Freesurfer

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optseq2 event duration definition
by Andrew Valdespino 14 May '12

14 May '12

(1) Version: optseq2.c,v 2.21.2.1 (2) Computer operating system: Mac OS X Version 10.7.3 (3) Command line: Not relavant here (4) Description of the problem: A trial in my experiment involves a countdown (duration 2 seconds) followed by the event of interest (0.5 seconds) followed by a blank screen (3.5 seconds). I am having trouble with the definition of 'event duration'. That is, for the argument --ev x *y* z, what do I specify for *y *(event duration)? the entire trial is 7 seconds in length, but the duration of the event of interest is only 0.5 seconds (embedded between a countdown, and a blank screen). As a second question, is psdmin always set at '0'? Would '0' be appropriate for the trial structure described above? (5) Log and/or summary files: Not relavant here ________

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Re: [Freesurfer] optseq
by Douglas N Greve 14 May '12

14 May '12

Hi Hanah, I found another bug with the way that tNullMin was being implemented which causes this problem. You can get the new version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2.linux doug On 05/14/2012 08:47 AM, Hanah Chapman wrote: > Dear Doug, > > Thank you for your response to my question about optseq and > tnullmin/max on the freesurfer listserv. The new file you sent did fix > the problem where some null trials exceeded the tnullmax, but I'm > still having difficulty calculating the correct number of timepoints. > I always get one very long (~60s) null event at the end. My starting > approach was to compute the average length of the null trial within > the range of tnullmin-tnullmax, and then allow that much time between > each trial. I also tried to reduce the number of timepoints in steps, > but I still get the problem of the long null at the end right up until > the point that optseq returns an error (presumably because there are > not enough timepoints). If you can offer any insight, that would be > much appreciated. The starting code in which I used an average of 7s > between each trial is this: > > > ./optseq2.linux --ntp 360 --tr 2 --tnullmin 4 --tnullmax 10 --psdwin 0 > 20 --nkeep 6 --o ./attention/360tp --nsearch 1000 \ > --ev DD 2 5 \ > --ev DF 2 5 \ > --ev DP 2 5 \ > --ev DN 2 5 \ > --ev FF 2 5 \ > --ev FD 2 5 \ > --ev FN 2 5 \ > --ev FP 2 5 \ > --ev PP 2 5 \ > --ev PD 2 5 \ > --ev PN 2 5 \ > --ev PF 2 5 \ > --ev NN 2 5 \ > --ev ND 2 5 \ > --ev NF 2 5 \ > --ev NP 2 5 > > Thanks for your help, > > Hanah > > -- > > Hanah Chapman > Postdoctoral Fellow > Department of Psychology > The Ohio State University -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Edit Aseg with Surfaces
by Matt Glasser 14 May '12

14 May '12

Is there a way to adjust the grey and white matter of the aseg automatically based on the surfaces? Thanks, Matt.

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mri_glmfit-sim error
by Juke Cha 14 May '12

14 May '12

Hi all, I've got an error while running mri_glmfit-sim. I ran this for several measures, and only for 'volume' and 'area' the function complained about missing CSD files stating "ERROR: cannot find any csd files" I don't know if this is a known issue. I saw several threads posted regarding this issue, but did not see a solution. Any suggestion? Best, Juke

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Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?
by Douglas N Greve 14 May '12

14 May '12

I don't know what that means. It is not an FS issue, it is something wrong on your system. doug On 05/14/2012 06:17 AM, Long wrote: > Hi Douglas, > > I used the command: > > tkmedit fslt1mnifs orig.mgz ./lh.zmap.mgh > > but it said: Resource temporarily unavailable. > > Best, > Xiangyu > > On Tue, Apr 24, 2012 at 5:01 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > How does it look in tkmedit? > > > On 04/23/2012 12:20 PM, Long wrote: > > Hi Douglas, > > I tried to do spatial normalization for volume data, all steps > are following: > > 1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s > subj01 --init-fsl --reg bb_register.dat > > I checked the result by tkregister2, it looked good. > > 2) mris_preproc --target fsaverage --hemi lh --iv > fsubj01_001.hdr bb_register.dat --projfrac 0.5 --out lh.zmap.mgh > > 3) mri_surf2vol --surfval lh.zmap.mgh --hemi lh --identity > fsaverage --outvol subj01_001.nii.gz --projfrac 0.5 > --fillribbon --template wfrest_res_co_001.hdr > > However, the output file subj01_001.nii.gz showed wrong > orientation when viewing in MRIcron, the image looked rotated. > Could you please help with it? > > Best, > Xiangyu > > On Mon, Apr 23, 2012 at 4:31 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Xiangyu, just add --identity fsaverage to the surf2vol > command line > doug > > > On 04/19/2012 05:57 PM, Long wrote: > > Hi all, > > > > I had a question when convert a surface to volume space. > > > > First, I converted a volume nifti data to fsaverage: > > > > mris_preproc --target fsaverage --hemi lh --iv data.nii > > bb_register.dat --out data.lh.mgh > > > > Then, I want to convert the data.lh.mgh to volume space, I tried > > mri_surf2vol, however, it needs register.dat. As I > understood, the > > data.lh.mgh was already registered to fsaverage surface, so how > can I > > get the required register.dat file? Thank you for your > attention. > > > > Best, > > Xiangyu > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the > person to > whom it is > addressed. If you believe this e-mail was sent to you in > error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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tfl single echo siemens ve‭rio te adjustment
by Jörg Pfannmöller 14 May '12

14 May '12

Dear freesurfers, currently the freesurfer single tfl protocol for the segmentation of the cortex surface was implemented at our scanner. Siemens Verio 3T MRT NumarisVer syngo MR B17 Gradientensystem (Tim 102x8) VQ-Engine Unfortunately the echo-time (te) could not be set to the recomended value of 3.31ms. The te is defined by the system and can not be changed. Is this critical for the segmentation quality? Sincerely yours A MRT-Physician

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Post-Doctoral position in brain imaging and computational morphometry – University of Geneva
by Narly GOLESTANI 13 May '12

13 May '12

Post-Doctoral applications are invited at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include the development of new data-driven computational morphometry methods for analysis of structural magnetic resonance imaging (MRI) data, and application of these to large datasets in the context of normal variability, disease, and expertise. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field with a strong mathematical and computational background, and ideally experience in pattern recognition and brain image analysis as well as excellent programming skills. We offer a competitive starting salary of 68, 964 CHF/year. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: Narly.Golestani(a)unige.ch.

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Re: [Freesurfer] tkregister2 wrong orientation
by Yosuke Morishima 11 May '12

11 May '12

Dear Doug, Great! I tried mri_vol2vol and it worked perfectly! Now I can proceed the steps. I really appreciate your helpful suggestions! Btw, do you think FSL made something wrong in my case and the problem in transformation would affect surface tracking? Best wishes, Yosuke > Try reversing the input and reference to flirt. Alternatively, you can > use mri_vol2vol instead. > doug > > On 05/11/2012 04:14 PM, Yosuke Morishima wrote: >> Dear Doug, >> >> Here's my command lines >> >> tkregister2 --mov ${SUBDIR}/mri/nifti/orig.nii --targ >> ${SUBDIR}/mri/nifti/rawavg.nii --regheader --reg junk --fslregout >> ${SUBDIR}/T1/freesurfer2struct.mat --noedit >> >> fsl4.1-flirt -in ${SUBDIR}/mri/nifti/orig.nii -ref >> ${SUBDIR}/mri/nifti/rawavg.nii.gz -out ${SUBDIR}/mri/nifti/testconform >> -applyxfm -init ${SUBDIR}/T1/freesurfer2struct.mat -interp >> nearestneighbour >> >> >> To check the transformation, I first created NIFTI format of orig and >> rawavg images to make sure the orientation, and then apply tkregister2 >> and FLIRT to those images. >> Both Freesurfer and FSL are the latest version. >> >> Best, >> Yosuke >> >> >> >> >> >> >> >>> How did you apply the matrix? What was your cmd line? >>> >>> On 05/11/2012 02:49 PM, Yosuke Morishima wrote: >>>> Dear Doug, >>>> >>>> I'm using FSL view to check the images, and see the bottle on the same >>>> side of 'R' in the transformed image, while I see the bottle on the >>>> 'L' side in original images. >>>> >>>> I first found the problem when I tried to open the mask label with >>>> tksurfer, which will be used for surface fiber tracking. I made a ROI >>>> on right hemisphere but I could not open the label. Then, I opened the >>>> ROI image transformed to freesurfer space with FSL view, and found ROI >>>> is flipped. >>>> >>>> Best, >>>> Yosuke >>>> >>>> >>>> >>>>> what tool are you using when you see it on the right? Note that the >>>>> image may be oriented any way in fslview, but if you look at the small >>>>> letters on the side of the image, you will see an indication of what the >>>>> actual orientation is >>>>> doug >>>>> >>>>> On 05/11/2012 01:53 PM, Yosuke Morishima wrote: >>>>>> Dear Doug, >>>>>> >>>>>> Thanks for your quick response and suggestion. >>>>>> Since I put a small saline bottle on subject's left forehead, I could >>>>>> make sure the L-R orientation. >>>>>> As you suggested I just checked the images in tkregister2 without >>>>>> --noedit, and it seems ok. >>>>>> But after apply image transformation by FLIRT in FSL, I see the saline >>>>>> bottle on right forehead, flipped. >>>>>> Do you think the problem is due to FSL? >>>>>> >>>>>> >>>>>> >>>>>> Best wishes, >>>>>> Yosuke >>>>>> >>>>>> >>>>>> >>>>>> 2012/5/11 Yosuke Morishima<yosukemorish...(a)gmail.com>: >>>>>>> Does it look flipped in tkregister2? If not, how are you judging that it >>>>>>> is flipped? >>>>>>> doug >>>>>>> >>>>>>> >>>>>>>> Date: Fri, 11 May 2012 14:11:09 +0200 >>>>>>>> From: Yosuke Morishima<yosukemorish...(a)gmail.com> >>>>>>>> Subject: [Freesurfer] tkregister2 wrong orientation >>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> Message-ID: >>>>>>>> >>>>>>>> <caodjftsje818-2dtthjrj5ii3g7wo-jdft7ox6kc1q7o7xr...(a)mail.gmail.com> >>>>>>>> Content-Type: text/plain; charset=ISO-8859-1 >>>>>>>> >>>>>>>> Dear Freesurfer specialits, >>>>>>>> >>>>>>>> I now have a problem that tkregister2 gives wrong orientation, >>>>>>>> specifically L-R orientation is flipped. >>>>>>>> I'm trying surface DTI fiber tracking by using FSL and Freesurfer as >>>>>>>> described in FSL documentation below and using tkregister2 to obtain >>>>>>>> transformation matrix from Freesurfer space to structural space. >>>>>>>> http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html >>>>>>>> >>>>>>>> I got transformation matrix with the following command. >>>>>>>> tkregister2 --mov mri/orig.mgz --targ mri/rawavg.mgz --regheader --reg >>>>>>>> junk --fslregout freesurfer2struct.mat --noedit >>>>>>>> >>>>>>>> Apply this transformation matrix (freesurfer2struct.mat) to a >>>>>>>> freesurfer-space image, and then >>>>>>>> I got L-R flipped image in structural space. >>>>>>>> >>>>>>>> I would really appreciate if you have any suggestions to solve the >>>>>>>> problem. >>>>>>>> Thanks. >>>>>>>> >>>>>>>> Best wishes, >>>>>>>> Yosuke >>>>>>>> >>>>>>>> >>>>>>>> Here is the message appeared in the terminal. >>>>>>>> >>>>>>>> tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl >>>>>>>> target volume >>>>>>>> /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz >>>>>>>> movable volume >>>>>>>> /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz >>>>>>>> reg file junk >>>>>>>> LoadVol 0 >>>>>>>> ZeroCRAS 0 >>>>>>>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ >>>>>>>> Diagnostic Level -1 >>>>>>>> INFO: loading target >>>>>>>> /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz >>>>>>>> INFO: target does not conform to COR format, so I'm going to >>>>>>>> reslice to COR. This will not affect the final registration. >>>>>>>> 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 >>>>>>>> /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz >>>>>>>> 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 >>>>>>>> Computing reg from header (and possibly input matrix) >>>>>>>> ---- Input registration matrix (computed) -------- >>>>>>>> 1.000 -0.000 -0.000 -0.000; >>>>>>>> -0.000 1.000 0.000 0.000; >>>>>>>> -0.000 0.000 1.000 0.000; >>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>> --------------------------------------- >>>>>>>> ---- Input registration matrix -------- >>>>>>>> 1.000 -0.000 -0.000 -0.000; >>>>>>>> -0.000 1.000 0.000 0.000; >>>>>>>> -0.000 0.000 1.000 0.000; >>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>> Determinant 1 >>>>>>>> subject = subject-unknown >>>>>>>> RegMat --------------------------- >>>>>>>> -1.000 0.002 -0.004 -0.000; >>>>>>>> 0.003 -0.162 -0.987 0.000; >>>>>>>> 0.003 0.987 -0.162 -0.000; >>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>> FSLOUTPUTTYPE NIFTIGZ >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> ------------------------------------------------------ >>>>>>> Yosuke Morishima M.D. Ph.D. >>>>>>> Laboratory for Social and Neural Systems Research >>>>>>> Institute for Empirical Research in Economics >>>>>>> University of Zurich >>>>>>> Blumlisalpstrasse 10 >>>>>>> CH-8006, Zurich >>>>>>> Switzerland >>>>>>> Phone: +41 44 634 51 69 >>>>>>> Fax: +41 44 634 49 07 >>>>>>> Email yosukemorish...(a)gmail.com >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> gr...(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------ >>>>> Dr. Yosuke Morishima M.D. Ph.D. >>>>> Laboratory for Social and Neural Systems Research >>>>> Department of Economics >>>>> University of Zurich >>>>> Blumlisalpstrasse 10 >>>>> CH-8006, Zurich >>>>> Switzerland >>>>> Phone: +41 44 634 51 69 >>>>> Fax: +41 44 634 49 07 >>>>> Email yosuke.morish...(a)econ.uzh.ch >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >> >> >> -- >> ------------------------------------------------------ >> Dr. Yosuke Morishima M.D. Ph.D. >> Laboratory for Social and Neural Systems Research >> Department of Economics >> University of Zurich >> Blumlisalpstrasse 10 >> CH-8006, Zurich >> Switzerland >> Phone: +41 44 634 51 69 >> Fax: +41 44 634 49 07 >> Email yosuke.morish...(a)econ.uzh.ch >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- > ------------------------------------------------------ > Dr. Yosuke Morishima M.D. Ph.D. > Laboratory for Social and Neural Systems Research > Department of Economics > University of Zurich > Blumlisalpstrasse 10 > CH-8006, Zurich > Switzerland > Phone: +41 44 634 51 69 > Fax: +41 44 634 49 07 > Email yosuke.morishima(a)econ.uzh.ch -- ------------------------------------------------------ Dr. Yosuke Morishima M.D. Ph.D. Laboratory for Social and Neural Systems Research Department of Economics University of Zurich Blumlisalpstrasse 10 CH-8006, Zurich Switzerland Phone: +41 44 634 51 69 Fax: +41 44 634 49 07 Email yosuke.morishima(a)econ.uzh.ch

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Re: [Freesurfer] tkregister2 wrong orientation
by Yosuke Morishima 11 May '12

11 May '12

Dear Doug, Here's my command lines tkregister2 --mov ${SUBDIR}/mri/nifti/orig.nii --targ ${SUBDIR}/mri/nifti/rawavg.nii --regheader --reg junk --fslregout ${SUBDIR}/T1/freesurfer2struct.mat --noedit fsl4.1-flirt -in ${SUBDIR}/mri/nifti/orig.nii -ref ${SUBDIR}/mri/nifti/rawavg.nii.gz -out ${SUBDIR}/mri/nifti/testconform -applyxfm -init ${SUBDIR}/T1/freesurfer2struct.mat -interp nearestneighbour To check the transformation, I first created NIFTI format of orig and rawavg images to make sure the orientation, and then apply tkregister2 and FLIRT to those images. Both Freesurfer and FSL are the latest version. Best, Yosuke > How did you apply the matrix? What was your cmd line? > > On 05/11/2012 02:49 PM, Yosuke Morishima wrote: >> Dear Doug, >> >> I'm using FSL view to check the images, and see the bottle on the same >> side of 'R' in the transformed image, while I see the bottle on the >> 'L' side in original images. >> >> I first found the problem when I tried to open the mask label with >> tksurfer, which will be used for surface fiber tracking. I made a ROI >> on right hemisphere but I could not open the label. Then, I opened the >> ROI image transformed to freesurfer space with FSL view, and found ROI >> is flipped. >> >> Best, >> Yosuke >> >> >> >>> what tool are you using when you see it on the right? Note that the >>> image may be oriented any way in fslview, but if you look at the small >>> letters on the side of the image, you will see an indication of what the >>> actual orientation is >>> doug >>> >>> On 05/11/2012 01:53 PM, Yosuke Morishima wrote: >>>> Dear Doug, >>>> >>>> Thanks for your quick response and suggestion. >>>> Since I put a small saline bottle on subject's left forehead, I could >>>> make sure the L-R orientation. >>>> As you suggested I just checked the images in tkregister2 without >>>> --noedit, and it seems ok. >>>> But after apply image transformation by FLIRT in FSL, I see the saline >>>> bottle on right forehead, flipped. >>>> Do you think the problem is due to FSL? >>>> >>>> >>>> >>>> Best wishes, >>>> Yosuke >>>> >>>> >>>> >>>> 2012/5/11 Yosuke Morishima<yosukemorish...(a)gmail.com>: >>>>> Does it look flipped in tkregister2? If not, how are you judging that it >>>>> is flipped? >>>>> doug >>>>> >>>>> >>>>>> Date: Fri, 11 May 2012 14:11:09 +0200 >>>>>> From: Yosuke Morishima<yosukemorish...(a)gmail.com> >>>>>> Subject: [Freesurfer] tkregister2 wrong orientation >>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>> Message-ID: >>>>>> >>>>>> <caodjftsje818-2dtthjrj5ii3g7wo-jdft7ox6kc1q7o7xr...(a)mail.gmail.com> >>>>>> Content-Type: text/plain; charset=ISO-8859-1 >>>>>> >>>>>> Dear Freesurfer specialits, >>>>>> >>>>>> I now have a problem that tkregister2 gives wrong orientation, >>>>>> specifically L-R orientation is flipped. >>>>>> I'm trying surface DTI fiber tracking by using FSL and Freesurfer as >>>>>> described in FSL documentation below and using tkregister2 to obtain >>>>>> transformation matrix from Freesurfer space to structural space. >>>>>> http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html >>>>>> >>>>>> I got transformation matrix with the following command. >>>>>> tkregister2 --mov mri/orig.mgz --targ mri/rawavg.mgz --regheader --reg >>>>>> junk --fslregout freesurfer2struct.mat --noedit >>>>>> >>>>>> Apply this transformation matrix (freesurfer2struct.mat) to a >>>>>> freesurfer-space image, and then >>>>>> I got L-R flipped image in structural space. >>>>>> >>>>>> I would really appreciate if you have any suggestions to solve the >>>>>> problem. >>>>>> Thanks. >>>>>> >>>>>> Best wishes, >>>>>> Yosuke >>>>>> >>>>>> >>>>>> Here is the message appeared in the terminal. >>>>>> >>>>>> tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl >>>>>> target volume >>>>>> /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz >>>>>> movable volume /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz >>>>>> reg file junk >>>>>> LoadVol 0 >>>>>> ZeroCRAS 0 >>>>>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ >>>>>> Diagnostic Level -1 >>>>>> INFO: loading target >>>>>> /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz >>>>>> INFO: target does not conform to COR format, so I'm going to >>>>>> reslice to COR. This will not affect the final registration. >>>>>> 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 >>>>>> /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz >>>>>> 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 >>>>>> Computing reg from header (and possibly input matrix) >>>>>> ---- Input registration matrix (computed) -------- >>>>>> 1.000 -0.000 -0.000 -0.000; >>>>>> -0.000 1.000 0.000 0.000; >>>>>> -0.000 0.000 1.000 0.000; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> --------------------------------------- >>>>>> ---- Input registration matrix -------- >>>>>> 1.000 -0.000 -0.000 -0.000; >>>>>> -0.000 1.000 0.000 0.000; >>>>>> -0.000 0.000 1.000 0.000; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> Determinant 1 >>>>>> subject = subject-unknown >>>>>> RegMat --------------------------- >>>>>> -1.000 0.002 -0.004 -0.000; >>>>>> 0.003 -0.162 -0.987 0.000; >>>>>> 0.003 0.987 -0.162 -0.000; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> FSLOUTPUTTYPE NIFTIGZ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------ >>>>> Yosuke Morishima M.D. Ph.D. >>>>> Laboratory for Social and Neural Systems Research >>>>> Institute for Empirical Research in Economics >>>>> University of Zurich >>>>> Blumlisalpstrasse 10 >>>>> CH-8006, Zurich >>>>> Switzerland >>>>> Phone: +41 44 634 51 69 >>>>> Fax: +41 44 634 49 07 >>>>> Email yosukemorish...(a)gmail.com >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> >>> -- >>> ------------------------------------------------------ >>> Dr. Yosuke Morishima M.D. Ph.D. >>> Laboratory for Social and Neural Systems Research >>> Department of Economics >>> University of Zurich >>> Blumlisalpstrasse 10 >>> CH-8006, Zurich >>> Switzerland >>> Phone: +41 44 634 51 69 >>> Fax: +41 44 634 49 07 >>> Email yosuke.morish...(a)econ.uzh.ch >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > -- ------------------------------------------------------ Dr. Yosuke Morishima M.D. Ph.D. Laboratory for Social and Neural Systems Research Department of Economics University of Zurich Blumlisalpstrasse 10 CH-8006, Zurich Switzerland Phone: +41 44 634 51 69 Fax: +41 44 634 49 07 Email yosuke.morishima(a)econ.uzh.ch -- ------------------------------------------------------ Dr. Yosuke Morishima M.D. Ph.D. Laboratory for Social and Neural Systems Research Department of Economics University of Zurich Blumlisalpstrasse 10 CH-8006, Zurich Switzerland Phone: +41 44 634 51 69 Fax: +41 44 634 49 07 Email yosuke.morishima(a)econ.uzh.ch

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Re: [Freesurfer] tkregister2 wrong orientation
by Yosuke Morishima 11 May '12

11 May '12

Dear Doug, Thanks for your quick response and suggestion. Since I put a small saline bottle on subject's left forehead, I could make sure the L-R orientation. As you suggested I just checked the images in tkregister2 without --noedit, and it seems ok. But after apply image transformation by FLIRT in FSL, I see the saline bottle on right forehead, flipped. Do you think the problem is due to FSL? Best wishes, Yosuke 2012/5/11 Yosuke Morishima <yosukemorishima(a)gmail.com>: > Does it look flipped in tkregister2? If not, how are you judging that it > is flipped? > doug > > >> Date: Fri, 11 May 2012 14:11:09 +0200 >> From: Yosuke Morishima <yosukemorishima(a)gmail.com> >> Subject: [Freesurfer] tkregister2 wrong orientation >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: >> <CAOdjfTSJE818-2dTthJrJ5ii3G7wo-JDfT7oX6Kc1Q7o7XRegQ(a)mail.gmail.com> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Dear Freesurfer specialits, >> >> I now have a problem that tkregister2 gives wrong orientation, >> specifically L-R orientation is flipped. >> I'm trying surface DTI fiber tracking by using FSL and Freesurfer as >> described in FSL documentation below and using tkregister2 to obtain >> transformation matrix from Freesurfer space to structural space. >> http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html >> >> I got transformation matrix with the following command. >> tkregister2 --mov mri/orig.mgz --targ mri/rawavg.mgz --regheader --reg >> junk --fslregout freesurfer2struct.mat --noedit >> >> Apply this transformation matrix (freesurfer2struct.mat) to a >> freesurfer-space image, and then >> I got L-R flipped image in structural space. >> >> I would really appreciate if you have any suggestions to solve the problem. >> Thanks. >> >> Best wishes, >> Yosuke >> >> >> Here is the message appeared in the terminal. >> >> tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl >> target volume /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz >> movable volume /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz >> reg file junk >> LoadVol 0 >> ZeroCRAS 0 >> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ >> Diagnostic Level -1 >> INFO: loading target >> /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz >> INFO: target does not conform to COR format, so I'm going to >> reslice to COR. This will not affect the final registration. >> 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 >> /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz >> 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 >> Computing reg from header (and possibly input matrix) >> ---- Input registration matrix (computed) -------- >> 1.000 -0.000 -0.000 -0.000; >> -0.000 1.000 0.000 0.000; >> -0.000 0.000 1.000 0.000; >> 0.000 0.000 0.000 1.000; >> --------------------------------------- >> ---- Input registration matrix -------- >> 1.000 -0.000 -0.000 -0.000; >> -0.000 1.000 0.000 0.000; >> -0.000 0.000 1.000 0.000; >> 0.000 0.000 0.000 1.000; >> Determinant 1 >> subject = subject-unknown >> RegMat --------------------------- >> -1.000 0.002 -0.004 -0.000; >> 0.003 -0.162 -0.987 0.000; >> 0.003 0.987 -0.162 -0.000; >> 0.000 0.000 0.000 1.000; >> FSLOUTPUTTYPE NIFTIGZ >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> ------------------------------------------------------ >> Yosuke Morishima M.D. Ph.D. >> Laboratory for Social and Neural Systems Research >> Institute for Empirical Research in Economics >> University of Zurich >> Blumlisalpstrasse 10 >> CH-8006, Zurich >> Switzerland >> Phone: +41 44 634 51 69 >> Fax: +41 44 634 49 07 >> Email? yosukemorishima(a)gmail.com >> >> > > > > > > -- > ------------------------------------------------------ > Yosuke Morishima M.D. Ph.D. > Laboratory for Social and Neural Systems Research > Institute for Empirical Research in Economics > University of Zurich > Blumlisalpstrasse 10 > CH-8006, Zurich > Switzerland > Phone: +41 44 634 51 69 > Fax: +41 44 634 49 07 > Email yosukemorishima(a)gmail.com -- ------------------------------------------------------ Yosuke Morishima M.D. Ph.D. Laboratory for Social and Neural Systems Research Institute for Empirical Research in Economics University of Zurich Blumlisalpstrasse 10 CH-8006, Zurich Switzerland Phone: +41 44 634 51 69 Fax: +41 44 634 49 07 Email morishi(a)iew.uzh.ch

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