Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

pediatric template vv. scaling or parcellation?
by Rhoshel Lenroot 14 Dec '09

14 Dec '09

Hello - We are planning to use freesurfer in a study of 2-5year olds; I understand from previous posts that image intensity should be ok at this age range, but was wondering whether there are issues related to scaling or parcellation such that it would still be optimal to use a pediatric template? Thank you very much, Rhoshel Lenroot, M.D. School of Psychiatry University of New South Wales r.lenroot(a)unsw.edu.au

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SetUp file error
by Ilana Hairston 14 Dec '09

14 Dec '09

Hi there, I moved my data to a new computer with Freesurfer installed. When i run the SetUpFreeSurfer.csh (or .sh for that matter) i get a strange configuration: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/ FSFAST_HOME /usr/local/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer//subjects MNI_DIR /usr/local/freesurfer//mni FSL_DIR /usr/local/fsl note the double slashes on SUBJECTS_DIR, FSFAST_DIR, and MNI_DIR. needless to say freesurfer can't find my data. I inspected the setup files and they don't have typo in them. what should i do? thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************

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Re: [Freesurfer] func2roi-sess bug?
by John Richey 14 Dec '09

14 Dec '09

Ok - I believe I figured out the problem, but I wanted to post it to the list, so that anyone else who encounters this error can hopefully spend less time than I did tracking down the culprit! Essentially, a break was being passed inappropriately to the mri_vol2roi subroutine called by func2roi-sess. The break (return/enter, etc) was located in the .txt file that specified the run numbers that I wanted to analyze (in my case, 007 008 009). These strings were separated by a space and a break, which caused the srcvol to equal srcvol = bold/007 /fmcsm8 And this caused func2roi-sess to terminate with errors when it couldn't find such a file. -----Original Message----- From: John Richey Sent: Friday, December 11, 2009 4:30 PM To: 'Freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] func2roi-sess bug? 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_C > 17 > mri_vol2roi > --srcreg bold/register.dat --label > /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C > 17/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_C > 17/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

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Re: [Freesurfer] func2roi-sess bug?
by John Richey 14 Dec '09

14 Dec '09

Dear experts, I was able to coax out a little bit more information on the nature of the error that I am encountering in func2roi-sess. Looking at the last line of the log (final 25 or so lines of the log are pasted below), it seems that the program is looking for bold/007/fmcsm8, but actually sees bold/007/ fmcsm8 Is it plausible that there is an errant space entered somewhere in the code that is causing the problem? I have looked through the source code and nothing is jumping out at me as obviously causing the error. /mnt/users.q.shares/jar62.GDfLZ35tI9j9pkcF2UKe/Analysis/freesurfer/SAD_C22 mri_vol2roi --srcvol bold/007 /fmcsm8 --roiavg bold/dotprobe_all_hrf/lh_lingual/fmcsm8-007 --srcreg bold/register.dat --label /mnt/users.q.shares/jar62.GDfLZ35tI9j9pkcF2UKe/Analysis/freesurfer/SAD_C22/l abel/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/lh_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/lh_lingual/fmcsm8-007 .txt ------------------------------------------- -------------------------------------------------------- /mnt/users.q.shares/jar62.GDfLZ35tI9j9pkcF2UKe/Analysis/freesurfer/SAD_C22 mri_vol2roi --srcvol bold/007 /fmcsm8 --roiavg bold/dotprobe_all_hrf/lh_lingual/fmcsm8-007 --srcreg bold/register.dat --label /mnt/users.q.shares/jar62.GDfLZ35tI9j9pkcF2UKe/Analysis/freesurfer/SAD_C22/l abel/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/lh_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/lh_lingual/fmcsm8-007 .txt version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/lh_lingual/fmcsm8-007 roitxtfile = bold/dotprobe_all_hrf/lh_lingual/fmcsm8-007 .txt oldtxtstyle = 0 srcvol = bold/007 /fmcsm8 srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /mnt/users.q.shares/jar62.GDfLZ35tI9j9pkcF2UKe/Analysis/freesurfer/SAD_C22/l abel/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 ERROR: could not find volume bold/007 /fmcsm8. Does it exist?

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Using segmentation for wm/pial edits
by Lena Palaniyappan 14 Dec '09

14 Dec '09

Though the pial surface and wm surface follow expected course, there are some regions that are misclassified when the colortable is overlaid. Please see the example below... Should I worry? Thanks in anticipation LKP _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Co-registration in FS
by Xinian Zuo 14 Dec '09

14 Dec '09

Hi FSers, I am new to freesurfer. now start to use it for looking at struc-func relationship. Normally, in fsl, I employ bet for both example_func and highresh anat. it means that the func_brain and anat_brain are fed into flirt to estimate the co-registration. here, i try to use reg_feat2anat to do this. but in this new version (4.5), it told me the betfunc command can not be found. thus I just used the version without --bet. the results in tksurfer looked not good. I am guessing it was caused by the highres with large neck areas. MY QUESTION is how can I trigger reg_feat2anat (or whatever other commands) to take skull-stripped highres for the co-registration (in fact, the brainmask.mgz already there)? Or I was wrong, reg_feat2anat did this consideration? Any suggestions would be appreciated! -- Xinian Zuo, Ph.D Associate Research Scientist Institute for Pediatric Neuroscience NYU Child Study Center 215 Lexington Ave., 14th Floor New York, NY 10016 Phone: 212-263-4735 Public: www.AboutOurKids.org Academic: http://publicationslist.org/xinian.zuo Personal: zuoxinian.googlepages.com Blog: http://restbrain.blogspot.com

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Recon error: Talairach Failure Detection
by Rodrigo Zepeda 14 Dec '09

14 Dec '09

Hi, I'm getting an error trying to run a reconstruction. I'm working on multnomah and my subjects directory is: /autofs/space/multnomah_002/users/Cashlab/ *I'm using the following command:* [multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject MG15_SurferOutput -i MG15/MG_15_SPGR/1.2.840.113619.2.176.3596.6688992.17364.1172489897.387.dcm *I get the following error:* #@# Talairach Failure Detection Sun Dec 13 11:51:46 EST 2009 /autofs/space/multnomah_002/users/Cashlab/MG15_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0308, pval=0.0034 < threshold=0.0050) Linux multnomah 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sun Dec 13 11:51:46 EST 2009 *My environment information is:* -------- freesurfer-Linux-centos4-stable-v4.5.0-20091124 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable4 FSFAST_HOME /usr/local/freesurfer/stable4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current Any help will be appreciated! Thanks, Rodrigo Zepeda

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Error: cannot open libXss.so.1?
by SG KIM 14 Dec '09

14 Dec '09

Dear Freesurfer, I ran recon-all with -all flag, and I've got an error message as below: >mris_volmask.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory >Linux compute-0-1.local 2.6.18-92.1.13.el5PAE #1 SMP Wed Sep 24 20:07:49 EDT 2008 i686 i686 i386 GNU/Linux >recon-all exited with ERRORS at Tue Dec 8 07:43:35 KST 2009 I ran it on {Intel(R) Xeon(R) CPU E5345 @ 2.33GHz (4096 KB cache)} with {Linux compute-0-1.local 2.6.18-92.1.13.el5PAE #1 SMP Wed Sep 24 20:07:49 EDT 2008 i686 i686 i386 GNU/Linux} I've googled it, only one case was posted via this mailing list. Yes, I want to know why this error occur but also how to fix it. Please help me out here! 'A` Mr. SG KIM.

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UC Berkeley RA position
by Elizabeth Mormino 12 Dec '09

12 Dec '09

Position in PET imaging at UC Berkeley/Lawrence Berkeley National Laboratory We're looking for a research assistant to work with multisite PET data. The position involves downloading PET images from archived sites, using existing software to extract numerical values from these images, analyzing data sets using values from these PET scans as well as associated clinical, demographic, cognitive, and biomarker data from databases of enrolled subjects. Education/Training: BA or BS preferably in neuroscience, engineering related fields, or psychology Skills: Familiarity with medical images and techniques used for image analysis, familiarity with multiple operating systems (Linux, Unix, OSX, Windows), familiarity with statistics (SPSS, R, etc.), experience in working with PET or MR images in SPM, FSL, and/or other analysis program, programming experience in Matlab or Python, experience working with databases Please apply online here (JOB ID#10185): http://jobs.berkeley.edu/ Jagust Laboratory Helen Wills Neuroscience Department, UC Berkeley Lawrence Berkeley National Laboratory

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Wm/pial edits misclassification
by Lena Palaniyappan 12 Dec '09

12 Dec '09

Hi all Please see the attached images slices 108 to 111 What is happening at precentral / middle frontal white matter? How should I be correcting this? The wm slices as you can see have missing volumes. I cannot fill these spaces in wm surface as there is no obvious white matter in the original surface. How should I go about correcting this? Many thanks in anticipation Lena _______________________________________________________ Lena Palaniyappan Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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