Freesurfer

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30070 discussions

question about strange results after talairach transform
by Bum Seok Jeong 03 Jan '07

03 Jan '07

Hi! I use axial LAS system 3D nifti and analyze format images to perform autorecon1 process. Skull stripping results looked fine. However, when I checked talairachs transform results (tkregister2 --mgz --s C1 --fstal), a part of original image was just shown at left upper corner and talairach template did not appear with white background. So I can not perform a manual registration. The message appeared as follows Thanks in advance bsJeong <259> fs/tmp% tkregister2 --mgz --s C1 --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 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 %Wed Jan 3 12:24:29 2007>>> /bin/freesurfer/mni/bin/minctracc -clobber -debug /tmp/mritotal_16322/src_8_dxyz.mnc /bin/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.auto.xfm -transformation /tmp/mritotal_16322/src_8tmp2c.xfm -lsq9 -xcorr -model_mask /bin/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -191.589493 222.719711 194.588959 -step 4 4 4 -tol 0.004 -simplex 2 talairach.xfm --------------------- 1.053 -0.003 -0.046 212.831; 0.006 1.123 0.061 -264.791; 0.045 -0.057 1.036 -186.491; 0.000 0.000 0.000 1.000; INFO: loading target /tmp/C1/mri/orig.mgzINFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 -62.500; 0.000 0.000 1.000 91.141; 0.000 -1.000 0.000 347.141; 0.000 0.000 0.000 1.000; INFO: loading movable /bin/freesurfer/average/mni305.cor.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 -------- 1.053 -0.003 -0.046 212.831; 0.006 1.123 0.061 -264.791; 0.045 -0.057 1.036 -186.491; 0.000 0.000 0.000 1.000; subject = C1 Zoom Factor = 2 FOV = 256 Opening window C1 Setting scale tkregister2: interface: /bin/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}

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free surfer installation questions
by Andrew Bolstad 03 Jan '07

03 Jan '07

Hi, We are trying to install Freesurfer on a Linux Fedora Core 6 platform. We downloaded the CentOS 4 platform and the FC 5 upgrade of tksurfer. We have two questions: 1. When we rename tksurfer_fc5 to tksurfer and move it into the Freesurfer directory, it is an executable file, whereas the old tksurfer was an executable text file. Do we need to do something to change the file type? In its current state, the tksurfer upgrade does not appear to work. We tried the command: tksurfer bert rh pial and got a "permission denied" message (we are logged in as root). The message was: /usr/share/freesurfer/bin//tksurfer: Permission denied. By the way, we have the freesurfer directory in /usr/share/. 2. We seem to be missing a library file of some kind. We ran these two commands to test freesurfer: tkmedit bert norm.mgz tkmedit bert orig.mgz and get this error message both times: /usr/share/freesurfer/bin/tkmedit.bin: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory Do we need to download libglut.so.3? If anyone on this list can answer these questions, please let us know what we need to do. Thanks, Andrew Bolstad

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mri_nu_correct: how to maintain original geometry?
by Stephen Towler 03 Jan '07

03 Jan '07

Hi all, Is there a way to get mri_nu_correct to output geometry identical to the input scan, with no interpolation? For example: if I run mri_nu_correct (only) on a T1 scan that is 124x256x256 (1.2mm x .9375 mm2), the output is 256x256x256 (.9375 mm3). Not desirable for my current application. Thanks! Stephen -- Stephen Towler stowler(a)mbi.ufl.edu 352-294-0048 office 352-258-6409 mobile 352-392-8347 fax Leonard Lab Department of Neuroscience PO Box 100244 University of Florida HSC Gainesville, FL 32610

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recon-all -autorecon2-cp
by Shi, Bo 03 Jan '07

03 Jan '07

Does recon-all -autorecon2-cp ... Remove all previous manual white-matter edits? Is there a way I can prevent this? -- Bo Shi 300 Longwood Ave Pavilion 152 Boston, MA 02115 (617) 355-5167

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WG: [Freesurfer] MRInormalize: could not find any valid peaks
by Juergen Haenggi 03 Jan '07

03 Jan '07

Dear Freesurfer user I posted this question already on the mailing list and understood the answer. But this failure only occures when running on the grid. When I run the Freesurfer locally with the same brains, the error did not occur. Unfortunately, I have Fs version 3.0.4 on the grid and 3.0.3 on my local machine. What other kind of problem could also produce that error message? When I looked in the directory of these subjects, only 3 folders are present (mri, scripts, touch) instead 10 as normal. I got the impression that not all environmental variables are set properly. Could it be that the missing folders caused the problem? Thanks in advance Best regards Juergen > > Hi Juergen, > > yes, this usually means the talairach is bad. Either run > without it or fix it manually I guess. > Bruce > On Tue, 19 Dec 2006, Juergen Haenggi, > Psychiatrische Uni-Klinik wrote: > > > Dear Freesurfer users > > > > > > While running recon-all, the following error occured: > > > > > > #-------------------------------------------- > > #@# Intensity Normalization Sat Dec 16 13:10:39 CET 2006 > > /scratch/bli/AN1792/subjects/Patient02_2002/mri > > mri_normalize -g 1 nu.mgz T1.mgz > > using max gradient = 1.000 > > reading from nu.mgz... > > normalizing image... > > talairach transform > > 0.796 -0.256 -0.057 -8195.100; > > 0.086 0.398 -0.583 12578.642; > > 0.224 0.596 0.440 21656.441; > > 0.000 0.000 0.000 1.000; > > INFO: Modifying talairach volume c_(r,a,s) based on average_305 > > MRInormalize: could not find any valid peaks > > mri_normalize: normalization failed > > Linux node0214 2.6.15.6-id-x86_64-k8-smp #1 SMP Wed Mar 22 12:35:20 > > CET 2006 > > x86_64 x86_64 x86_64 GNU/Linux > > recon-all exited with ERRORS at Sat Dec 16 13:10:41 CET 2006 > > > > > > > > If I try to check the talairach.xfm with tkregister2, I see only a > > little part of the brain in the left upper corner of the graphic > > window. Because the DICOM files used > > > > were converted from ANALYSE files, I guess that there is a problem > > with the coordinate origin of the DICOMs. > > > > > > Could it be that this is the cause of my problem? > > > > The transformation matrix seems also not OK. > > > > Because I have about 250 brains which is the fastest way to > fix that problem? > > > > > > Thanks in advance > > > > Best regards > > > > Juergen > > > > > > ----------------------------------------------- > > Juergen Haenggi, Ph.D. student > > Psychiatric University Hospital > > Division of Psychiatry Research > > University of Zurich, Switzerland > > PO Box 1931 > > Lenggstrasse 31, 8032 Zurich > > 0041 44 384 26 10 (office phone) > > 0041 76 445 86 84 (mobile phone) > > 0041 44 384 26 86 (fax) > > H 115 (office room number) > > juergen.haenggi(a)bli.unizh.ch (division email) > http://www.dpr.unizh.ch/ > > (division website) http://www.juergenhaenggi.ch (private website) > > ----------------------------------------------- > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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talairach questions
by Dominick, Kelli, Ray Carpenter 02 Jan '07

02 Jan '07

Hi All, We have had a number of brains with very bad talairach transforms however aparc+aseg looks fine. In addition, while the talairach.xfm transform is very bad talairach.Ita is not. Is the bad xfm transform still a problem even though it is not affecting the labels. And if so which transform should I attempt to correct in tkregister2 in order to fix the problem? (I ask because it looks like that some of the tutorials still refer to old file names that have changed in the stable versions). I am using v3.03. Thanks in advance for your help! Kelli

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DICOM format
by Kaoru Amano 02 Jan '07

02 Jan '07

Though I need Dicom data, files in the MGH format (.bshort, .bfloat) are currently available. "mri_convert" seems to accept dicom format only as an input. Is there a way to get Dicom data from MGH data? Regrds, Kaoru Amano

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mris_preproc
by Lars M. Rimol 31 Dec '06

31 Dec '06

Hi, When I try to run mris_preproc wiht the nocleanup flag I get an error message: flag --nocleanup not recognized Same thing happens for --cleanup (i.e., not recognized), and "--tmpdir tmpdir" doesn't seem to work (it still does cleanup). But all these flags are listed under the help function for mris_preproc: --tmpdir dir : use tmpdir. Implies --nocleanup. --nocleanup : do not delete tmpdir --cleanup : delete tmpdir (default) I'm using /RH4-x86_64-R302. Thank you! -- yours, LMR

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once more: Cortical thickness group analyses
by Dziobek, Isabel 29 Dec '06

29 Dec '06

Hi, I posted the message below about a week ago but didn't get a reply. Any help is much appreciated! Thanks and best, Isabel -----Original Message----- From: Dziobek, Isabel Sent: Wednesday, December 20, 2006 11:38 AM To: Freesurfer(a)nmr.mgh.harvard.edu Subject: Cortical thickness group analyses Dear All, I have some questions in regard to the FreeSurfer group analyses (I am using the 3.0 Version), for which I would appreciate your help. I am trying to compare a patient to a control group with respect to cortical thickness (regressing out variables such as age and IQ) and also to see if associations exist in specific ROIs between cortical thickness and cognitive variables (for the groups separately). I started constructing a group descriptor file containing the two classes (patient and control) and the variable age. First, I wanted to compare the groups disregarding any other variable and so I constructed the following contrast vector: (1 -1 0), assuming doss and thinking that the ³0² meant that this column of the design matrix would not be taken into account in the model. However, this yielded the same result as running (1 -1 1). Do I have to construct a separate fsgd file only containing the classes and then a contrast vector (1 -1)? What about regressing out more than 1 variable (e.g. age and IQ), how does the contrast vector have to look like then? Also, how do I look at correlations between those variables and cortical thickness for the groups separately? When loading the scatter plots of the fsgd, the regression line for the separate groups seems to run always parallel, which does not seem very likely (see attached jpg). Are these regression lines at all? Where can I obtain the Rs in numbers? Can I, alternatively, stream out the numbers for the cortical thickness of a defined ROI to then run correlations in SPSS. Where would I find those numbers? I was also wondering about corrections for intracranial vault. Does the registration to the group¹s average brain takes care of differences in overall head size or is it advisable to put icv as a separate regressor (as is done in very few studies)? Thanks a lot for your help and happy holidays, Isabel ************************************** Isabel Dziobek, PhD Postdoctoral Research Fellow Independent Junior Research Group Neurocognition of Decision-Making Max-Planck Institute for Human Development Lentzeallee 94 14195 Berlin Phone: +49 30 82406 619 Fax: +49 30 82406 616 dziobek(a)mpib-berlin.mpg.de

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mri_convert does not recognize dicom files
by Julia Hamstra 22 Dec '06

22 Dec '06

Hello, I am unable to use mri_convert to import dicom files. Below are examples of the errors. For a GE scan: mri_convert -it ge -ot mgz -i 01.v2 -o orig.mgz reading from 01.v2... genesisRead(): can't determine file name format for ./01.v2 For a Siemens scan: mri_convert -it siemens_dicom -ot mgz -i 0001.dcm -o orig.mgz reading from 0001.dcm... ERROR (ScanSiemensSeries): ./0001.dcm is not a Siemens DICOM file ERROR: could not find any files (SeriesList==NULL) Similar errors are given when the generic dicom is used. Other programs, such as Osirix and Analyze are able to process the DICOM files. Is there an obvious error in the command? What else should I consider? Thank you ~julia -- UC Davis Neuroscience Graduate Group The M.I.N.D. Institute - Amaral Lab (916) 703-0376

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