Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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

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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

Merging the labels to T1 image
by Anupa AV 22 Apr '13

22 Apr '13

Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image? If yes, which method I should follow?

3 7

QDEC questions
by Tudor Popescu 21 Apr '13

21 Apr '13

Dear experts, Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from misbehaving, and so after running a first whole-brain group cortical thickness analysis on my structural data, I have some questions: 1. After running recon-all with the –qcache flag (i.e. presmoothing), files of the type lh.thickness.*.mgh were created for all 38 subjects (19 in each group), however files of the type *rh*.thickness.*.mgh were not created for 5 out of the 19 subjects of the first group. Log files *recon-all-status.log * and *recon-all.log* (attached, for one of those 5 subjects) both mention that the process ran on Mar22nd ended with errors, although I can't quite see what that was 2. When I take age as a continuous factor (covariate), the list of clusters in my results look dramatically different from the clusters that I get for the same contrast ran without the covariate. Why is that, given that normally adding a covariate very rarely changes the results by a great deal? Also in my case, I had quite a narrow (and well-balanced between the groups) age range! 3. I know that discrete factors cannot be taken as nuisance factors, but it seems they also can't be taken as covariates. How does one, then, control for the effects of e.g. gender in a group comparison? 4. When should values other than 10 be used for the FWHM parameter of the smoothing? 5. How come QDEC allows you to set the FWHM parameter, when in fact it is also set in the qcache stage of recon-all, which precedes QDEC? Many thanks in advance!! Tudor

4 6

Re: [Freesurfer] Hippo-subfields
by Marcos Martins da Silva 20 Apr '13

20 Apr '13

Thank you for your answer, Juan. Yes, I want a surface of the whole hippocampus and I thought I had just obtained that using freeview and adding all hippo-subfield files. That resulted in the screenshot I previously attached. I just do not know how I can save the resultant surface. After I checked "show as isosurface in 3D view" the low and high threshold controls appeared. The default threshold values on Freeview for low was 127.5 and high was 255. When I played with these controls, the size of the surfaces changed on 3D view. That is why I made the second question. I was trying to select the correct values for low and high threshoulds so I get an image consistent with the volume values we get after running kvlQuantifyPosteriorProbabilityImages. After setting the correct values I would like to save the work as a surface so I could load the whole surface instead of loading each individual subfield file. But I did not find a "save as surface" option. So I used the screenshot tool to "save" the work. This way I could at least show you what I got but I thought it was not the best way to do it. Relating to the last question about generating a new segmentation (anterior, body and posterior), you said I could use simple geometric rules to get it. Could you tell me where I can find instructions about how to do it? Sorry, I am afraid I am a novice here and my questions are the best proof of this, so I would like to thank you for all your patience. Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu: Dear Marcos, > > > 1- How do I save the combined 3D view I got as a surface? > > Do you want a surface of the whole hippocampus? In that case I would > suggest adding up the probability volumes from all the subfields and > thresholding the resulting volume. > > > > 2-I know the hippo-subifields .mgz files are probability maps and if I > > guess right kvlQuantifyPosteriorProbabilityImages read these files to > > count how many voxels you have in each subfield. I also guess it count > > only the voxels with reasonable high probability to be part of each > > subfield. If so, what is the minimum value between 1 and 255 the > > program use to decide if a particular voxel is valid? > > The estimates of the volumes are based on soft probabilities, so all > voxels with non-zero probability contribute towards the estimate. For > instance, a voxel with value 255 contributes to the volume 255 times as > much as a voxel with a value of 1. > > > > 3- Is it possible to merge hippo-subfield .mgz files data and to > > generate a different segmentation like anterior (anterior quarter), > > body (the2 intermediate quarters) and posterior (posterior quarter). > > There are currently no scripts in FreeSurfer to generate such a > partition. But you could always take a mask of the whole hippocampus > (either from aseg.mgz of from the combination of all the subfields, like > I mentioned in 1) and define some simple geometric rules to create it. > > Kind regards, > > Eugenio > > > > > > > > TY in advance > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Technical Assistant Position Available at MIT
by Satrajit Ghosh 19 Apr '13

19 Apr '13

For details of the position and for applying see: http://sh.webhire.com/servlet/av/jd?ai=631&ji=2681168&sn=I

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