wh.org.au > >>>> > >>>> > >>>> > >>>> > >>>> > >>> > >>> > >>> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _________________________________________________ > Itamar Kahn > Department of Psychology > Stanford University > Jordan Hall, Bldg 420 > Mail Code 2130 > Stanford, CA 94305 > office: 650-724-9515 fax: 650-725-5699 > url: http://web.mit.edu/kahn/www > _________________________________________________ > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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