Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

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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Question on FWHM in surface smoothing
by Hae-Jeong Park, PhD 28 Jun '05

28 Jun '05

Hi, I would like to know the relationship between number of iteration in surface smoothing and Gaussian kernel size in FWHM. Would you give me some information on this? Thank you in advance. Hae-Jeong -- Hae-Jeong Park, PhD Assistant Professor, Department of Diagnostic Radiology, Yonsei University, College of Medicine and Division of Nuclear Medicine, Severance Hospital Director, Laboratory of Molecular Neuroimging Technology <http://neuroimage.yonsei.ac.kr/> http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax) 82-2-393-3035 Cellur) 82-10-4220-1003

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

28 Jun '05

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 _________________________________________________

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Getting there but still stuck
by David Soscia 28 Jun '05

28 Jun '05

Hey guys, I sent one messge before but it was very vague, but now that I am a little bit more knowledgeable about what I am doing, let me be more specific. I have a bunch of images (individual slices) in .dcm format. What EXACTLY should I type in the command line to convert these to .cor files? I've been fiddling with the mri_convert command, and I thought it worked at first, but the files themselves didn't say .cor after I was finished with the "conversion." Also, should I FIRST move the files into an orig directory that I have created, THEN convert them, visa versa, or does it not matter what order I do that in? When I convert the files, I dont know how to convert ALL of the slices in the folder, but I was rather trying to individually convert the files at first, which would take forever. I have gotten several errors wheile trying to convert, but mostly I get ones having to do with the output I am putting into the command. One more thing. Suppose this converion/moving the files works...I am confused as to why you need to make subdirectories under the orig directory labled 001 002 003. Are there more than just 3 I am supposed to make, and what exactly do I put in these subcategories? Once I get over this road block I should be alright because I was able to do everything properly with the bert file. Thanks. Dave

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RE: [Freesurfer] mris_glm
by Fornito, Alexander 27 Jun '05

27 Jun '05

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

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