Freesurfer July 2005

freesurfer@nmr.mgh.harvard.edu

39 participants
68 discussions

RE: [Freesurfer] mri_vol2surf
by Fornito, Alexander 03 Jul '05

03 Jul '05

Hi, I've managed to get the mask to a point where it's in the correct position if I load it through tkmedit (as a binary in analyze format). I then run mri_vol2surf, which seems to work (output below). However, If I try to load the mask (now saved as a .w file) though tksurfer as file > label > load, nothing happens (nothing happens if I try to load it as an overlay with the register.dat file either). If I try to load it as a label in tkmedit, I get the following: Couldn't load the label. Tkmedit couldn't read the label you specified. This could be because the format wasn't valid or the file wasn't found. Am I missing something? I though .w was the correct format for labels of this type. Here's the mri_vol2surf output. Thanks again! mri_vol2surf --src 186_corconv_native_testmask_binary_y --src_type analyze --srcreg register.dat --hemi lh --out ./186_native_flip_y_mask_surf.w --out_type paint INFO: output format is paint srcvol = 186_corconv_native_testmask_binary_y 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_native_testmask_binary_y ----------------------------------------------------------------- INFO: could not find /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y.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_native_testmask_binary_y.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 avg = 1.000, stdev = 0.000, min = 1.000, max = 1.000 -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Fri 7/1/2005 10:11 PM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Sorry, I gave you a slightly wrong tkmedit command-line, it should have been -overlay-reg ... As for tkmedit, the mask is probably too dark. Click in the window and hit 'i'. This will turn on intensity normalization, which will probably fix the problem. You may want to load in the volume that you traced the mask on instead of the mask itself. doug Fornito, Alexander wrote: >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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Rotating Images in Analyze
by rhaynes＠neuro.gatech.edu 02 Jul '05

02 Jul '05

We are trying to rotate images in Analyze to align the midline. We have to do this by getting series from a PAX system to a PC with Analyze, rotating the images, sending back to PAX, and then transfering to a linux box with FreeSurfer. For some reason, FreeSurfer loads only a thin slice from the series as the volume. When loading the same volume in Slicer, the volume appears normal. Have you encountered this problem before? Thanks. Ryan Haynes Radiology Research Assistant Children's Healthcare of Atlanta

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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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Freesurfer July 2005