Freesurfer October 2005

freesurfer@nmr.mgh.harvard.edu

49 participants
62 discussions

good news and bad news
by Bruce Fischl 21 Oct '05

21 Oct '05

Hi All, I'll start with the good: thanks to Anders Dale (UCSD), Howard Pinsky (CorTechs) and Christian Euseman (MGH), we have finally signed an open source agreement for FreeSurfer. We will be posting a "read-only" tarball on the website in the next couple of weeks, and anyone is free to download it and look at it. We will *not* be supporting a make/configure type env for people to download and build, as we simply aren't ready to do so. We plan to implement such a procedure, but it will be a while. Instead of waiting until that was ready, I thought people would like to have access to the source to at least see what things are doing, and be able to see file formats and such. Now the bad news. I know we've been promising a new release, but it is being delayed for another month or two. Partially this is due to the opensourcing, which has taken our time and resources, but it is also because we *really* don't want to release something that is half broken. There are also a number of features that we want to get into the release, and not have updates to it right away. We have continued to post current versions on the website as prereleases, but *please* be aware that we can't guarantee that these versions will be compatible with the one we ultimately release. I think they will be, but can't say for sure. Our hope is that datasets processed with the prerelease versions can be rerun automatically with recon-all --rerun or something like that, but again, no guarantees. cheers, Bruce

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FS-FAST Registration Question: registration across sessions within subjects
by Tommi Raij 20 Oct '05

20 Oct '05

Hi Doug/All, This is a question about registering several functional scans from the same subject in the same space. The functional scans are from different sessions, so even if the slice recording parameters are identical, the head will inavoidably be in different locations and with different rotation. The data have already been collected, so we cannot use any on-line corrections. Four different techniques come to mind that could be used to achieve this, but I would expect that the accuracy of the methods varies a lot. Optimally IMHO one should register the different functional runs with respect to each other directly, simply because the EPI images are very similar with respect to each other (or at least their T1 contrast is). The high-resolution structural image is very different compared to the EPI images so functional-to-structural registration is expected to be much more inaccurate. Here are the four different techniques (please tell me if you can think of more): 1. One possibility would be to use mc-sess for all runs from the same subject (place all the runs from the different sessions in a single "bold" directory and just run mc-sess). Possible problem: If I have understood correctly, mc-sess only corrects for motion within slices. Therefore the different head rotations would make this technique very inaccurate. Or does there exist an updated version of mc-sess that could handle even large displacements and rotations? 2. A second possibility would be to use one of the automatic functional-to-structural registration programs and register each functional run to the same hires structural image. However, based on the discussion above, there are expected to be inaccuracies in the functional-to- structural registration that could be large enough to make comparisons across the functional sessions meaningless (i.e., the differences would mainly be driven by inaccuracies in the registration). 3. A third possibility would be to use the same technique as for registration across subjects, i.e., resampling the different runs from the same subject into a spherical space calculated from this specific subject. Again this is just as variety of registration from functional to structural, and would be expected to provide suboptimal results. 4. A fourth possibility would be to find a method for registering all the functional images in a single space with respect to each other, e.g. by picking one of the functional sessions as the target space and resampling all other functional sessions from this subject into this space (without using the hires structurals at all). I guess this would be kind of motion correction but capable of handling rotations. If such a tool exists, it might be more accurate than any of the methods above, simply because the functional images are more similar compared to each other than compared to the subject's hires structural image. Any ideas/suggestions which method would give the most accurate result? And what kind of tools currently exist? Thanks, Tommi --- Tommi Raij MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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mris_glm
by antao＠itsa.ucsf.edu 20 Oct '05

20 Oct '05

Hi, I processed all data in older version (20040218). Can I do group comparison with mris_glm? I just wanted to try, I got the following error message: gdfReadHeader: reading ./ad_cn_fsgd.txt INFO: ignoring tag vs. INFO: ignoring tag SomeTag INFO: gd2mtx_method is doss INFO: Normalized Design Matrix Condition Number is 18.894 INFO: found 3 elements in group contrast vector 1.000 -1.000 0.000; $Id: mris_glm.c,v 1.43 2005/08/17 22:19:35 greve Exp $ setenv SUBJECTS_DIR /home/antao/freesurfer/subjects /home/antao/freesurfer/subjects/stats mris_glm lh --trgsubj average_ftd --fsgd ./ad_cn_fsgd.txt doss --beta_in ./lh_beta_ad_cn.mgz --var_in ./lh_var_ad_cn.mgz --gcv 1 -1 0 --ces ./lh_ces_ad_cn.mgz --t ./lh_t_ad_cn.mgz --sigt ./lh_sigt_ad_cn.mgz Design Matrix ------------------------------------ 1.000 0.000 71.000; 1.000 0.000 63.000; 1.000 0.000 60.000; 1.000 0.000 63.000; 0.000 1.000 62.000; 1.000 0.000 51.000; 0.000 1.000 77.000; 0.000 1.000 60.000; 0.000 1.000 57.000; 0.000 1.000 65.000; Design Covariance Matrix ------------------------------------ 5.000 0.000 308.000; 0.000 5.000 321.000; 308.000 321.000 40027.000; Contrast Matrix: ----------------------------- 1.000 -1.000 0.000; DOF = 7 INFO: loading surface /home/antao/freesurfer/subjects/average_ftd/surf/lh.sphere.reg nvertices = 163842 surface nvertices 163842 surface area 125674.750000 INFO: loading beta_in ./lh_beta_ad_cn.mgz ERROR: number of components in input beta does not match the number of regressors in the design matrix [antao@freesurfer stats]$ Thanks, Antao

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determining significance levels
by d.g.lawyer＠medisin.uio.no 20 Oct '05

20 Oct '05

Hi, We've been having alot of discussion in our group regarding how one should set significance levels. Since you include FDR in the newer releases, I take it that is your current reccomendation (see also Doug's slides: http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsfsl-mris_glm.pdf) Correct? Put very roughly, the FDR rate controls the (expected) percent of your positive results that are false. So what level is appropriate? All that Genovese says is that "it is common to set q to conventional levels ...(e.g. 0.01-0.05) ... values in the range of 0.10-0.20 are reasonable in many problems (Benjamini, personal communication)" [quote from pg 872, 2nd column]. What sort of rates do you think are reasonable, and under what conditions? +glenn

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mapping left hemi into right hemi coordinates
by Irina Sigalovsky 19 Oct '05

19 Oct '05

Hi, I was wondering if there is a way to map one hemisphere onto the other (e.g., left on right) so that I could average data from the two hemispheres. Thank you. Irina

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Optseq2
by Christie Chung 19 Oct '05

19 Oct '05

Hi, I have a question regarding programming fMRI experiments. I am programming a source memory experiment and would like to do ROC modeling with the data. Therefore, I would need to record two responses from participants in each test trial (i.e., Red, Blue, New; and 1, 2, 3). I am wondering if it's fine to do that in the scanner. I used Optseq2 to randomize the trials and have accounted for the total amount of time I would need to get both responses (8 sec/trial -- 4 for each response). I just wanted to make sure that's the right approach before testing participants on the task. Thanks, Christie -- Christie Chung, Ph.D. Postdoctoral Associate Department of Brain and Cognitive Sciences 46-5127D Massachusetts Institute of Technology Cambridge, MA 02139 chung_c(a)mit.edu http://web.mit.edu/bnl/ Office No.: 617-253-8976

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Re: [Freesurfer] tkregister2
by Sasha Wolosin 19 Oct '05

19 Oct '05

My subject's anatomical scan seems to be relatively well aligned with the fuzzy talairach brain, but the green 'orig' surface is completely off. How is this possible? Why do we need the surface at all if it's not used for alignment? The tutorial advises using the 'final objective function value' from mritotal.log to determine if the registration is off before making any edits. If the registration needs to be modified, and if it's important to have an accurate talairach.xfm, how do I determine if it is aligned sufficiently after making edits? Thanks, Sasha >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 10/18/2005 12:23 PM >>> Hit the "compare" button to flip back and forth between the talairach brain and your subjects anatomical. On Tue, 18 Oct 2005, Sasha Wolosin wrote: > How can I check the registration if I can't see the surface? > -Sasha > >>>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 10/18/2005 12:07 PM >>> > > If you don't have a surface, then don't run it with --surf. It's > important to have an accurate talairach.xfm. > > doug > > > > > On Mon, 17 Oct 2005, Sasha Wolosin wrote: > >> Dear Nick, >> >> I recently installed the dev release from October 3rd, but tkregister2 still does not work after autorecon1. (It will not load the orig volume because rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I not using the correct inputs for this step (my inputs are the same as that of the tutorial)? How important is it to have a correct registration before running autorecon2? >> >> Here is the script for a subject who has only been run with autorecon1: >> >> % [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal --surf orig >> surfname set to orig >> INFO: no target volume specified, assuming FreeSurfer orig volume. >> target volume orig >> movable volume (null) >> reg file (null) >> LoadVol 1 >> $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ >> Diagnostic Level -1 >> talairach.xfm --------------------- >> 1.020 -0.138 0.036 -2.498; >> 0.151 1.100 -0.045 -8.636; >> -0.033 0.052 1.156 -11.535; >> 0.000 0.000 0.000 1.000; >> WARNING: can't find the talairach xform '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' >> WARNING: transform is not loaded into mri >> INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz >> WARNING: can't find the talairach xform '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' >> WARNING: transform is not loaded into mri >> INFO: changing target type to float >> Ttarg: -------------------- >> -1.000 0.000 0.000 128.538; >> 0.000 0.000 1.000 -132.197; >> 0.000 -1.000 0.000 137.708; >> 0.000 0.000 0.000 1.000; >> INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz >> 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 = 0, float2int = 0 >> ---- Input registration matrix -------- >> 1.020 -0.138 0.036 -2.498; >> 0.151 1.100 -0.045 -8.636; >> -0.033 0.052 1.156 -11.535; >> 0.000 0.000 0.000 1.000; >> subject = 2333 >> Reading lh surface orig >> MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open file >> No such file or directory >> tkregister2: could not read surface orig >> No such file or directory >> [root@bwy-1-113mm mri]$ >> >> If I instead run the command: >> tkregister2 --mgz --s 2333 --fstal >> tkregister2 does load, but there is no green orig outline to guide any corrections. >> >> If I run tkregister2 after running autorecon2, it also loads, but the registration is all wrong. (It was about as far off as the tutorial subject) Here is the output: >> >> [root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s 2338 --fstal --surf orig >> surfname set to orig >> INFO: no target volume specified, assuming FreeSurfer orig volume. >> target volume orig >> movable volume (null) >> reg file (null) >> LoadVol 1 >> $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ >> Diagnostic Level -1 >> talairach.xfm --------------------- >> 1.131 -0.107 0.009 -12.066; >> 0.107 1.119 -0.133 -2.885; >> 0.003 0.141 1.186 -27.267; >> 0.000 0.000 0.000 1.000; >> WARNING: can't find the talairach xform '/freesurfer/subjects/2338/mri/transforms/talairach.xfm' >> WARNING: transform is not loaded into mri >> INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz >> WARNING: can't find the talairach xform '/freesurfer/subjects/2338/mri/transforms/talairach.xfm' >> WARNING: transform is not loaded into mri >> INFO: changing target type to float >> Ttarg: -------------------- >> -1.000 0.000 0.000 136.359; >> 0.000 0.000 1.000 -135.309; >> -0.000 -1.000 0.000 159.346; >> 0.000 0.000 0.000 1.000; >> INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz >> 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 = 0, float2int = 0 >> ---- Input registration matrix -------- >> 1.131 -0.107 0.009 -12.066; >> 0.107 1.119 -0.133 -2.885; >> 0.003 0.141 1.186 -27.267; >> 0.000 0.000 0.000 1.000; >> subject = 2338 >> Reading lh surface orig >> Done reading surface >> Reading rh surface orig >> Done reading surface >> Zoom Factor = 2 >> FOV = 256 >> Opening window 2338 >> Setting scale >> tkregister2: interface: /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} >> >> >> Looking through the script I noticed it never mentions the path to the correct .xfm file, which is in the subjects directory (the subjects directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off. >> >> Any help is greatly appreciated, >> Thanks, >> Sasha >> >> >> >> >> >> >> Sasha Wolosin >> Research Assistant >> Developmental Cognitive Neurology >> Kennedy Krieger Institute >> 707 N. Broadway >> Baltimore, MD 21205 >> ph: (443) 923-9270 >> wolosin(a)kennedykrieger.org >>>>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 09/15/05 2:40 PM >>> >> Sasha, >> >> An alternative solution is to create the COR files for the talairach >> subject: >> >> cd $SUBJECTS_DIR/talairach/mri >> mri_convert -it mgz -ot cor orig.mgz orig/ >> >> This will deposit COR files into the orig/ directory, and your current >> tkregister2 should then work. >> >> We are recommending using .mgz files over the older COR format, and are >> still trying to make all the tools fully compliant. >> >> A new 'dev' release containing the updated tkregister2 will be posted in >> the next couple days. >> >> Nick >> >> >> On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote: >>> I just fixed this error. For those in the nmr center, the fix will be >>> live tomorrow. For those outside, you can download a new Linux version >>> from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> Sasha Wolosin wrote: >>> >>>> Dear all, >>>> >>>> I am having trouble running tkregister2. >>>> >>>> I get an error when I run tkregister2 on a subject after running autorecon1 (see below.) However, I also get an error when I run it on bert. >>>> It seems tkregister2 is searching for COR files, but I am using mgz format. Am I not using the correct flags? >>>> >>>> My subjects directory contains the talairach subject included in the dev release. Do I need to download talairach separately? >>>> >>>> Here is the output for subject 2335 and bert: >>>> [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal >>>> INFO: no target volume specified, assuming FreeSurfer orig volume. >>>> target volume orig >>>> movable volume (null) >>>> reg file (null) >>>> LoadVol 1 >>>> $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ >>>> Diagnostic Level -1 >>>> talairach.xfm --------------------- >>>> 1.002 0.050 -0.017 -3.539; >>>> -0.053 1.034 -0.076 -12.275; >>>> 0.014 0.081 1.091 -14.424; >>>> 0.000 0.000 0.000 1.000; >>>> corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info >>>> ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 >>>> >>>> >>>> [root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal >>>> INFO: no target volume specified, assuming FreeSurfer orig volume. >>>> target volume orig >>>> movable volume (null) >>>> reg file (null) >>>> LoadVol 1 >>>> $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ >>>> Diagnostic Level -1 >>>> talairach.xfm --------------------- >>>> 1.154 -0.024 0.046 -5.813; >>>> 0.014 0.941 0.131 -21.893; >>>> -0.048 -0.155 1.123 -0.730; >>>> 0.000 0.000 0.000 1.000; >>>> WARNING: can't find the talairach xform '/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm' >>>> WARNING: transform is not loaded into mri >>>> corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info >>>> ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 >>>> [root@bwy-1-113mm subjects]$ >>>> >>>> >>>> Any help is greatly appreciated. >>>> >>>> Thanks, >>>> Sasha >>>> >>>> >>>> Sasha Wolosin >>>> Research Assistant >>>> Developmental Cognitive Neurology >>>> Kennedy Krieger Institute >>>> 707 N. Broadway >>>> Baltimore, MD 21205 >>>> ph: (443) 923-9270 >>>> wolosin(a)kennedykrieger.org >>>> >>>> >>>> >>>> Disclaimer: >>>> The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >>>> >>>> _______________________________________________ >>>> 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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aparc.annot
by antao＠itsa.ucsf.edu 18 Oct '05

18 Oct '05

Hi, I just updated the freesurfer. I have processed a large amount of data using older recon-all. I just found that aparc.annot generated by oldered and newer recon-all are different. I want to generate new aparc.annot to calculate the cortical thinckness in different regions. What is the best way to do it without re-processing all data? Thanks, Antao

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Re: [Freesurfer] tkregister2
by Sasha Wolosin 18 Oct '05

18 Oct '05

How can I check the registration if I can't see the surface? -Sasha >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 10/18/2005 12:07 PM >>> If you don't have a surface, then don't run it with --surf. It's important to have an accurate talairach.xfm. doug On Mon, 17 Oct 2005, Sasha Wolosin wrote: > Dear Nick, > > I recently installed the dev release from October 3rd, but tkregister2 still does not work after autorecon1. (It will not load the orig volume because rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I not using the correct inputs for this step (my inputs are the same as that of the tutorial)? How important is it to have a correct registration before running autorecon2? > > Here is the script for a subject who has only been run with autorecon1: > > % [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal --surf orig > surfname set to orig > INFO: no target volume specified, assuming FreeSurfer orig volume. > target volume orig > movable volume (null) > reg file (null) > LoadVol 1 > $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ > Diagnostic Level -1 > talairach.xfm --------------------- > 1.020 -0.138 0.036 -2.498; > 0.151 1.100 -0.045 -8.636; > -0.033 0.052 1.156 -11.535; > 0.000 0.000 0.000 1.000; > WARNING: can't find the talairach xform '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' > WARNING: transform is not loaded into mri > INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz > WARNING: can't find the talairach xform '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' > WARNING: transform is not loaded into mri > INFO: changing target type to float > Ttarg: -------------------- > -1.000 0.000 0.000 128.538; > 0.000 0.000 1.000 -132.197; > 0.000 -1.000 0.000 137.708; > 0.000 0.000 0.000 1.000; > INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz > 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 = 0, float2int = 0 > ---- Input registration matrix -------- > 1.020 -0.138 0.036 -2.498; > 0.151 1.100 -0.045 -8.636; > -0.033 0.052 1.156 -11.535; > 0.000 0.000 0.000 1.000; > subject = 2333 > Reading lh surface orig > MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open file > No such file or directory > tkregister2: could not read surface orig > No such file or directory > [root@bwy-1-113mm mri]$ > > If I instead run the command: > tkregister2 --mgz --s 2333 --fstal > tkregister2 does load, but there is no green orig outline to guide any corrections. > > If I run tkregister2 after running autorecon2, it also loads, but the registration is all wrong. (It was about as far off as the tutorial subject) Here is the output: > > [root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s 2338 --fstal --surf orig > surfname set to orig > INFO: no target volume specified, assuming FreeSurfer orig volume. > target volume orig > movable volume (null) > reg file (null) > LoadVol 1 > $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ > Diagnostic Level -1 > talairach.xfm --------------------- > 1.131 -0.107 0.009 -12.066; > 0.107 1.119 -0.133 -2.885; > 0.003 0.141 1.186 -27.267; > 0.000 0.000 0.000 1.000; > WARNING: can't find the talairach xform '/freesurfer/subjects/2338/mri/transforms/talairach.xfm' > WARNING: transform is not loaded into mri > INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz > WARNING: can't find the talairach xform '/freesurfer/subjects/2338/mri/transforms/talairach.xfm' > WARNING: transform is not loaded into mri > INFO: changing target type to float > Ttarg: -------------------- > -1.000 0.000 0.000 136.359; > 0.000 0.000 1.000 -135.309; > -0.000 -1.000 0.000 159.346; > 0.000 0.000 0.000 1.000; > INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz > 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 = 0, float2int = 0 > ---- Input registration matrix -------- > 1.131 -0.107 0.009 -12.066; > 0.107 1.119 -0.133 -2.885; > 0.003 0.141 1.186 -27.267; > 0.000 0.000 0.000 1.000; > subject = 2338 > Reading lh surface orig > Done reading surface > Reading rh surface orig > Done reading surface > Zoom Factor = 2 > FOV = 256 > Opening window 2338 > Setting scale > tkregister2: interface: /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} > > > Looking through the script I noticed it never mentions the path to the correct .xfm file, which is in the subjects directory (the subjects directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off. > > Any help is greatly appreciated, > Thanks, > Sasha > > > > > > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 > wolosin(a)kennedykrieger.org >>>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 09/15/05 2:40 PM >>> > Sasha, > > An alternative solution is to create the COR files for the talairach > subject: > > cd $SUBJECTS_DIR/talairach/mri > mri_convert -it mgz -ot cor orig.mgz orig/ > > This will deposit COR files into the orig/ directory, and your current > tkregister2 should then work. > > We are recommending using .mgz files over the older COR format, and are > still trying to make all the tools fully compliant. > > A new 'dev' release containing the updated tkregister2 will be posted in > the next couple days. > > Nick > > > On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote: >> I just fixed this error. For those in the nmr center, the fix will be >> live tomorrow. For those outside, you can download a new Linux version >> from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> Sasha Wolosin wrote: >> >>> Dear all, >>> >>> I am having trouble running tkregister2. >>> >>> I get an error when I run tkregister2 on a subject after running autorecon1 (see below.) However, I also get an error when I run it on bert. >>> It seems tkregister2 is searching for COR files, but I am using mgz format. Am I not using the correct flags? >>> >>> My subjects directory contains the talairach subject included in the dev release. Do I need to download talairach separately? >>> >>> Here is the output for subject 2335 and bert: >>> [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal >>> INFO: no target volume specified, assuming FreeSurfer orig volume. >>> target volume orig >>> movable volume (null) >>> reg file (null) >>> LoadVol 1 >>> $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ >>> Diagnostic Level -1 >>> talairach.xfm --------------------- >>> 1.002 0.050 -0.017 -3.539; >>> -0.053 1.034 -0.076 -12.275; >>> 0.014 0.081 1.091 -14.424; >>> 0.000 0.000 0.000 1.000; >>> corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info >>> ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 >>> >>> >>> [root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal >>> INFO: no target volume specified, assuming FreeSurfer orig volume. >>> target volume orig >>> movable volume (null) >>> reg file (null) >>> LoadVol 1 >>> $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ >>> Diagnostic Level -1 >>> talairach.xfm --------------------- >>> 1.154 -0.024 0.046 -5.813; >>> 0.014 0.941 0.131 -21.893; >>> -0.048 -0.155 1.123 -0.730; >>> 0.000 0.000 0.000 1.000; >>> WARNING: can't find the talairach xform '/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm' >>> WARNING: transform is not loaded into mri >>> corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info >>> ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 >>> [root@bwy-1-113mm subjects]$ >>> >>> >>> Any help is greatly appreciated. >>> >>> Thanks, >>> Sasha >>> >>> >>> Sasha Wolosin >>> Research Assistant >>> Developmental Cognitive Neurology >>> Kennedy Krieger Institute >>> 707 N. Broadway >>> Baltimore, MD 21205 >>> ph: (443) 923-9270 >>> wolosin(a)kennedykrieger.org >>> >>> >>> >>> Disclaimer: >>> The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >>> >>> _______________________________________________ >>> 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] tkregister2
by Sasha Wolosin 18 Oct '05

18 Oct '05

Dear Nick, I recently installed the dev release from October 3rd, but tkregister2 still does not work after autorecon1. (It will not load the orig volume because rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I not using the correct inputs for this step (my inputs are the same as that of the tutorial)? How important is it to have a correct registration before running autorecon2? Here is the script for a subject who has only been run with autorecon1: % [root@bwy-1-113mm mri]$ tkregister2 --mgz --s 2333 --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz WARNING: can't find the talairach xform '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.538; 0.000 0.000 1.000 -132.197; 0.000 -1.000 0.000 137.708; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz 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 = 0, float2int = 0 ---- Input registration matrix -------- 1.020 -0.138 0.036 -2.498; 0.151 1.100 -0.045 -8.636; -0.033 0.052 1.156 -11.535; 0.000 0.000 0.000 1.000; subject = 2333 Reading lh surface orig MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open file No such file or directory tkregister2: could not read surface orig No such file or directory [root@bwy-1-113mm mri]$ If I instead run the command: tkregister2 --mgz --s 2333 --fstal tkregister2 does load, but there is no green orig outline to guide any corrections. If I run tkregister2 after running autorecon2, it also loads, but the registration is all wrong. (It was about as far off as the tutorial subject) Here is the output: [root@bwy-1-113mm /freesurfer_subjects]$ tkregister2 --mgz --s 2338 --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/freesurfer/subjects/2338/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz WARNING: can't find the talairach xform '/freesurfer/subjects/2338/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 136.359; 0.000 0.000 1.000 -135.309; -0.000 -1.000 0.000 159.346; 0.000 0.000 0.000 1.000; INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz 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 = 0, float2int = 0 ---- Input registration matrix -------- 1.131 -0.107 0.009 -12.066; 0.107 1.119 -0.133 -2.885; 0.003 0.141 1.186 -27.267; 0.000 0.000 0.000 1.000; subject = 2338 Reading lh surface orig Done reading surface Reading rh surface orig Done reading surface Zoom Factor = 2 FOV = 256 Opening window 2338 Setting scale tkregister2: interface: /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} Looking through the script I noticed it never mentions the path to the correct .xfm file, which is in the subjects directory (the subjects directory is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file to the folder it was looking for, and the registration was still just as far off. Any help is greatly appreciated, Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 09/15/05 2:40 PM >>> Sasha, An alternative solution is to create the COR files for the talairach subject: cd $SUBJECTS_DIR/talairach/mri mri_convert -it mgz -ot cor orig.mgz orig/ This will deposit COR files into the orig/ directory, and your current tkregister2 should then work. We are recommending using .mgz files over the older COR format, and are still trying to make all the tools fully compliant. A new 'dev' release containing the updated tkregister2 will be posted in the next couple days. Nick On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote: > I just fixed this error. For those in the nmr center, the fix will be > live tomorrow. For those outside, you can download a new Linux version > from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > Sasha Wolosin wrote: > > >Dear all, > > > > I am having trouble running tkregister2. > > > > I get an error when I run tkregister2 on a subject after running autorecon1 (see below.) However, I also get an error when I run it on bert. > > It seems tkregister2 is searching for COR files, but I am using mgz format. Am I not using the correct flags? > > > > My subjects directory contains the talairach subject included in the dev release. Do I need to download talairach separately? > > > >Here is the output for subject 2335 and bert: > >[root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal > >INFO: no target volume specified, assuming FreeSurfer orig volume. > >target volume orig > >movable volume (null) > >reg file (null) > >LoadVol 1 > >$Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ > >Diagnostic Level -1 > >talairach.xfm --------------------- > > 1.002 0.050 -0.017 -3.539; > >-0.053 1.034 -0.076 -12.275; > > 0.014 0.081 1.091 -14.424; > > 0.000 0.000 0.000 1.000; > >corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info > >ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 > > > > > >[root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal > >INFO: no target volume specified, assuming FreeSurfer orig volume. > >target volume orig > >movable volume (null) > >reg file (null) > >LoadVol 1 > >$Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ > >Diagnostic Level -1 > >talairach.xfm --------------------- > > 1.154 -0.024 0.046 -5.813; > > 0.014 0.941 0.131 -21.893; > >-0.048 -0.155 1.123 -0.730; > > 0.000 0.000 0.000 1.000; > >WARNING: can't find the talairach xform '/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm' > >WARNING: transform is not loaded into mri > >corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info > >ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 > >[root@bwy-1-113mm subjects]$ > > > > > >Any help is greatly appreciated. > > > >Thanks, > >Sasha > > > > > >Sasha Wolosin > >Research Assistant > >Developmental Cognitive Neurology > >Kennedy Krieger Institute > >707 N. Broadway > >Baltimore, MD 21205 > >ph: (443) 923-9270 > >wolosin(a)kennedykrieger.org > > > > > > > >Disclaimer: > >The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > > > >_______________________________________________ > >Freesurfer mailing list > >Freesurfer(a)nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > >

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Freesurfer October 2005