Freesurfer

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30088 discussions

consult
by 传玺 11 Apr '12

11 Apr '12

Dear FS expert： Today i put two contrast in the file {subjects},and run the command line "recon-all -s mgz -all", several minutes later,the terminal tells error,it says: [brain@localhost ~]$ recon-all -s mgz -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.25-14.fc9.i686 #1 SMP Thu May 1 06:28:41 EDT 2008 i686 i686 i386 GNU/Linux #-------------------------------------------- #@# MotionCor Wed Apr 11 17:49:05 HKT 2012 Found 3 runs /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/mgz mri_robust_template --mov /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz --average 1 --template /usr/local/freesurfer/subjects/mgz/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/mgz/mri/orig/002-iscale.txt /usr/local/freesurfer/subjects/mgz/mri/orig/003-iscale.txt /usr/local/freesurfer/subjects/mgz/mri/orig/004-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/mgz/mri/orig/002.lta /usr/local/freesurfer/subjects/mgz/mri/orig/003.lta /usr/local/freesurfer/subjects/mgz/mri/orig/004.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/mgz/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz'... reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz'... reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz ) Registration::setSourceAndTarget ... Mov: (0.4688, 0.4688, 1.19996)mm and dim (512, 512, 156) Dst: (0.4688, 0.4688, 1.20005)mm and dim (512, 512, 156) Asserting both images: 0.4688mm isotropic and (512, 512, 400) voxels Original : (0.4688, 0.4688, 1.19996) mm size and (512, 512, 156) voxels. Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 400) voxels. Reslicing using trilinear interpolation Original : (0.4688, 0.4688, 1.20005) mm size and (512, 512, 156) voxels. Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 400) voxels. Reslicing using trilinear interpolation Registration::findSaturation - Gaussian Pyramid MRIalloc(512, 512, 400): could not allocate 1048576 bytes for 367th slice Cannot allocate memory Linux localhost.localdomain 2.6.25-14.fc9.i686 #1 SMP Thu May 1 06:28:41 EDT 2008 i686 i686 i386 GNU/Linux recon-all -s mgz exited with ERRORS at Wed Apr 11 17:51:20 HKT 2012 For more details, see the log file /usr/local/freesurfer/subjects/mgz/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting could you tell me what is wrong in the process? Thank you very much.

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consult
by 传玺 11 Apr '12

11 Apr '12

-------- 转发邮件信息 -------- 发件人："传玺" <shandongren2084(a)163.com> 发送日期：2012-04-11 19:26:41 收件人：freesurfer <freesurfer(a)nmr.mgh.harvard.edu> 主题：[Freesurfer] consult Dear FS expert： Today i put two contrast in the file {subjects},and run the command line "recon-all -s mgz -all", several minutes later,the terminal tells error,it says: [brain@localhost ~]$ recon-all -s mgz -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.25-14.fc9.i686 #1 SMP Thu May 1 06:28:41 EDT 2008 i686 i686 i386 GNU/Linux #-------------------------------------------- #@# MotionCor Wed Apr 11 17:49:05 HKT 2012 Found 3 runs /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/mgz mri_robust_template --mov /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz --average 1 --template /usr/local/freesurfer/subjects/mgz/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/mgz/mri/orig/002-iscale.txt /usr/local/freesurfer/subjects/mgz/mri/orig/003-iscale.txt /usr/local/freesurfer/subjects/mgz/mri/orig/004-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/mgz/mri/orig/002.lta /usr/local/freesurfer/subjects/mgz/mri/orig/003.lta /usr/local/freesurfer/subjects/mgz/mri/orig/004.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/mgz/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz'... reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz'... reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz ) Registration::setSourceAndTarget ... Mov: (0.4688, 0.4688, 1.19996)mm and dim (512, 512, 156) Dst: (0.4688, 0.4688, 1.20005)mm and dim (512, 512, 156) Asserting both images: 0.4688mm isotropic and (512, 512, 400) voxels Original : (0.4688, 0.4688, 1.19996) mm size and (512, 512, 156) voxels. Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 400) voxels. Reslicing using trilinear interpolation Original : (0.4688, 0.4688, 1.20005) mm size and (512, 512, 156) voxels. Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 400) voxels. Reslicing using trilinear interpolation Registration::findSaturation - Gaussian Pyramid MRIalloc(512, 512, 400): could not allocate 1048576 bytes for 367th slice Cannot allocate memory Linux localhost.localdomain 2.6.25-14.fc9.i686 #1 SMP Thu May 1 06:28:41 EDT 2008 i686 i686 i386 GNU/Linux recon-all -s mgz exited with ERRORS at Wed Apr 11 17:51:20 HKT 2012 For more details, see the log file /usr/local/freesurfer/subjects/mgz/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting could you tell me what is wrong in the process? Thank you very much.

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What is MNI coordinates
by bowang21＠mail.ustc.edu.cn 10 Apr '12

10 Apr '12

Dear FreeSurfer experts Recently,I am learning FreeSurfer and I see a word 'MNI coordinates'.What is MNI coordinates?Can you give me some essays about it? thanks very much BOBO

2 1

Gcut contrast change
by Gabriel Gonzalez Escamilla 10 Apr '12

10 Apr '12

2 2

Freeview bus error
by Jeni Chen 10 Apr '12

10 Apr '12

Hi, I was recently at the FreeSurfer workshop in Boston and learned about the "Freeview" tool in Freesurfer. However, when I tried to run it from my own laptop (Mac book pro), it crashes and gives the error message: "Bus error". I didn't get a chance to have this problem solved while I was there, and after coming back from Boston, I tried running the program on the Mac Pro in my lab, and I got the same error message. Does Freeview have known issue on Mac? Here are some info about the Mac in my lab: Mac Pro Mac OS X version 10.6.8 2x2.4GHz quad core 8GB memory FreeSurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I'd really appreciate it if someone could help me figure it out. Thank you in advance! Jeni

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Empty Segmentations
by Allie Rosen 10 Apr '12

10 Apr '12

Hi Freesurfers, I am attempting to get total GM and WM volumes for two populations. I ran asegstats2table. For the following segmentations, 6/8 control measures are empty: lhCortexVol rhCortexVol CortexVol lhCorticalWhiteMatterVol rhCorticalWhiteMatterVol SubCortGrayVol TotalGrayVol For the following segmentations, all patients and 2 controls are empty: Left-Cerebral-White-Matter Left-Cerebral-Cortex Right-Cerebral-White-Matter Right-Cerebral-Cortex BrainSegVol I'm not sure why these are empty, or how to check for problems with the segmentations. Any help would be appreciated! Allie

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Re: [Freesurfer] question abt fsaverage_sym
by Douglas N Greve 10 Apr '12

10 Apr '12

On 04/10/2012 10:04 AM, Ritobrato Datta wrote: > Hi Doug, > > I am following up on the post below > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-February/022613… > > Question 1) How is the new fsaverage_sym different from the old one ? There was a small bug in the construction of the old one that caused the left hemi target to give slightly different results than the right hemi target. thus, if you did two different analyses, one targeting the lh and on targeting the rh, then they would give different results. Even now, you won't get exactly the same, but it will be very close. > > Question 2) The multiple comparison correction shud be untar'ed' to 'average' folder and not fsaverage_sym folder ? > > in the email you have the following - > ######## Untar fsaverage_sym.mcc.tar.gz into > $FREESURFER_HOME/average/mult-comp-cor/ > cd $FREESURFER_HOME/average/mult-comp-cor/ > tar xvfz fsaverage_sym.mcc.tar.gz > ######## Those instructions are correct. > > Question 3) Is there a mac version of mri_convert.linux I just put one there called mri_convert.macos. The uname from the machine it came from is: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 let me know if that does not work. doug > > Please let me know. > > Thanks > > Rito > > Ritobrato Datta, Ph.D. > Post Doctoral Researcher > Department of Neurology > University of Pennsylvania School of Medicine > 3rd Floor, Room 312 > 3710 Hamilton Walk (Goddard Laboratories) > Philadelphia, PA 19104-6241 > > -- 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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Identifying meridia in retinotopic maps
by Greg Burgess 10 Apr '12

10 Apr '12

HI freesurfers, I have a few questions that were asked previously, but I don't seem to be able to find (or possibly understand) the answers. 1) I'm displaying polar and eccentricity maps using the rtview script. However, no color wheel appears, and I do not seem to be able to find an option to display it in the tksurfer menus. What colors correspond to the horizontal and vertical meridia? Is there a way to display the color wheel as a legend? 2) If, instead of using rtview, I display the heat maps in tksurfer, how do I know what values correspond to the horizontal and vertical meridia? 3) My fieldsign maps appear very speckled, like red and blue polka dots across all of cortex. However, as far as I can determine, the polar and eccentricity maps look reasonable. As suggested elsewhere, I've applied various amounts of smoothing in the fieldsign-sess call. More smoothing makes it look better, but even with 10mm of smoothing, it's unclear if the fieldsigns are correct. How can I track down the problems with the fieldsign maps? Thanks in advance! --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burgessg(a)pcg.wustl.edu

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How to let fsfast process the data not named f.nii.gz?
by Zhen Zonglei 10 Apr '12

10 Apr '12

My raw BOLD data is named func.nii.gz in each run directory. It preprocess-sess reported the ERROR: could not determine format for S0001/obj/004/f, even I provide the –i func option. Is there an easy way to let fsfast process the data not named f.nii.gz ? The version I used is FS 5.1. Thanks Zonglei

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recon-all processing stages
by Ed Gronenschild 10 Apr '12

10 Apr '12

Hi I'm not sure but does the Talairach stage precede the nu-correct stage in version v5.1.0? If so, is there an option to switch these two stages? Cheers, Ed

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