Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

postdoc position in Leiden, The Netherlands: studies on resting-state and activation EEG-fMRI during sleep and wakefulness in healthy subjects and patient with sleep disorders including insomnia and narcolepsy
by Diederick Stoffers 12 Dec '09

12 Dec '09

LEIDEN UNIVERSITY MEDICAL CENTER The Leiden University Medical Center (LUMC) has initiated the interdisciplinary Sleep Neuroscience Center Leiden. Its focus is fundamental and strategic scientific and clinical research on sleep Within the Departments of Neurology and Neuroradiology, and in close collaboration with Dr. E.J.W. van Someren’s Sleep & Cognition group at the Netherlands Institute for Neuroscience, a position is available for a Postdoc (m/f) 38 hours per week Project information: This project is funded by a LUMC starting grant for the Sleep Neuroscience Center Leiden. It has become evident over the last decade that sleep is an essential component of normal cognitive functioning and maintenance of brain structure and function at the cellular to the systems level. In addition, disturbed sleep crucially contributes to major health problems associated with metabolic regulation, aging and psychiatry. The present project aims to elucidate the association between activatiion of the default mode resting state network, it’s structural backbone, and travelling slow oscillations during sleep. A second focus is on the involvement of the default mode network in deviant switching between sleep and wakefulness in narcolepsy and insomnia. Philips 7T and 3T scanners are available for structural and functional MRI. The aim is to do EEG-MRI with the new Electrical Geodesics Inc (EGI) system. The project will be performed in close collaboration with Dr. S. Rombouts (director of the Leiden Institute for Brain and Cognition: LIBC) and with the Sleep & Cognition group at the Netherlands Institute for Neuroscience. A 0.5 FTE lab technician will support the project. Requirements: A strong scientific track record including publications is essential for the Postdoc. The Postdoc will be responsible for studies on resting-state and activation EEG-fMRI during sleep and wakefulness in healthy subjects and patient with sleep disorders including insomnia and narcolepsy. Appoinment: This position involves a temporary appointment for three years. Salary: Depending on training and work experience according to the collective Agreement for Dutch Universities (CAO-Nederlandse Universiteiten), including 8% holiday pay and a 8.3% year-end bonus. We offer an extensive package of fringe benefits. Work location: The Leiden University Medical Center, Leiden. Information: For further information about this position, you may contact Dr. EJW Van Someren (e-mail e.van.someren(a)nin.knaw.nl) or Dr. SARB Rombouts (s.a.r.b.rombouts(a)lumc.nl ). Information on the groups is found at http://www.nin.knaw.nl/research_groups/van_someren_group/ and at http://www.libc-leiden.nl Application: You may send your application letter, curriculum vitae and the names of 2 references to Dr. EJW Van Someren (Laboratory for Neurophysiology, Department of Molecular Cell Biology, LUMC S-05-P, PO Box 9600, 2300 RC Leiden, The Netherlands) or preferably by email: e.van.someren(a)nin.knaw.nl. Application deadline: January 14, 2010. Any acquisition further to this advertisement will not be appreciated

1 0

how to evaluate our own template without creating our own atlas
by Guang Zeng 11 Dec '09

11 Dec '09

Hi, there, We created our own template using 10 subjects, now we'd like to know how good it is compare to FS's default template. We do not create our own atlas yet which need manully label all the regions in the training set. Is there a way to do this kind of comparison? Is it possible to do some kind registration using ?h.white and ?h.sphere. reg, and load the registered ?h.white using tkmedit? Thanks a lot! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/

1 0

Re: [Freesurfer] func2roi-sess bug?
by John Richey 11 Dec '09

11 Dec '09

I am using v4.5.0, on CentOS 5.4. Here is the log: [jar62@meehl freesurfer]$ func2roi-sess -roidef l_lingual -analysis dotprobe_all_hrf -anatlabel lh.lingual -maskcontrast AllvFix -maskthresh 0 -masktail pos -maskmap sig.nii -sf subjectlist.txt -d /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer/ ---------------------------------------------------------- func2roi-sess logfile is /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/log/func2ro i-sess.log ---------------------------------------------------------- ----------------------------------------------------- Session: SAD_C17 1/26 Fri Dec 11 16:05:23 EST 2009 Fri Dec 11 16:05:23 EST 2009 --------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h --roiavg bold/dotprobe_all_hrf/l_lingual/h --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h.txt --------------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h --roiavg bold/dotprobe_all_hrf/l_lingual/h --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h.txt version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/h roitxtfile = bold/dotprobe_all_hrf/l_lingual/h.txt oldtxtstyle = 0 srcvol = bold/dotprobe_all_hrf/h.nii srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 srcreg Dsrc ------------- 0.999 -0.001 -0.043 -6.051; 0.036 -0.523 0.852 -10.837; 0.024 0.852 0.522 1.743; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -0.320 0.000 0.000 32.000; -0.000 -0.000 -0.320 32.000; -0.000 0.227 -0.000 16.000; 0.000 0.000 0.000 1.000; ---------------------------------- Reading bold/dotprobe_all_hrf//AllvFix/sig.nii NOT INVERTING Loading volume bold/dotprobe_all_hrf/h.nii ...done INFO: Source volume detected as selxavg format INFO: Adjusting Frame Power Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 1142 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 93 hits in final mask label2mask_linear: done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 3673 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 277 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 93 Done averging over ROI (nhits = 93) INFO: Readjusting Frame Power --------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h-offset --roiavg bold/dotprobe_all_hrf/l_lingual/h-offset --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h-offset.txt --------------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h-offset --roiavg bold/dotprobe_all_hrf/l_lingual/h-offset --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h-offset.txt version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/h-offset roitxtfile = bold/dotprobe_all_hrf/l_lingual/h-offset.txt oldtxtstyle = 0 srcvol = bold/dotprobe_all_hrf/h-offset.nii srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 srcreg Dsrc ------------- 0.999 -0.001 -0.043 -6.051; 0.036 -0.523 0.852 -10.837; 0.024 0.852 0.522 1.743; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -0.320 0.000 0.000 32.000; -0.000 -0.000 -0.320 32.000; -0.000 0.227 -0.000 16.000; 0.000 0.000 0.000 1.000; ---------------------------------- Reading bold/dotprobe_all_hrf//AllvFix/sig.nii NOT INVERTING Loading volume bold/dotprobe_all_hrf/h-offset.nii ...done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 1142 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 93 hits in final mask label2mask_linear: done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 3673 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 277 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 93 Done averging over ROI (nhits = 93) 009ist: 007 ------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 ------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 .txtxtfile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 oldtxtstyle = 0 /fmcsm8= bold/007 srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 /fmcsm8. Does it exist?lume bold/007 [jar62@meehl freesurfer]$ mri_modify Usage: mri_modify <-xras xr xa xs> <-yras yr ya ys> <-zras zr za zs> <-cras cr ca cs> \ <-xsize size> <-ysize size> <-zsize size> \ <-tr recoverytime> <-te echotime> <-ti inversiontime> <-fa angledegree> \ <-xform new_file_name> \ involume outvolume [jar62@meehl freesurfer]$ func2roi-sess -roidef l_lingual -analysis dotprobe_all_hrf -anatlabel lh.lingual -maskcontrast AllvFix -maskthresh 0 -masktail pos -maskmap sig.nii -sf subjectlist.txt -d /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer/ -rawstem fmcsm8 -rawrlf dotprobe.txt ---------------------------------------------------------- func2roi-sess logfile is /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/log/func2ro i-sess.log ---------------------------------------------------------- ----------------------------------------------------- Session: SAD_C17 1/26 Fri Dec 11 16:57:34 EST 2009 Fri Dec 11 16:57:34 EST 2009 --------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h --roiavg bold/dotprobe_all_hrf/l_lingual/h --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h.txt --------------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h --roiavg bold/dotprobe_all_hrf/l_lingual/h --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h.txt version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/h roitxtfile = bold/dotprobe_all_hrf/l_lingual/h.txt oldtxtstyle = 0 srcvol = bold/dotprobe_all_hrf/h.nii srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 srcreg Dsrc ------------- 0.999 -0.001 -0.043 -6.051; 0.036 -0.523 0.852 -10.837; 0.024 0.852 0.522 1.743; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -0.320 0.000 0.000 32.000; -0.000 -0.000 -0.320 32.000; -0.000 0.227 -0.000 16.000; 0.000 0.000 0.000 1.000; ---------------------------------- Reading bold/dotprobe_all_hrf//AllvFix/sig.nii NOT INVERTING Loading volume bold/dotprobe_all_hrf/h.nii ...done INFO: Source volume detected as selxavg format INFO: Adjusting Frame Power Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 1142 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 93 hits in final mask label2mask_linear: done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 3673 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 277 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 93 Done averging over ROI (nhits = 93) INFO: Readjusting Frame Power --------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h-offset --roiavg bold/dotprobe_all_hrf/l_lingual/h-offset --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h-offset.txt --------------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h-offset --roiavg bold/dotprobe_all_hrf/l_lingual/h-offset --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h-offset.txt version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/h-offset roitxtfile = bold/dotprobe_all_hrf/l_lingual/h-offset.txt oldtxtstyle = 0 srcvol = bold/dotprobe_all_hrf/h-offset.nii srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 srcreg Dsrc ------------- 0.999 -0.001 -0.043 -6.051; 0.036 -0.523 0.852 -10.837; 0.024 0.852 0.522 1.743; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -0.320 0.000 0.000 32.000; -0.000 -0.000 -0.320 32.000; -0.000 0.227 -0.000 16.000; 0.000 0.000 0.000 1.000; ---------------------------------- Reading bold/dotprobe_all_hrf//AllvFix/sig.nii NOT INVERTING Loading volume bold/dotprobe_all_hrf/h-offset.nii ...done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 1142 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 93 hits in final mask label2mask_linear: done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 3673 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 277 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 93 Done averging over ROI (nhits = 93) 009ist: 007 ------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 ------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 .txtxtfile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 oldtxtstyle = 0 /fmcsm8= bold/007 srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 /fmcsm8. Does it exist?lume bold/007 that is bizarre. What version of freesurfer and what operating system are you using? doug John Richey wrote: > Dear freesurfer experts: > > I am trying to extract roi from my fMRI data using func2roi-sess. However, I > encounter an error that I wonder might be a bug in the code? My input is > func2roi-sess -roidef l_lingual -analysis hrf -anatlabel lh.lingual > -maskcontrast AllvFix -maskthresh 0 -masktail pos -maskmap sig -sf > subjects.txt > > (the last 25 or so lines of the log are pasted below). Basically, I believe > that line in the log that reads: > > /fmcsm8= bold/007 > > should read: > > srcvol = bold/007/fmcsm8.nii > > The result is that the func2roi-sess routine terminates with the error > displayed on the last line: /fmcsm8. Does it exist?lume bold/007 > > Has anyone else encountered this problem? Or maybe I am skipping a step? I > am using v4.5.0. If it helps, I can also paste my source code that seems to > produce this error. Thanks in advance > > John Richey > > > -------------------------------------------------------- > /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 > mri_vol2roi > --srcreg bold/register.dat --label > /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab > el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii > --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol > bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt > bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 > version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ > -------------------------------------------------------- > roifile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 > .txtxtfile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 > oldtxtstyle = 0 > /fmcsm8= bold/007 > srcfmt = bvolume > srcreg = bold/register.dat > srcregold = 0 > srcwarp unspecified > label file = > /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab > el/lh.lingual.label > labelreg unspecified > label fill thresh = 1e-07 > mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii > mskfmt unspecified > msk volume same as source > msk tail = pos > msk threshold = 0.000000 > msk invert = 0 > msk frame = 0 > /fmcsm8. Does it exist?lume bold/007 > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

how to load lh.jacobian_white in tkmedit
by Guang Zeng 11 Dec '09

11 Dec '09

Hi, there, I'd like to load lh.jacobian_white using tkmedit to check how much the white surface was distorted in order to register to the spherical atlas my command line is tkmedit subj_id brainmask.mgz rh.white -aux T1.mgz -aux-surface lh.jacobian_white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt But I got an error, =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to analysis-bugs(a)nmr.mgh.harvard.edu : : Now exiting... : Anyone can help? Thanks a lot! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/

2 1

FW: a question about the mris_volmask ERROR
by Guang Zeng 10 Dec '09

10 Dec '09

Hello, Allison, Thanks a lot for your help and sorry for my delay! Yes, I agree. If I use -autorecon3 to rerun it, everything should be fine. But I also find something interesting. Please check the attached recon-all.log, >From line 10812 to line 10847, you will see "ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x270e3480): Unable to create a thread. pthread_create() returned 12" Normally, after this line, we will see something like, "Segmentation fault (core dumped) recon-all exited with ERRORS at Thu Dec 10 00:58:33 CST 2009" Once, I call -autorecon3, we can see the following lines in the recon-all.log, and the results will be fine. " New invocation of recon-all Thu Dec 10 15:50:19 CST 2009 /data1/radiology/m047599/subjects/002_S_0413_20060519 /usr/local/biotools/freesurfer/freesurfer-v4.5.0/bin/recon-all -s 002_S_0413_20060519 -autorecon3 -no-isrunning " However, in the recon-all.log I sent to you, we only can see something like, " ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x30bf9d90): Unable to create a thread. pthread_create() returned 12 loading input data... hemi masks overlap voxels = 4 writing volume /data1/radiology/m047599/subjects/002_S_0413_20060502/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# AParc-to-ASeg Wed Dec 9 20:07:25 CST 2009 /data1/radiology/m047599/subjects/002_S_0413_20060502 mri_aparc2aseg --s 002_S_0413_20060502 --volmask " The trick thing is I do not do anything, it looks like to me, after few rounds of calling vtkMultiThreader and getting ERRORs, FS automatically go to the next step with a wrong ribbon.mgz by itself. And it will finish the whole process without "errors", however, when we load the results into tkmedit, we find lots of wm parcellation are wrong. I have 38 subjects have this kind of problem, do you think it is because of FS or the SGE I use to run the subjects? Thanks a lot! Guang > Date: Tue, 8 Dec 2009 17:43:09 -0500 > From: astevens(a)nmr.mgh.harvard.edu > To: freesurfer_zg(a)hotmail.com > Subject: Re: [Freesurfer] a question about the mris_volmask ERROR > > Oh I just saw your earlier message which had a bit more detail. > > If you are using -autorecon3 to rerun it so it finishes, you shouldn't see > a difference in the stats. You may see a difference if you are running on > different platforms. > > -- > > On Mon, 7 Dec 2009, Guang Zeng wrote: > > > > > Hi, there, > > > > I have question about the mris_volmask ERROR. > > > > I ran multiple subjects on our SUN Grid Engine system. sometimes some subjects are sent to the same cluster node, and limited memory is assigned to each subject. > > Because of this, I often met an ERROR at the mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance sub1 step > > in autorecon3., which gave me an error like: > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 > > vtkMultiThreader (0x33d05a90): Unable to create a thread. pthread_create() returned 12 > > > > I knew this error is caused by some VTK function FS used to allocate memory. What I did is everytime when I met this kind of error, > > I use recon-all -s subj -autorecon3 -no-isrunning , and the process will finish. > > > > However, I found if I did something like this, it will cause problems at the wm parcellation step. For example, I have the same subject which is sent to SGE, fails at mris_volmask, and then I call autorecon3 to finish the process, and I go to wmparc.stats, lotf of rois such as isthumus ctx-cingluate, ctx-posterior singulate are 0. > > While I ran the same subject at a local machine, and finished without any problems, I looked at isthumus cingluate and posterior singulate, they are not zeros. > > > > So, does it mean that I need start from beginning when I met the errors cause by mris_volmask? > > > > Thanks a lot! > > guang > > > > _________________________________________________________________ > > Chat with Messenger straight from your Hotmail inbox. > > http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?o… Windows Live Hotmail gives you a free,exclusive gift. Click here to download. _________________________________________________________________ Windows Live Hotmail gives you a free,exclusive gift. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?o…

1 0

func2roi-sess bug?
by John Richey 10 Dec '09

10 Dec '09

Dear freesurfer experts: I am trying to extract roi from my fMRI data using func2roi-sess. However, I encounter an error that I wonder might be a bug in the code? My input is func2roi-sess -roidef l_lingual -analysis hrf -anatlabel lh.lingual -maskcontrast AllvFix -maskthresh 0 -masktail pos -maskmap sig -sf subjects.txt (the last 25 or so lines of the log are pasted below). Basically, I believe that line in the log that reads: /fmcsm8= bold/007 should read: srcvol = bold/007/fmcsm8.nii The result is that the func2roi-sess routine terminates with the error displayed on the last line: /fmcsm8. Does it exist?lume bold/007 Has anyone else encountered this problem? Or maybe I am skipping a step? I am using v4.5.0. If it helps, I can also paste my source code that seems to produce this error. Thanks in advance John Richey -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 .txtxtfile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 oldtxtstyle = 0 /fmcsm8= bold/007 srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 /fmcsm8. Does it exist?lume bold/007

2 1

rebuild_gca_atlas.csh
by Jared Price 10 Dec '09

10 Dec '09

Freesurfer gurus: When using rebuild_gca_atlas.csh it fails due to the fact that not all of the TRs TEs and FlipAngles are identical across all scans I am using for the atlas. Is there any major concern if we artificially change these values using mri_modify so that they are identical? Much thanks, Jared

2 1

Rotating to chiasmato-commissural plane
by Jordan Poppenk 10 Dec '09

10 Dec '09

Dear list, I would like to rotate my orig.mgz volume into chiasmato-commissural space to assess the length of a freesurfer-obtained hippocampal segmentation along the main axis of the hippocampus. I am doing this to enable use of a slice-counting method. Now, I know that tkregister2 allows me to both rotate volumes and load aseg files, but I can only rotate the movable volume. I'm not clear on how I would set this up a) to rotate my target image in native / subject space (orig.mgz), so as not to disturb the raw length values; or b) to rotate the aseg segmentation along with it. Is anyone able to offer any suggestions on how I might be able to use freesurfer to accomplish this task (or whether there is a different approach that would be simpler)? Thanks in advance for any help. Cheers, Jordan _____________________________________ Jordan Poppenk Ph.D. Candidate, Department of Psychology University of Toronto, Canada http://individual.utoronto.ca/poppenk There is no way to peace; peace is the way. - A.J. Muste

2 3

2009 Destrieux Parcellation for FSAverage?
by Michael Waskom 09 Dec '09

09 Dec '09

Hi all, Is there a way to get aparc.a2009s.annot files (the updated Destrieux parcellation) for fsaverage? Doesn't seem to be in the labels directory for fsaverage for 4.5.0. Thanks! Best, Mike

2 1

linux ppc64 build
by Bradley Buchsbaum 09 Dec '09

09 Dec '09

Hi, There was a previous request from Andre Gouws (Nov. 19th 2009) about the possiblity of obtaining a linux-ppc build. We would also like to run freesurfer on a (64-bit) linux-ppc IBM cluster. Here's hoping two independent requests in the last three weeks constitutes overwhelming demand... cheers, Brad Buchsbaum -- Bradley R. Buchsbaum, Ph.D. Rotman Research Institute 3560 Bathurst St. Toronto, ON Canada M6A 2E1 email: bbuchsbaum(a)rotman-baycrest.on.ca

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer