Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

segmentation question
by Andrew H Bell 01 Jul '05

01 Jul '05

Happy soon-to-be Independence Day FreeSurfers, I am in the process of trying to fix the segmentation of my surface and I had a few general questions: Is editing the voxels the only way one can change what is counted as white vs. grey matter? Is there any way to indicate with control points what is grey vs. white vs. CSF? It has been particularly trying with monkey data considering how much extra tissue they have surrounding their brain :) that doesn't always get clipped using the strip skull step. Thanks! Andy Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health 49 Convent Drive Building 49, RM 1B80 Bethesda, MD 20892 office: (301) 496-5625 ext.260 fax: (301) 402-0921 mobile: (202) 679-1279 bellah(a)mail.nih.gov

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Converting RGB to COR
by Sarah Rugheimer 01 Jul '05

01 Jul '05

Hello, I manipulated some of the slices in matlab and would like to convert them back into COR format so I can bring them back into Freesurfer to complete the reconstruction. I can save these images into any matlab supported format or RGB. Since freesurfer can convert COR to RGB I thought there might be a way to convert from RGB to COR, but I have been unable to find it. Any help would be appreciated! Thanks. Sarah

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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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