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30132 discussions

Re: [Freesurfer] Help with generation of surface after WM edits
by Douglas N Greve 01 Dec '10

01 Dec '10

You can ignore that error. Does the lh.orig.nofix look the same before and after the wm edits? doug SK wrote: > Hi, > > I ran the command > >> recon-all -autorecon2-wm -subjid George -noaseg >> > after reading your comments and it finally finished just now. But I > still cannot see any changes in the places where I have modified the > white matter. > > So, i tried loading the lh.orig.nofix using > > >> tkmedit Paul wm.mgz lh.orig.nofix >> > > It shows a zagged yellow line on top of the wm.mgz. There is also an > error saying.. > > >> mrisReadTriangleFile(/data/kodaly/r/sk/FreeSurfer/Paul/surf/lh.orig): surface >doesn't match /data/kodaly/r/sk/FreeSurfer/Paul/surf/lh.orig.nofix >> > > Any suggestions?? > > regards, > krishna > > > > On 11/30/10, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > >> That is strange. The -autorecon2-wm should have changed those surfaces. >> What's in your xopts file? Can you load the lh.orig.nofix surface in >> tkmedit to see if that has changed? >> >> doug >> >> Krishna Srihasam wrote: >> >>> Hi, >>> >>> I am trying to generate surfaces of a monkey brain and I have run into >>> some problem after the initial surface creation. I had some problems >>> with wm.mgz and I corrected them (check the two images I have >>> attached). I then ran >>> >>> recon-all -autorecon2-wm -subjid George -noaseg –xopts-use –nocortribbon >>> >>> The pial and wm surfaces output was exactly similar to the older one >>> (i.e. before the white matter edits).I , then, tried running recon-all >>> with >>> >>> recon-all -autorecon2-pial -subjid George -noaseg –xopts-use >>> –nocortribbon >>> >>> with pretty much the same result. Any help , suggestions or input is >>> more that welcome. >>> >>> Regards, >>> >>> Krishna >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> ------------------------------------------------------------------------ >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 >> greve(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 >> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(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

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mask.mgh to volume
by Ritobrato Datta 01 Dec '10

01 Dec '10

Hello All , I have a binary mask - mask.mgh. I want create a binary volumetric mask from it in the same space and dimension as orig.mgz Can mri_label2vol be used ? How ? If not, how can this be done ? Thanks a lot Ri

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func2roi-sess question : label2mask_linear: there were 0 label hits
by Yuko Yotsumoto 01 Dec '10

01 Dec '10

Hi all, Mac OS 10.6.5 freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I want to run func2roi-sess with a functionally defined label (lh_MT.label). I have a label stored as : subjects/VM20/label/lh_MT.label and I can see this label with tksurfer-sess. When I ran: func2roi-sess -roidef lh_MT -analysis VMfwhm5lh -motioncor -rawstem fmcsm5 -df sessdirfile -reg register.dof6.dat -s VM20 -anatlabel lh_MT I got an error (roisummary-sess results filled with 0). Below shows some lines from log file that might be related to this problem. All logs are pasted at the end of this message. > Lxyz2Scrs: > -1.000 -0.020 0.021 69283.891; > 0.019 -1.000 -0.021 -1.705; > 0.022 -0.021 1.000 -19.485; > 0.000 0.000 0.000 1.000; > > INFO: label2mask_linear: there were 0 label hits > voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 > INFO: label2mask_linear: there were 0 hits in final mask > label2mask_linear: done > > Lxyz2Scrs: > -1.000 -0.020 0.021 69283.891; > 0.019 -1.000 -0.021 -1.705; > 0.022 -0.021 1.000 -19.485; > 0.000 0.000 0.000 1.000; > > INFO: label2mask_linear: there were 0 label hits > voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 > INFO: label2mask_linear: there were 0 hits in final mask > label2mask_linear: done > Averging over ROI Looks like somehow my label was rejected, or didn't meet some criteria? I don't want any functional thresholds for this analysis, though I see clear activation within this label during task. Please let me know what I need to add/change to make func2roi-sess work. Thank you! Yuko Yotsumoto ############################################### fucn2roi-sess log file $Id: func2roi-sess,v 1.16 2010/03/25 16:22:53 greve Exp $ /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan /Applications/freesurfer/fsfast/bin/func2roi-sess -roidef lh_MT -analysis VMfwhm5lh -motioncor -rawstem fmcsm5 -df sessdirfile -reg register.dof6.dat -s VM20 -anatlabel lh_MT Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 Tue Nov 30 13:08:07 JST 2010 ----------------------------------------------------- Session: VM20 1/1 Tue Nov 30 13:08:07 JST 2010 Tue Nov 30 13:08:07 JST 2010 --------------------------------------------------- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h --roiavg bold/VMfwhm5lh/lh_MT/h --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h.txt --------------------------------------------------- -------------------------------------------------------- /Users/yuko/Documents/freesurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h --roiavg bold/VMfwhm5lh/lh_MT/h --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h.txt version $Id: mri_vol2roi.c,v 1.31 2010/03/25 16:00:50 greve Exp $ -------------------------------------------------------- roifile = bold/VMfwhm5lh/lh_MT/h roitxtfile = bold/VMfwhm5lh/lh_MT/h.txt oldtxtstyle = 0 srcvol = bold/VMfwhm5lh/h.nii srcfmt = bvolume srcreg = bold/register.dof6.dat srcregold = 0 srcwarp unspecified label file = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/VMfwhm5lh/h.nii ...done srcreg Dsrc ------------- 1.000 0.020 -0.021 -0.890; 0.022 -0.021 1.000 -19.985; -0.019 1.000 0.021 2.205; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -1.000 0.000 0.000 69283.000; -0.000 -0.000 -1.000 0.500; -0.000 1.000 -0.000 0.500; 0.000 0.000 0.000 1.000; ---------------------------------- INFO: Source volume detected as selxavg format INFO: Adjusting Frame Power Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 0 WARNING: there were no voxels in the input mask > 0.5 Done averging over ROI (nhits = 0) INFO: Readjusting Frame Power --------------------------------------------------- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h-offset --roiavg bold/VMfwhm5lh/lh_MT/h-offset --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h-offset.txt --------------------------------------------------- -------------------------------------------------------- /Users/yuko/Documents/freesurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h-offset --roiavg bold/VMfwhm5lh/lh_MT/h-offset --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h-offset.txt version $Id: mri_vol2roi.c,v 1.31 2010/03/25 16:00:50 greve Exp $ -------------------------------------------------------- roifile = bold/VMfwhm5lh/lh_MT/h-offset roitxtfile = bold/VMfwhm5lh/lh_MT/h-offset.txt oldtxtstyle = 0 srcvol = bold/VMfwhm5lh/h-offset.nii srcfmt = bvolume srcreg = bold/register.dof6.dat srcregold = 0 srcwarp unspecified label file = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/VMfwhm5lh/h-offset.nii ...done srcreg Dsrc ------------- 1.000 0.020 -0.021 -0.890; 0.022 -0.021 1.000 -19.985; -0.019 1.000 0.021 2.205; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -1.000 0.000 0.000 69283.000; -0.000 -0.000 -1.000 0.500; -0.000 1.000 -0.000 0.500; 0.000 0.000 0.000 1.000; ---------------------------------- Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 0 WARNING: there were no voxels in the input mask > 0.5 Done averging over ROI (nhits = 0) ------------------------------------------- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/001/ --roiavg bold/VMfwhm5lh/lh_MT/-001 --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/-001.txt ------------------------------------------- corRead(): can't open file bold/001/COR-.info -------------------------------------------------------- /Users/yuko/Documents/freesurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/001/ --roiavg bold/VMfwhm5lh/lh_MT/-001 --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/-001.txt version $Id: mri_vol2roi.c,v 1.31 2010/03/25 16:00:50 greve Exp $ -------------------------------------------------------- roifile = bold/VMfwhm5lh/lh_MT/-001 roitxtfile = bold/VMfwhm5lh/lh_MT/-001.txt oldtxtstyle = 0 srcvol = bold/001/ srcfmt = bvolume srcreg = bold/register.dof6.dat srcregold = 0 srcwarp unspecified label file = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/001/ ...

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occipital label without v1
by Ritobrato Datta 01 Dec '10

01 Dec '10

Hello All, I have an occipital label and a v1 label and I have created binary masks from them. Is there a way to create an "Occipital label - V1 label" ie excluding v1 from occipital label. Please let me know. Thank you Ri

2 1

some pial-like tissues aroud Coronal 117 slices
by xuemei lei 01 Dec '10

01 Dec '10

Hi, experts I found my data with a problem like the attached picture: around Coronal 117 slice there are some pial-like tissue included in gray matter。I am not sure this kind of things are pials or gray matter and if I should remove them from the GM. Any help will be appreciated. Thanks in advance -- Xuemei Lei National Key Laboratory of Cognitive Neuroscience and Learning<http://psychbrain.bnu.edu.cn> Beijing Normal University Beijing, China. 100875 Tel: +86-13269171259 ============================================== Welcome to visit my blog: www.mobiye.com

2 1

asegstats2table error
by Jesse Bledsoe 30 Nov '10

30 Nov '10

Hello, I am having difficulty generating an aseg_stats.txt table. When I use the following: asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile aseg_stats.txt I get the following error: 'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os I am on Linux-centos4-stable-pub-v4.2.0 Any suggestions are much appreciated, Jesse

1 0

Help with generation of surface after WM edits
by Krishna Srihasam 30 Nov '10

30 Nov '10

Hi, I am trying to generate surfaces of a monkey brain and I have run into some problem after the initial surface creation. I had some problems with wm.mgz and I corrected them (check the two images I have attached). I then ran recon-all -autorecon2-wm -subjid George -noaseg -xopts-use -nocortribbon The pial and wm surfaces output was exactly similar to the older one (i.e. before the white matter edits).I , then, tried running recon-all with recon-all -autorecon2-pial -subjid George -noaseg -xopts-use -nocortribbon with pretty much the same result. Any help , suggestions or input is more that welcome. Regards, Krishna

2 1

recon-all fsaverage error and re-running
by Joakim Vinberg 30 Nov '10

30 Nov '10

Hi everybody, I received the following error running recon-all on a new subject. It looks like the directory this subject was moved to didn't have the fsaverage link, and so it didn't quite complete. I've replaced the link, and am going to finish processing this subject. My question is: based on the error below and reading ReconAllDevTable, I believe I only have to re-run the final few steps, all in autorecon3. Is this correct, or should I re-run earlier steps as well? Thanks in advance for all of your help! Joakim #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Wed Nov 24 20:40:47 EST 2010 mris_preproc --s 9211 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh ERROR: cannot find fsaverage in /data/freesurfer/round5

2 1

Run skullstrip only?
by Lisa F. Akiyama 30 Nov '10

30 Nov '10

Hello FreeSurfers, By reading through the wiki, it seems like the skullstrip command uses nu.mgz and T1.mgz, but is there a way to just run the skullstrip command without nuintensitycor or normalization? I have MRIs of a few subjects in which the intensity normalization seems to not have beneficial for preparing the MRIs for skullstripping. I've attached the snapshot of brainmask.mgz to this email. Thanks in advance. Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment before printing this e-mail.

2 2

recon-all exited with ERRORS
by Zhangyuanchao 30 Nov '10

30 Nov '10

Dear expert， We compute the MRI data with FREESURFER using instruction recon-all -s < > -all,but some data will show recon -all exited with ERRORS in the recon-all-status.log. The flowing display error information :status file for recon-allThu Nov 11 19:22:13 HKT 2010recon-all finished without error at Thu Nov 11 19:22:17 HKT 2010 New invocation of recon-all status file for recon-allThu Nov 11 20:26:17 HKT 2010#@# MotionCor Thu Nov 11 20:26:17 HKT 2010#@# Nu Intensity Correction Thu Nov 11 20:26:33 HKT 2010#@# Talairach Thu Nov 11 20:26:57 HKT 2010#@# Talairach Failure Detection Thu Nov 11 20:27:50 HKT 2010#@# Intensity Normalization Thu Nov 11 20:27:50 HKT 2010#@# Skull Stripping Thu Nov 11 20:31:17 HKT 2010Linux ccm.web 2.6.18-194.17.1.el5xen #1 SMP Wed Sep 29 13:30:21 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Nov 11 23:17:40 HKT 2010 OR LIKE THIS: status file for recon-allThu Nov 11 19:33:11 HKT 2010recon-all finished without error at Thu Nov 11 19:33:15 HKT 2010 New invocation of recon-all status file for recon-allMon Nov 22 00:51:21 HKT 2010#@# MotionCor Mon Nov 22 00:51:21 HKT 2010#@# Nu Intensity Correction Mon Nov 22 00:51:37 HKT 2010#@# Talairach Mon Nov 22 00:52:34 HKT 2010#@# Talairach Failure Detection Mon Nov 22 00:53:20 HKT 2010#@# Intensity Normalization Mon Nov 22 00:53:20 HKT 2010#@# Skull Stripping Mon Nov 22 00:56:37 HKT 2010#@# EM Registration Mon Nov 22 02:36:07 HKT 2010#@# CA Normalize Mon Nov 22 03:17:48 HKT 2010#@# CA Reg Mon Nov 22 03:20:05 HKT 2010#@# CA Reg Inv Mon Nov 22 07:03:03 HKT 2010#@# Remove Neck Mon Nov 22 07:04:31 HKT 2010#@# SkullLTA Mon Nov 22 07:06:08 HKT 2010#@# SubCort Seg Mon Nov 22 08:12:28 HKT 2010Linux ccm.web 2.6.18-194.17.1.el5xen #1 SMP Wed Sep 29 13:30:21 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Nov 22 08:35:10 HKT 2010 Could you explain to me the reason for the problem and could you solve me the problem? I will appreciate your help very much. Best regards, Liang Gao

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