Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

longitudinal processing (base-tps error)
by Sabin Khadka 11 Apr '12

11 Apr '12

HI all, I ran longitudinal processing with reco-all -base <templateID> -tp <MRI_T1> -tp <MRI_T2> -all but in base-tps file of template ID I found the subject ID of MRI_T1 twice instead of MRI_T1 and MRI_T2. I want to run recon-all -long which I am able to do for MRI_T1 but could not do the same for MRI_T2. ANy help would be appreciated. Thanks SK

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Re: [Freesurfer] consult
by Bruce Fischl 11 Apr '12

11 Apr '12

Hi haochuanxi please post to the list so that others can help! It looks to me like your voxel size is (0.4688, 0.4688, 1.19996). Is that the case? If so, it's going to be har to reconstruct good surfaces even if you find a machine with enough memory. "in plane" means the resolution of your data in one of the acquisition planes cheers Bruce On Wed, 11 Apr 2012, ?? wrote: > Dear Bruce? > Something you said I could not understand fully: what is ".46 mm in plane", and what is > anisotropic (0.4688, 0.4688, 1.19996). the data I processed is 3D volume data. > > haochuanxi > > > > > > > > > > At 2012-04-11 21:44:38,"Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >are your data really .46 mm in plane? It looks you are running out of > >memory, but even if you weren't it's very hard to reconstruct data that is > >that anisotropic (0.4688, 0.4688, 1.19996). You are better off getting 1mm > >isotropic and using it, which these days with 3T and 32 channels is only >4-6 min of imaging time.>>cheers>Bruce>> > >On Wed, 11 Apr 2012, ?? wrote:> >> >> >> >> 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 > /fr>> eesurfer/subjects/mgz/mri/orig/004.mgz --average 1 --template /usr/local/freesurfer/subjects/mgz/mri/rawavg.mgz --satit --inittp 1 --fixtp -- > noi>> t --iscale --iscaleout /usr/local/freesurfer/subjects/mgz/mri/orig/002-iscale.txt /usr/local/freesurfer/subjects/mgz/mri/orig/003-iscale.txt ?? ?/us>> r/local/freesurfer/subjects/mgz/mri/orig/004-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/mgz/mri/orig/002.lta /usr/local/ > fre >> esurfer/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. >> >> >> >> >> >> >>>> > >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. > > > >

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-cm switch error
by Oya, Hiroyuki (UI Health Care) 11 Apr '12

11 Apr '12

Hello When I run recon-all with -cm switch, that generates error as follows: /* mri passed volume size is different from the one used to create M3D data ERROR: mri_ca_register with non-zero status 0 */ Without -cm switch, recon-all completes all processing without error. Any help would be appreciated. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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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

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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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Freesurfer April 2012