Freesurfer January 2006

freesurfer@nmr.mgh.harvard.edu

32 participants
47 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain 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=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

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retinotopy and FsFast
by Jane Aspell 17 May '06

17 May '06

Hi Thanks for all your previous help with freesurfer. I am trying to use FsFast to do retinotopy analysis and have been following the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I come undone at the stage of running the actual analysis, where the command should be: >sfa-sess -s avdk -a rtopy what does 'avdk' refer to? when i run it i get: ERROR: could not find session avdk when i try it with the arguments: >sfa-sess -analysis rtopy -sf sessid which is similar to the arguments needed for 'selxavg-sess' i get a similar error of not been able to find my (particular subject's) session. i believe i have set up the all the directory structures etc correctly for the sessions format as previous steps worked fine. any ideas what's going wrong? thanks Jane Aspell

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Re: [Freesurfer] Re: mk-fieldsign problems
by Jane Aspell 03 May '06

03 May '06

Hi I would be really grateful if someone could help me with the problems I am having with mk-fieldsign. Even after installing a new version of freesurfer and making various changes to libraries etc. when i run: "paint-sess -sf sessid -a rtopy -hemi rh" i get the error below: tksurfer: run tcl script: mk-fieldsign.tcl couldn't read file "mk-fieldsign.tcl": no such file or directory even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl (which works fine). i am running Red Hat Linux release 9 (Shrike) and installed from freesurfer-Linux-rh9-v2.2.tar.gz any idea what to do? thanks again for your help! Jane In message <1134599450.17318.34.camel(a)minerva.nmr.mgh.harvard.edu> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> writes: > Jane, > > Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does > not use these libraries any more (I think the older -20040218 release > did, however). > > Do you have the environment variable ITCL_LIBRARY defined in your > startup .cshrc file? You can test if it is set by typing (in csh or > tcsh): > > env|grep ITCL > > If it is set (which it might be, from your older freesurfer > installation), then it should be deleted or commented-out from > your .cshrc (or possibly it was placed in your > $FREESURFER_HOME/SetUpFreeSurfer.csh file). > > You can also just type this: > > unsetenv ITCL_LIBRARY > > and then try tkmedit. > > If this is not the problem, can you tell me which OS you are running? > Type: > > cat /etc/redhat-release > > and > > uname -a > > A last ditch effort is to install the itcl libs, from this site: > > http://rpmfind.net/linux/rpm2html/search.php?query=itcl > > But this should not be necessary, as tkmedit that you have does not use > this library (I am truly puzzled why 'ldd' shows that it needs these > libs). > > Thanks, > > Nick > > > On Mon, 2005-12-12 at 11:40 +0000, Jane Aspell wrote: > > hi nick > > > > when i type >ldd `which tkmedit` i get the ouput pasted below this email. > > libitk3.2.so and libitcl3.2.so are not found - could be the problem? > > > > uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in FreeSurferEnv.csh > > (and typing 'unsetenv TCLLIBPATH') had no effect. > > > > an earlier version of freesurfer(freesurfer-20040218) didn't give me any of > > these problems and tkmedit etc worked fine. > > > > also, does ANYONE know how to interpret the colour coding (for fovea/vertical > > meridian etc) produced by the FsFast retinotopy analysis?! > > > > thanks again! > > > > jane > > > > > > >ldd `which tkmedit` > > libtix8.1.8.3.so => > > /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0x40017000) > > libtk8.4.so => /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so > > (0x40051000) > > libtcl8.4.so => > > /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000) > > libglut.so.3 => /usr/lib/libglut.so.3 (0x401ba000) > > libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401ef000) > > libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401f8000) > > libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x40210000) > > libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x40226000) > > libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x4022e000) > > libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x402ab000) > > libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x402ef000) > > libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x403ce000) > > libtiff.so.3 => /usr/lib/libtiff.so.3 (0x403ed000) > > libcrypt.so.1 => /lib/libcrypt.so.1 (0x4042e000) > > libz.so.1 => /usr/lib/libz.so.1 (0x4045b000) > > libm.so.6 => /lib/tls/libm.so.6 (0x40469000) > > libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4048b000) > > libc.so.6 => /lib/tls/libc.so.6 (0x42000000) > > libitk3.2.so => not found > > libitcl3.2.so => not found > > libdl.so.2 => /lib/libdl.so.2 (0x4049a000) > > libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x4049e000) > > libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x404f0000) > > libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x404ff000) > > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x405b2000) > > /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) > > > > > > > > In message <1133802940.21136.14.camel(a)minerva.nmr.mgh.harvard.edu> Nick > > Schmansky <nicks(a)nmr.mgh.harvard.edu> writes: > > > Jane, > > > > > > This is an unusual error, since tkmedit and tksurfer do not use the ITK > > > library. To figure out how libitk3.2.so is being referenced, can you > > > send me the output of this command: > > > > > > ldd `which tkmedit` > > > > > > I suspect there is some conflict between the FSL setup and Freesurfer, > > > as FSL does use ITK, and Freesurfer does not, but performs the FSL setup > > > (as a convenience to MGH-NMR users). Along this line, one option is to > > > edit the file FreeSurferEnv.csh (found in your $FREESURFER_HOME) and > > > comment-out this line: > > > > > > source ${FSL_DIR}/etc/fslconf/fsl.csh > > > > > > like this: > > > > > > # source ${FSL_DIR}/etc/fslconf/fsl.csh > > > > > > Another option is to type this after sourcing the freesurfer setup file: > > > > > > unsetenv TCLLIBPATH > > > > > > This last option is just a guess at a fix though. > > > > > > Nick > > > > > > > > > On Mon, 2005-12-05 at 15:37 +0000, Jane Aspell wrote: > > > > hi > > > > > > > > i installed a newer version of freesurfer (using download > > > > freesurfer-Linux-rh9-v2.2.tar.gz) but when i try and run tkmedit or tksurfer i > > > > get the error: > > > > > > > > "error while loading shared libraries: libitk3.2.so: cannot open shared object > > > > file: No such file or directory" > > > > > > > > this is my output when i source SetUpFreeSurfer.csh: > > > > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > FREESURFER_HOME /home/jaspell/freesurfer > > > > FSFAST_HOME /home/jaspell/freesurfer/fsfast > > > > SUBJECTS_DIR /home/jaspell/freesurfer/subjects > > > > FUNCTIONALS_DIR /home/jaspell/freesurfer/sessions > > > > MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin > > > > MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib > > > > TCLLIBPATH /home/jaspell/freesurfer/lib/tcltktixblt/lib > > > > FSL_DIR /usr/local/fsl > > > > > > > > and these are the contents of /home/jaspell/freesurfer/lib/tcltktixblt/lib: > > > > > > > > blt2.4/ libBLTlite24.a libtclstub8.4.a libtk8.4.so* > > > > tix8.1/ > > > > libBLT24.a* libBLTlite.2.4.dylib* libtix8.1.8.3.so libtk.so.0* > > > > tixConfig.sh > > > > libBLT.2.4.dylib* libBLTlite.a libtix8.1.8.4.so libtkstub8.4.a > > > > tk8.4/ > > > > libBLT.2.dylib* libtcl8.4.so* libtixsam8.1.8.4.so tcl8.4/ > > > > tkConfig.sh > > > > libBLT.a* libtcl.so.0* libtix.so.0 tclConfig.sh > > > > > > > > > > > > any idea how to fix it? > > > > > > > > i don't suppose there's a way of updating an old version of freesurfer without > > > > reinstalling the entire (new version) package? > > > > > > > > thanks! > > > > > > > > jane > > > > > > > > > > > > > > > > > > > > In message <Pine.LNX.4.62.0512021326490.5676(a)icebox.nmr.mgh.harvard.edu> Doug > > > > Greve <greve(a)nmr.mgh.harvard.edu> writes: > > > > > > > > > > That's a pretty old version. Can you download and install a new version? > > > > > > > > > > I actually don't know that much about the interpretation of the color > > > > > wheel. Maybe Nouchine or Sari can help with this. > > > > > > > > > > doug > > > > > > > > > > > > > > > On Fri, 2 Dec 2005, Jane Aspell wrote: > > > > > > > > > > > hi again > > > > > > > > > > > > i'm still really stuck with my retinotopy analysis as i'm not sure if my > > > > > > version of paint-sess $Id: paint-sess,v 1.2 2003/08/06 00:53:50 greve Exp $ > > > > > > FAST Version 20031218) has a bug in it (it doesn't make the field sign > > map). i > > > > > > originally downloaded freesurfer-20040218-Linux.tar.gz (for RedHat 9). > > > > > > > > > > > > also, can someone also confrim the colour coding is: red=upper field/fovea, > > > > > > blue=horizontal meridian/parafovea, green=lower visual field/periphery? > > > > > > > > > > > > i can't work out what the overlay threshold settings should be in > > tksurfer to > > > > > > correctly display the colours to code the retinotopy, is there some > > rationale > > > > > > for choosing them? > > > > > > > > > > > > thanks a lot for your help! > > > > > > > > > > > > Jane > > > > > > > > > > > > > > > > > > In message > > <Pine.LNX.4.62.0511280225500.19611(a)icebox.nmr.mgh.harvard.edu> Doug > > > > > > Greve <greve(a)nmr.mgh.harvard.edu> writes: > > > > > >> > > > > > >> What version of freesurfer (and paint-sess) are you using? This was a > > > > > >> problem in some versions about 6 mo ago, but I thought I fixed them > > > > > >> all. > > > > > >> > > > > > >> doug > > > > > >> > > > > > >> > > > > > >> > > > > > >> On Thu, 24 Nov 2005, Jane Aspell wrote: > > > > > >> > > > > > >>> hi again > > > > > >>> I have been proceeding with the retinotopy analysis using FsFast, > > > > > > following the > > > > > >>> instructions at: > > > > > >>> > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > > > > > >>> and i believe i have successfully overlaid the results on my surfaces and > > > > > > now > > > > > >>> have two questions: > > > > > >>> > > > > > >>> i wasn't able to create the fieldsign with 'paint-sess' because it > > > > > > couldn't find > > > > > >>> tksurfer.new. when i run 'surf-sess' i use the flag -old which forces it > > > > > > to use > > > > > >>> tksurfer.old but this doesn't work in the former case. how can i make > > > > > >>> 'paint-sess' use tksurfer.old and thus create the fieldsign? > > > > > >>> > > > > > >>> there are no instructions on how to relate the colours seen when viewing > > > > > > eccen > > > > > >>> and polar to the location of the ring and wedge. is there a map somewhere > > > > > > that > > > > > >>> can be loaded that tells me what order the colours run from fovea to > > > > > > periphery > > > > > >>> and from vertical to horizontal meridian etc.? > > > > > >>> > > > > > >>> thanks again for your help! > > > > > >>> > > > > > >>> jane > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >> > > > > > >> -- > > > > > >> Douglas N. Greve, Ph.D. > > > > > >> MGH-NMR Center > > > > > >> greve(a)nmr.mgh.harvard.edu > > > > > >> Phone Number: 617-724-2358 > > > > > >> Fax: 617-726-7422 > > > > > >> > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve(a)nmr.mgh.harvard.edu > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > >

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Short Course in fMRI
by Doug Greve 10 Apr '06

10 Apr '06

Mark Vangel and I are offering a short course in the statistical signal processing of fMRI. October 31 (Mon) & November 1 (Tue), 2005 7th Floor Auditorium Building 149 Charlestown Navy Yard Free, but limited to 40 attendees. Register at: http://www.nmr.mgh.harvard.edu/martinos/training/shortCoursefMRIStats.php doug

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FS-FAST registration across sessions
by Jane Aspell 08 Mar '06

08 Mar '06

Hi My question was asked last year by Tommi Raij (see email pasted below) but I couldn't find a reply to it in the archives. I am analysing retinotopy data that was collected over several sessions but I cannot see how to register scans from multiple sessions together, and to the subject's anatomical scan. Although Fs-Fast appears to combine the data from multiple sessions during the retinotopy analysis it only seems to be possible to use one registration file (register.dat) when overlaying the results onto the anatomical. I would have thought that registering scans from multiple sessions together would be a feature that many people would require. Is there anyway to do it? Tommi gives some possible methods in his email below. When I do try and overlay my data onto a surface I see 'gaps' in the blue/yellow colouring of the fieldsign map overlaid onto the cortical surface. I wonder if this could be due to the inaccuracy of the registration given that I only used the register.dat from the registration of the first session. hope that makes sense! i'd be grateful for any help with this! Jane -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ------------------------------------------- [Freesurfer] FS-FAST Registration Question: registration across sessions within subjects Tommi Raij Thu, 20 Oct 2005 15:43:46 -0700 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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newest dev question
by Sasha Wolosin 31 Jan '06

31 Jan '06

Dear all, Is the latest January dev release compatible with the previous one (Oct 2005) with regards to surface-based measures? Are there any differences in the segmentation algorithms or in the implementation of these algorithms which might cause differences in the surface files? Thanks, Sasha 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.

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Display of thickness measurement
by Antao Du 31 Jan '06

31 Jan '06

Hi, I am interested in measuring the cortical thickness in entorhinal cortex. I can display the thickness measurement by " tkmedit AD1232 brain.mgz lh.white " to look at the measurement in entorhinal region, but I don't know the boundary of entorhinal cortex by this way. Is there any way that I can only display the measurement of cortical thckness in the entorhinal cortex? Thanks, Antao

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feat2surf
by Strien, N van 31 Jan '06

31 Jan '06

Hi, I am having several problems with the feat2surf script when using this on my own data. For privacy purposes I renamed my subject to bert, however this refers not to the sample dataset: The problems that I face with the feat2surf script are as follows: 1) If I do not edit the script manually it stops when not finding a data file (zstat1.img) in analyze format. If I edit the feat2surf script so it only finds a zstat1.nii file it continues. 2) Results are not stored under 4 new subdirectories in the .feat main directory (as suggested in the tutorial). They are stored (and overwritten) in the /root directory. (I know it’s a bad habit of mine to work under the root account, but I expect the outputdir will only change to /home/$username/ if I change user. Ẃhen the script only looks for .nii files (and finds them) it exits nicely (after commenting away some of the images the feat2surf script looks for such as cluster* and rendered*). 3) When opening for example the rh volume in tksurfer, I get an error message that the .mgh volume is incorrect. This is the output when I run the feat2surf script without editing it. Mon Jan 30 13:32:00 CET 2006 /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_lev el mri_vol2surf --src mblok1+.feat/stats/*.img --srcreg mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out /*.mgh --surf white --out_type mgh srcvol = mblok1+.feat/stats/*.img srcreg = mblok1+.feat/reg/freesurfer/anat2exf.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = bert2 surfreg = sphere.reg interp = nearest float2int = round INFO: float2int code = 0 ERROR: analyzeRead(): cannot find any files for mblok1+.feat/stats/*.img ERROR: could not read mblok1+.feat/stats/*.img as type 16 ERROR: with mri_vol2surf --src mblok1+.feat/stats/*.img --srcreg mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out /*.mgh --surf white --out_type mgh When I ran mri_vol2surf manually (see command line below; $out1 = the output dir I created manually to store the results in), the computer runs forever displaying a vol2surf_linear message. I left it running overnight and it didn't finish. Any suggestions in what I could alter to get it right? The functional overlay works fine with tkmedit. Thanks in advance, Niels van Strien mri_vol2surf --src $datalocation/mblok1+.feat/stats/zstat1.nii --srcreg $datalocation/mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out $out1/zstat1.nii.mgh --surf white --out_type mg srcvol = /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_lev el/mblok1+.feat/stats/zstat1.nii srcreg = /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_lev el/mblok1+.feat/reg/freesurfer/anat2exf.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = bert2 surfreg = sphere.reg interp = nearest float2int = round INFO: float2int code = 0 WARNING: missing NIfTI-1 orientation (qform_code = 0) WARNING: your volume will probably be incorrectly oriented Done loading volume Reading surface /media/userdata/subjects/bert2/surf/lh.white INFO: NOT fixing vertex area Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 vol2surf_linear: nhits = 74277/126030 2 0 0 0 vol2surf_linear: nhits = 74277/126030 3 0 0 0 vol2surf_linear: nhits = 74277/126030 4 0 0 0 vol2surf_linear: nhits = 74277/126030 5 0 0 0 vol2surf_linear: nhits = 74277/126030 6 0 0 0 vol2surf_linear: nhits = 74277/126030 7 0 0 0 vol2surf_linear: nhits = 74277/126030 8 0 0 0

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Multiple warnings and errors in autorecon1
by Daniel Goldenholz 29 Jan '06

29 Jan '06

Hi Freesurfers, It has been a long time since I had the pleasure of recon-all'ing anything. Many things have changed. I ran recon-all today (based on the dev installation) and I got all sorts of interesting warnings. Should I care? If so, what should I do? Below are a few selected lines from the huge pile of output from autorecon1... ... $Id: fsl_rigid_register,v 1.13 2006/01/24 19:51:34 greve Exp $ Sun Jan 29 12:44:41 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /autofs/space/megraid_043/seder/freesurfer/nmr00036 calling eval flirt -in /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/cor-2.hdr -out /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/cor-1.hdr -omat /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image ... mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2831/nu0.mnc Can't find the talairach xform '/autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/transforms/talairach.xfm does not exist ... ... trying /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/transforms/talairach.xfm ...which does not exist .... Iteration 1 Sun Jan 29 12:53:19 EST 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.2831/nu0.mnc ./tmp.mri_nu_correct.mni.2831/nu1.mnc Not implemented yet in cache_volume_range_has_changed() Mode: atlas analysis ****VALIDATION*** THE SEGMENTATION IS PROBABLY NOT CORRECT .... -- Daniel Goldenholz ----------------------------------------------------- Cell: 617-935-9421 http://people.bu.edu/danielg/ "Mavet v'chaim b'yad halashon" "Life and death are in the hands of language" - Proverbs 18:21

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[Freesurfer] problem in autorecon1, checking the talairach transform
by Ryu-Ichiro Hashimoto 27 Jan '06

27 Jan '06

Dear all, I am trying "RecommendedReconstruction", following Wiki instruction. My problem is, after the first step of recon-all ("recon-all -autorecon1") when I try to check the talairach transform (by tkregister2 --mgz ... --fstal), I get an image incorrectly aligned ... image is displayed in quadrant (pls see ac_aft_reconall1_target.jpg). In this display, I cannot manually adjust it for coregistration. When I continue to run autorecon2, it crashes. For checking skull strip, it is correctly displayed (ac_aft_reconall1_tkmedit.jpg). I thought problem could be already present in converting from dicom to mgz, as there seems to be some missing info (message_conv.txt), though I am not sure whether it is really relevant. The image was obtained by 3T GE magnet with SPGR at BWH. Any thoughts regarding above are greatly appreciated. Thanks in advance for your help. Ryu Hashimoto mri_convert -it dicom -ot mgz 001/ 001.mgz reading from 001/... 256 DICOM 3.0 files in list Found 256 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 256. reading DICOM image... ------------------------------------------------- DICOM meta-header file name 001/dspgr_wa_001.dcm Date and time study date not found study time not found series time acquisition time Identification patient name not found manufacturer not found Dimensions number of rows 256 number of columns 256 number of frames 256 pixel width 0.94 pixel height 0.94 slice thickness 0.94 field of view 240.64 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time not found repetition time not found inversion time not found echo number not found flip angle not found bits allocated 16 Spatial information first image position 0 0 0 last image position 0 0 239.7 image orientation -1 0 0 0 -1 0 ------------------------------------------------- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, -0, 0) j_ras = (-0, 1, 0) k_ras = (0, 0, 1) writing to 001.mgz...

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Freesurfer January 2006