Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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 > > > > > > > > > >

2 1

morph_subject error
by Lars Tjelta Westlye 18 Oct '05

18 Oct '05

Dear all, I'm encountering following error when running morph_subject <subject>. What is wrong? ............. registration took 0.67 hours writing registered surface to ../surf/lh.rh.sphere.reg... /var/lab-data/genetic/id106 /var/lab-data/genetic/id106/scripts /var/lab-data/genetic/id106/scripts ------------------------------------- /var/lab-data/genetic/id106/scripts mris2rgb -o id106.reg -both -c /var/lab-data/genetic/id106/surf/lh.sulc -canon /var/lab-data/genetic/id106/surf/lh.sphere.reg /var/lab-data/genetic/id106/surf/lh.sphere.reg /var/lab-data/genetic/id106/rgb ------------------------------------- using id106.reg as output stem reading canonical coordinates from /var/lab-data/genetic/id106/surf/lh.sphere.reg. Segmentation fault mris2rgb exited with errors [brain@amygdala genetic]$ Also, when typing check_subject <subject> I get the following warnings: _______ [brain@amygdala genetic]check_subject id106 CHECKING SUBJECT id106 WARN: time for rh.orig is older than rh.qsphere WARN: file rh.inflated is not equal in size to rh.smoothwm WARN: file rh.white is not equal in size to rh.smoothwm WARN: file rh.sphere is not equal in size to rh.smoothwm WARN: file rh.pial is not equal in size to rh.smoothwm WARN: file rh.sphere.reg is not equal in size to rh.smoothwm WARN: time for lh.orig is older than lh.qsphere WARN: file lh.inflated is not equal in size to lh.smoothwm WARN: file lh.white is not equal in size to lh.smoothwm WARN: file lh.sphere is not equal in size to lh.smoothwm WARN: file lh.pial is not equal in size to lh.smoothwm WARN: file lh.sphere.reg is not equal in size to lh.smoothwm WARN: file lh.rh.sphere.reg is not equal in size to lh.smoothwm --------- My guess is that these problems are connected? Anyone know how to fix this? I am the using the FS version from june (?) 2005 on this project. Cheers, Lars T .Westlye

4 3

recon-all -autorecon1 failure
by Elizabeth Fenstermacher 17 Oct '05

17 Oct '05

I am having difficulty running mri_watershed within autorecon1 on two scans, visually the orig volumes look completely normal, but mri_watershed exits with intensity-related errors The data I have been trying to run this on is located in /space/krupa/9/users/PPG_STR/Reisa/PPG10/mri /space/krupa/9/users/PPG_STR/Reisa/PPG19/mri recon-all-log error message: mri_watershed T1.mgz brain.mgz ************************************************************ The input file is T1.mgz The output file is brain.mgz If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=127 y=135 z=131 r=101 first estimation of the main basin volume: 4371827 voxels Error w=White Matter =Intensity too high (>240)...valid input ? ERROR: mri_watershed exited with non-zero status Linux node0078 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686 i386 GNU/Linux recon-all exited with errors at Wed Oct 12 14:45:26 EDT 2005

1 0

parcellation atlas
by marc ruiz 17 Oct '05

17 Oct '05

2 1

Error with morph_subject
by sbasho＠nmr.mgh.harvard.edu 14 Oct '05

14 Oct '05

Hi, I have been getting an error message when I try to run morph_subject and I was wondering if it has anything to do with my link to the average7 brain. The error message is below: stable2 ####################################### INFO: SUBJECTS_DIR is /autofs/space/tango_001/users/recon_modygp/surina ERROR: cannot find /autofs/space/tango_001/users/recon_modygp/surina/average7/label/lh-avg_ calcarine_sulcus.label ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on tango:/local_mount/space/tango/1 46474056 41683544 2429768 95% /autofs/space/tango_001 ------------------------------------------ recon-all exited with errors at Fri Oct 14 18:26:26 EDT 2005 Any insight would be most appreciated. Thank you! *************************************************************** Surina Basho Department of Radiology MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th Street, CNY 2301 Charlestown, MA 02129-2020 USA sbasho(a)nmr.mgh.harvard.edu ***************************************************************

1 0

Group analysis
by Sunaina Fotedar 14 Oct '05

14 Oct '05

Dear all, Would it be feasible to do a group analysis with the present developmental release of freesurfer on the subjects which were individually analyzed on the previous(old) version of freesurfer? In other words, is the Group analysis module of present version sensitive to the version in which the data was preprocessed/ reconstructed ? Thanks Sunaina Fotedar 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.

12 26

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