Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30096 discussions

transformation between cvs and native space
by Kami Koldewyn 23 Apr '13

23 Apr '13

Hi All, We have contiguous ROIs in cvs template (volume) space. We need to move this to each individual subject's surface. What's the best way of doing this? We tried going from template volume to individual volume to individual surface, but these rois were not all contiguous on the surface -- in some cases they were split nearly in half (most likely because they were placed on either side of a sulcus). We could try to correct for this problem in each individual, but that would be very labor-intensive and pretty subjective across individuals. We're thinking that it would be better to go from template volume to template surface and then from template surface to individual surface -- this way we can make all of our corrections on the template surface, which would make ad hoc corrections not different across subjects. But we're not sure what the best way to do this is as the cvs transform that allows us to get back to subject-specific native space is a volume transform: 1. Do people think that going to template surface rather than individual volume is the better intermediate step? 2. If yes, do you think it's best to move to the CVS surface and then use spherical surface alignment transform to move from the template surface to each individual surface - or is there a better way to do this? Any pointers on how to do this with the smallest number of transformations and/or steps that require morphing or interpolation would be greatly appreciated. sorry for the long email, and thanks in advance! -kami --------------------------------------------------------------- Kami Koldewyn, PhD. McGovern Institute for Brain Research MIT, Building 46 Room 4141 (Kanwisher Lab) Cambridge, MA 02139 kamik(a)mit.edu

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GLM | group comparison and correlation on surface with whole-brain DTI/tractography results | How to setup fsgd and contrast matrix?
by Robert Schulz 23 Apr '13

23 Apr '13

Hi Freesurfers, I managed to project tractography results (seed-based whole-brain tractography performed in FSL) onto the surface of each individual subject (19 OLD, 19 YOUNG). Each individual surface (including the results) has been transferred to fsaverage to allow statistical group comparison on the group surface level: mri_surf2surf --srcsubject SUBJ --srcsurfval ${main}/${study}/voxelnum_IN_STRUCT_fs_DILF.mgh --trgsubject fsaverage --trgsurfval ${main}/${study}/voxelnum_IN_STRUCT_fs_DILF_average.mgh --hemi ${side[$i]}h I concatenated all the subjects (first 19 old, then 19 young) and smoothed it with fwhm of 10 using the following commands: mri_concat ${main}/${study}/*voxelnum_IN_STRUCT_fs_DILF_average.mgh --o ${main}/${study}/all.mgh mri_surf2surf --srcsubject fsaverage --srcsurfval ${main}/${study}/all.mgh --fwhm 10 --trgsubject fsaverage --hemi ${side[$i]}h --trgsurfval ${main}/${study}/all_smooth.mgh My questions: 1) To answer the question where the "tractograophy_results_on_surface" are higher in OLD then in YOUNG I used the follwong command mri_glmfit --glmdir ${main}/${study}/fs/glmout --y ${main}/${study}/all_smooth.mgh --fsgd ${main}/${study}/fs/glmout/glmout/glm.fsgd --C ${main}/${study}//fs/glmout/omy.mtx --surf fsaverage ${side[$i]}h --cortex with glm.fsdg GroupDescriptorFile 1 Class Old Class Young Input co_001 Old Input co_002 Old Input co_003 Old Input co_004 Old Input co_005 Old Input co_006 Old Input co_007 Old Input co_008 Old Input co_009 Old Input co_010 Old Input co_011 Old Input co_012 Old Input co_013 Old Input co_014 Old Input co_015 Old Input co_016 Old Input co_017 Old Input co_018 Old Input co_019 Old Input cy_001 Young Input cy_002 Young Input cy_003 Young Input cy_004 Young Input cy_005 Young Input cy_006 Young Input cy_007 Young Input cy_008 Young Input cy_009 Young Input cy_012 Young Input cy_016 Young Input cy_019 Young Input cy_020 Young Input cy_021 Young Input cy_022 Young Input cy_024 Young Input cy_014 Young Input cy_025 Young Input cy_028 Young and the contrast file omy.mtx 1 -1 This approach gave me plausible results compared to my pilot FSL analysis. 2) Second I'd like to perform a simple correlation analysis correlating the result_on_surface in OLD with another behavioural measure (e.g. performance in a motor task). Therefore I concatenated the surfaces of all OLD subjects. I wonder how the fsgd file and the contrast file would look like for the GLM_FIT? If I put GroupDescriptorFile 1 Class Old Variables Learning Input co_001 Old x Input co_002 Old x Input co_003 Old x Input co_004 Old x Input co_005 Old x Input co_006 Old x Input co_007 Old x Input co_008 Old x Input co_009 Old x Input co_010 Old x Input co_011 Old x Input co_012 Old x Input co_013 Old x Input co_014 Old x Input co_015 Old x Input co_016 Old x Input co_017 Old x Input co_018 Old x Input co_019 Old x in the fsdg with x = behavioural result and " 0 1 " in the contrast file corr.mtx (looking for positive correlation between surface_result and behaviour), I don't get any significant results. And I am not sure whether I performed the analysis correctly. Can anybody tell me whether the GLM, fsgd and contrast files are set up correctly, both for the group comparison in 1) and for the correlation analysis in 2). Thank you very much! Kind regards, Robert -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus

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Research Assistant position
by Olivier Coulon 23 Apr '13

23 Apr '13

Dear All, please find below an announcement for a research assistant position. ----------------------------------------------------------------------------------- Neuroimaging Research Engineer - Centre IRMf de La Timone, Marseille, France *Recruitment date:* May 2013 *Application closing date:* May 15th, 2013 *Contract duration:* 30 months *Salary*: 19.000 -- 24.000 Euros / year, depending on experience *Context* The La Timone fMRI Centre (http://irmfmrs.free.fr/) of the Institut des Neurosciences de La Timone (http://www.int.univ-amu.fr/) in Marseille provides neuroscientists, medical researchers, and psychologists from the Aix - Marseilles area and beyond with Magnetic Resonance Imaging (MRI) services. The Centre operates a 3 Tesla MR system fully dedicated to neuroscience and psychology research in human and non-human primates and equipped with high-end stimulation and recording systems. The Centre, affiliated to CNRS and Aix-Marseille University, is involved in clinical, fundamental and methodological research and technical development through collaboration with local, national and international research groups and with a strong involvement in training and teaching. *Mission* The post holder will have for mission to assist the user community with basic and advanced analysis of cerebral MRI data (functional and structural). Specifically, tasks include: - Advise and help users with standard analysis of brain MR data - Help users with advanced analyses such as functional connectivity, diffusion tensor imaging, tractography, multivariate analysis, morphometry, ... - Develop and optimize software pipelines - Assist with the design and set-up of new studies - Contribute to education and training of the users *Profile of the candidate* Background in neuroimaging essential Experience with brain image analysis packages (e.g., SPM, Freesurfer, BrainVISA or FSL) Experience with development of brain image analysis methods or/and their application to neuroimaging studies desirable Good knowledge of statistical methods and tools Expertise with one or several programming languages (Matlab, Python, C/C++) Autonomy, initiative, ability to work at the interface between multidisciplinary teams *Information requests and applications should be addressed to **Jean-Luc.Anton(a)univ-amu.fr**, **Patricia.Romaiguere(a)univ-amu.fr**, and **Pascal.Belin(a)univ-amu.fr* -- signatureMail2011 Olivier Coulon, CNRS research Fellow, Head of the Images&Models team olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univmed.fr> Tel: +33491828527 fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr <http://olivier.coulon.perso.esil.univmed.fr/> LSIS Laboratory, I&M Team ESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE BrainMorph logo http://www.lsis.org/brainmorph

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Where does a sulcus end and a gyrus begin in FreeSurfer?
by Yang, Daniel 23 Apr '13

23 Apr '13

Dear FreeSurfer Experts and Users, This is probably a basic question, so please bear with me. I'm looking at the Coronal view in tkmedit, and I am wondering how does FreeSurfer knows where a gyrus ends and a sulcus begins (and vice versa). For example, I'm looking at the superior temporal sulcus. But I'm not sure how FS figures out which part is superior temporal gyrus, middle temporal gyrus, or superior temporal sulcus? Thanks! Daniel

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Zip File for Freesurfer (Hippocampal Subfields)
by Erin Walsh 22 Apr '13

22 Apr '13

Hi, I recently found a thread that is similar to an error I am experiencing when running the automated hippocampal subfield segmentation: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27551.html . I was wondering if anyone might be able to provide access to the zip files referenced in the email? (I clicked on the link but was unable to see the files-- I assume I do not have access or they are gone.) I was hoping to try the fix listed first before making a more formal report. Thank you for any assistance you can offer! Best, Erin -- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwalsh(a)gmail.com

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T2 pial
by Eduard Vilaplana Martinez 22 Apr '13

22 Apr '13

Dear FreeSurfer experts, First of all, congrats for this new 5.2 stable version. My name is Eduard, and I'm trying to perform de T2 pial refinement in a pre-processed subject with the B0 image from a DTI. I used that command: recon-all -autorecon3 -T2pial -s ACC019/ -T2 /home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii Being "ACC019" the subject ID and "/home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii" the path to the T2 nifti. Whatever I do, it always return me the following error. Any suggestions would be greatly appreciated. Thanks in advance. @# Refine Pial Surfs w/ T2/FLAIR Wed Apr 17 14:37:42 CEST 2013 bbregister --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.log Wed Apr 17 14:37:42 CEST 2013 setenv SUBJECTS_DIR /home/linux/Escritorio/COHORTE_T2 cd /home/linux/Escritorio/COHORTE_T2/ACC019/scripts /usr/local/freesurfer/bin/bbregister --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz... TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996796, 0.0725774, -0.0336276) j_ras = (0.065149, 0.980551, 0.185135) k_ras = (-0.0464102, -0.182351, 0.982138) writing to /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii... fslregister --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister --dof 6 --fsvol brainmask Log file is /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fslregister.log Wed Apr 17 14:37:42 CEST 2013 --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ linux-To-be-filled-by-O-E-M Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mri_convert ERROR: could not determine file for /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR: /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR: /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii... TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996796, 0.0725774, -0.0336276) j_ras = (0.065149, 0.980551, 0.185135) k_ras = (-0.0464102, -0.182351, 0.982138) keeping frame 0 writing to /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii... Mov determinant is -5.12001 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts tkregister2_cmdl --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat --regheader --fslregout /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0 --s ACC019 --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii reg file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat 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/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz 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/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.600 0.000 0.000 128.000; 0.000 0.000 2.000 -80.000; 0.000 -1.600 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) -------- 0.997 -0.073 0.034 0.214; -0.046 -0.182 0.982 -30.911; -0.065 -0.981 -0.185 1.512; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.997 -0.073 0.034 0.214; -0.046 -0.182 0.982 -30.911; -0.065 -0.981 -0.185 1.512; 0.000 0.000 0.000 1.000; Determinant 1 subject = ACC019 RegMat --------------------------- 0.997 -0.073 0.034 0.214; -0.046 -0.182 0.982 -30.911; -0.065 -0.981 -0.185 1.512; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -5.12001, ref det = -1 Wed Apr 17 14:37:44 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts flirt.fsl -ref /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii -in /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister ERROR: Could not open image /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Wed Apr 17 14:37:44 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts flirt.fsl -ref /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii -in /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat -init /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister ERROR: Could not open image /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) tkregister2_cmdl --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --fslreg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ERROR: cannot open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat cat: /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Wed Apr 17 14:37:42 CEST 2013 Ended at Wed Apr 17 14:37:44 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --surf orig mri_segreg --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --init-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --out-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat mri_segreg --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --init-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat --out-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat tkregister2_cmdl --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --noedit --ltaout /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta regio_read_register(): No such file or directory Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz reg file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ERROR: reading /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat Cleaning up Started at Wed Apr 17 14:37:42 CEST 2013 Ended at Wed Apr 17 14:37:45 CEST 2013 BBR-Run-Time-Sec 3 bbregister Done To check results, run: tkregister2 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --surf mri_convert -at /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz mri_convert -at /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz ltaReadFile(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta): can't open file $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz... TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996796, 0.0725774, -0.0336276) j_ras = (0.065149, 0.980551, 0.185135) k_ras = (-0.0464102, -0.182351, 0.982138) INFO: Reading transformation from file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() No such file or directory ERROR: Reading transform from file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ACC019 exited with ERRORS at Wed Apr 17 14:37:45 CEST 2013 For more details, see the log file /home/linux/Escritorio/COHORTE_T2/ACC019/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

5 8

gender differences in qdec
by Hélène Bretschneider 22 Apr '13

22 Apr '13

Dear freesurfers, I want to look at the gender differences of a correlation between cortical thickness and some impulsivity-tests. When I use qdec, the question "Does the thickness-BIS-correlation differ between 0 and 1?" is displayed. So, 0 and 1 are female/male. But there are positive and negative correlations (red and blue voxels)...what does it mean? There can not be a negative difference...?? Thank you very much! Leni

2 3

segmentation error
by HOSSU Gabriela 22 Apr '13

22 Apr '13

Hi all, I am working with FreeSurfer version 5.10 from some months. We have some problems with some segmentations see attached files (images are acquired at 3T). How can we explain and solve these errors? Thanks for any help; Gabriela HOSSU, Ph.D. Chef de projet CIC-IT Nancy (Inserm CIT801) CHU de Nancy Brabois 4ème étage Tour Drouet Rue du Morvan 54511 VANDOEUVRE-LES-NANCY FRANCE

2 1

mri_segstats SNR calculation
by Jordi Delgado 22 Apr '13

22 Apr '13

Dear Freesurfers, After running the first tests of freesurfer 5.2, I found a file named $hemi.w-g.pct.stats on the stats folder. The last column of the file is a SNR calculation, i found on the help manual, that is required to add --snr to perform this calculation. I'm interested to know how this SNR is calculated. Is there any method or paper related? Thank you in advance, /Jordi

2 1

22 Apr '13

Dear All, I was trying to create register.dat for a single subject. Command line: autoreg-sess -s SZ01 -d $SUBJECTS_DIR/SZ01 But it showed some error like this... Logfile is /home/mbial/JPJ/freesurfer/SZ01/log/autoreg-sess.log setenv SUBJECTS_DIR /home/mbial/JPJ/freesurfer/SZ01 _______________________________________________________ --- ERROR: ----------- _______________________________________________________ Inside the log I got some thing like this: autreg-sess log file $Id: autoreg-sess,v 1.4 2007/01/09 22:41:16 nicks Exp $ /usr/local/freesurfer/fsfast/bin/autoreg-sess Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux Tue Apr 23 14:11:09 IST 2013 setenv SUBJECTS_DIR /home/mbial/JPJ/freesurfer/SZ01 _______________________________________________________ --- ERROR: ----------- _______________________________________________________ What might be the trouble with this..? Please help..

2 1

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