Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

MNC label to Freesurfer
by Caspar M. Schwiedrzik 06 Jan '14

06 Jan '14

Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, Caspar

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recon-all exited w/errors
by Boric, Katica A. 06 Jan '14

06 Jan '14

Happy New Year freesuerfers! I run into this error while doing recon-all : ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would really appreciate if someone could give me some advice on how to fix this error. Thank you very much! Katica Boric, ps: Here is the error log: #@# Talairach Failure Detection Thu Jan 2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Thu Jan 2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan 2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install it from the CPAN distribution Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, line 460. Thu Jan 2 14:21:43 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Jan 2 14:21:44 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan 2 14:21:45 EST 2014

2 3

recon-all error
by Emad Ahmadi 06 Jan '14

06 Jan '14

Hello & Happy New Year! I'm running recon-all for one subject on MGH clusters (ERISone), and it exits with error. I would appreciate it if you help me figure out what the problem is. The log file is attached. All the best throughout 2014! Emad Emad Ahmadi, MD ------------------------------------------------ Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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converting .thickness files of T1 MRI from FreeSurfer into AFNI
by Muhammad Naveed Iqbal Qureshi 06 Jan '14

06 Jan '14

Hi, I want to know that how can I convert FreeSurfer .thickness files to AFNI readable format I tried the following Command but it gives error mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik... AFNI BRIK write unsupported ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik UN:/media> Please let me help me to solve this problem Thank you :) Best Regards, Muhammad Naveed Iqbal Qureshi

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erroneuos segmentation labeling of skull outside of brain
by Yuliya Yoncheva 05 Jan '14

05 Jan '14

Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question. In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools. Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate? Thus, voxels, which have not been automatically labelled would not impact volume computations? Thank you kindly for your help.

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Re: [Freesurfer] Motion correction for SPACE FLAIR
by Octavian Lie 05 Jan '14

05 Jan '14

Dear Bruce, Best wishes for 2014! I will heed your advice and cc to the list. Indeed, the MGH protocol I obtained from Andre has one acquisition (NSA). Related, I cc this post: We have been trying adaptations of the T2spaceFLAIR MGH protocol on our Phillips 3T scanners (sequences called VISTA). Incorporation of the T2 space FLAIR has been mostly successful at editing out the dura from the pial surface. The only concern are minute differences occasionally appearing as small indentations (at most times <1-2mm) between the woFLAIR.pial and the final pial surfaces, including in intrasulcal (duraless) areas; the amount of these small mismatches is variable from patient to patients, with some trials with almost perfect overlap, and others with visible, if small, differences. I wonder if this has been your experience too, and if this is due mostly to bb registration limits or to differences in pixel bandwidth between mprage and space flair sequences (in our case, see below). In FSwiki, the recommendation is that T2 space flair “should be bandwidth, geometry and readout matched to the mprage”. 1. Speaking about pixel bandwidth, logistics most likely would not allow application of a MEMPR sequence on our Phillips. According to Siemens MPRAGE MGH specs, "exceptions indicate that if a multiple echo sequence is not available, one should choose a bandwidth of 195 Hz/pixel for the MPRAGE". In that case/ using the Siemens Trio MPRAGE protocol as if the MEMPR is not available, how one would adjust the bandwidth in T2spaceFLAIR protocol (currently ~650 in the Siemens space flair and MEMPR protocols) to "match" it to the "simple" MPRAGE protocol (decreasing it to 195 ?). Would it be a workaround? (Please comment on the Siemens case, obviously, I do not expect any light on Phillips without further testing). 2. Could you clarify what geometry matched means? Please advise, Thank you, Octavian On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Octavian > > can you cc the list so that others can answer? What is NSA? We don't have a > ton of experience with it, but 1 has seemed ok (not sure if we've ever tried > two) > Bruce > > > > On Thu, 2 Jan 2014, Octavian Lie wrote: > >> Dear Bruce, >> >> Thank you. We used one vs 2 NSA T2 space FLAIR sequences, without a >> consistent difference in results, with the 2-NSA run obviously doubling >> the >> scan time. Is there a preferred number of NSA you recommend, or we should >> be >> fine with one? Both are at resolution 1X1X1 mm. >> Thank you, >> >> Octavian >> >> >> >> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Octaviaan >> no, not really. You should motion correct and average them using >> something like mri_motion_correct* >> >> We do typically bandwidth/readout match them to the memprages so >> that there is no differential distortion >> >> cheers >> Bruce >> >> >> On Wed, 1 Jan 2014, Octavian Lie wrote: >> >> Dear All, >> >> We recently implemented pial correction using T2 >> space FLAIR with freesurfer >> v 5.3, mostly successfully. We use 2-3 MPRAGE >> (sagittal + axial and/or >> coronal) volumes as 001.mgz, 002/003.mgz for the >> motion correction step in >> recon-all pipeline. >> The typical times for acquiring space FLAIR in our >> settings vary from 2.5 to >> 6 min, depending on the resolution/NSA no. I was >> wondering how freesurfer >> deals with motion artifacts in the space FLAIR >> sequence (especially with >> longer acquisition times), and if there is a >> strategy to minimize motion >> distortion with these (such as getting second runs >> for averaging, etc). >> Please advise, >> >> Octavian. >> >> >> >> >> 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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wm.mgz edits get overwritten & surfs not correctly re-generated
by Tudor Popescu 05 Jan '14

05 Jan '14

Hi everyone and happy new year! I made a couple of manual edits to a wm.mgz file and then relaunched part of that subject's recon (-autorecon2-wm -autorecon3). After it finished, however, the wm.mgz had lost its manual edits - even though I had saved the edited version under the same name, in the right folder. Any ideas why it got overwritten? Comparing filesizes, the post-recon wm.mgz was different not just from my edited version, but also slightly different from the pre-edited wm.mgz! I then redid my edits and repeated the procedure. Strangely, this time the wm.mgz edits were kept, however the redone surfaces still looked bad, as if the wm.mgz hadn't been edited at all. I am running FS 5.3.0 from inside VirtualBox 4.2.12, on a Windows PC. Recon jobs are run remotely on a server running FSL software and output files are then copied over to my local PC. Any help much appreciated, thanks in advance! Tudor

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Fw: Re: Re: problems about freeview
by charujing 04 Jan '14

04 Jan '14

发件人："charujing"<charujing(a)gmail.com> 发送时间：2014-01-05 09:55 主题：Re: Re: [Freesurfer] problems about freeview 收件人："zkaufman"<zkaufman(a)nmr.mgh.harvard.edu>,"Ruopeng Wang"<rpwang(a)nmr.mgh.harvard.edu>,"charujing"<charujing(a)gmail.com> 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Hi Ruopeng and Zeke, Thanks. I will try the latest version. CentOS has 6.0,6.1,6.2,6.3,6.4 and 6.5, also part of them have desktop, server and alternate version. And in Freesurfer download page we can see: OSPlatformVersionRelease DateDownloadSize LinuxCentOS 6 x86_64 (64b)stable v5.3.015 May 2013freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz4.2G LinuxCentOS 4 x86_64 (64b)stable v5.3.015 May 2013freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz4.0G LinuxCentOS 4 (32b)stable v5.3.015 May 2013freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz3.8G MacLion OX X 10.7 (64b Intel)stable v5.3.015 May 2013freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg3.5G MacSnowLeopard OS X 10.6 (32b Intel)stable v5.3.015 May 2013freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg3.2G VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G Also I want to know which CentOS version(6.0,6.1,6.2,6.3,6.4 or 6.5?) and its desktop, alternate or server I should installed or all of them are appropriate for freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz. Thanks Ruopeng and Zeke. All the best. Rujing Zha 2014-01-05 charujing 发件人：zkaufman(a)nmr.mgh.harvard.edu 发送时间：2014-01-05 07:10 主题：Re: [Freesurfer] problems about freeview 收件人："charujing"<charujing(a)gmail.com> 抄送："Ruopeng Wang"<rpwang(a)nmr.mgh.harvard.edu>,"freesurfer"<freesurfer(a)nmr.mgh.harvard.edu>,"Z K"<zkaufman(a)nmr.mgh.harvard.edu> Hello Rujing, You can download the most up to date version of freeview using the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/dev/ In order to use this version, you will need to replace the file $FREESURFER_HOME/bin/freeview.bin currently on your system, with the file you download from the link above. Let me know if you need additional assistance. -Zeke > Hi Rujing, > > I am able to replicate the issue with 5.3.0 release. The good news is the > issue does not appear in the current dev version (so I think it has been > fixed). Zeke, would it be possible for Rujing to download a copy of the > latest freeview build? > > Best, > Ruopeng > > On Jan 4, 2014, at 10:40 AM, "charujing" <charujing(a)gmail.com> wrote: > >> Dear doug, bruce and others, >> Previously I could not view " >> freeview -f >> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot >> " from the >> "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis". The >> freeview did represent 3 images. But it reported a something about no >> geomatric information and I couldnot configure the overlay(When I >> clicked the "configure overlay", it stopped without any response). My OS >> is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX >> 650 and setup the NVIDIA driver. Freesurfer version is >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has >> 2G memory and 4 processors. >> I need help to fix it. >> If anyone have viewed sample data or other data(*.inflated, >> *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by >> freeview just as above, would you please tell me some information? The >> information I need is Freesurer version, Centos version(desktop or >> others) and something in CentOS setup, graphic card version and its >> driver, memory size. >> Thanks very much, doug, brucen and others. >> Any reply will be highly appreciated. >> All the best. >> Rujing Zha >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > 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.

2 1

Re: [Freesurfer] problems about freeview
by charujing123 04 Jan '14

04 Jan '14

发件人："charujing" <charujing(a)gmail.com> 发送时间：2014-01-05 10:26 主题：Fw: Re: Re: [Freesurfer] problems about freeview 收件人："charujing123"<charujing123(a)163.com> 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 发件人："charujing"<charujing(a)gmail.com> 发送时间：2014-01-05 09:55 主题：Re: Re: [Freesurfer] problems about freeview 收件人："zkaufman"<zkaufman(a)nmr.mgh.harvard.edu>,"Ruopeng Wang"<rpwang(a)nmr.mgh.harvard.edu>,"charujing"<charujing(a)gmail.com> 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Hi Ruopeng and Zeke, Thanks. I will try the latest version. CentOS has 6.0,6.1,6.2,6.3,6.4 and 6.5, also part of them have desktop, server and alternate version. And in Freesurfer download page we can see: OSPlatformVersionRelease DateDownloadSize LinuxCentOS 6 x86_64 (64b)stable v5.3.015 May 2013freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz4.2G LinuxCentOS 4 x86_64 (64b)stable v5.3.015 May 2013freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz4.0G LinuxCentOS 4 (32b)stable v5.3.015 May 2013freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz3.8G MacLion OX X 10.7 (64b Intel)stable v5.3.015 May 2013freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg3.5G MacSnowLeopard OS X 10.6 (32b Intel)stable v5.3.015 May 2013freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg3.2G VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G Also I want to know which CentOS version(6.0,6.1,6.2,6.3,6.4 or 6.5?) and its desktop, alternate or server I should installed or all of them are appropriate for freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz. Thanks Ruopeng and Zeke. All the best. Rujing Zha 2014-01-05 charujing 发件人：zkaufman(a)nmr.mgh.harvard.edu 发送时间：2014-01-05 07:10 主题：Re: [Freesurfer] problems about freeview 收件人："charujing"<charujing(a)gmail.com> 抄送："Ruopeng Wang"<rpwang(a)nmr.mgh.harvard.edu>,"freesurfer"<freesurfer(a)nmr.mgh.harvard.edu>,"Z K"<zkaufman(a)nmr.mgh.harvard.edu> Hello Rujing, You can download the most up to date version of freeview using the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/dev/ In order to use this version, you will need to replace the file $FREESURFER_HOME/bin/freeview.bin currently on your system, with the file you download from the link above. Let me know if you need additional assistance. -Zeke > Hi Rujing, > > I am able to replicate the issue with 5.3.0 release. The good news is the > issue does not appear in the current dev version (so I think it has been > fixed). Zeke, would it be possible for Rujing to download a copy of the > latest freeview build? > > Best, > Ruopeng > > On Jan 4, 2014, at 10:40 AM, "charujing" <charujing(a)gmail.com> wrote: > >> Dear doug, bruce and others, >> Previously I could not view " >> freeview -f >> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot >> " from the >> "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis". The >> freeview did represent 3 images. But it reported a something about no >> geomatric information and I couldnot configure the overlay(When I >> clicked the "configure overlay", it stopped without any response). My OS >> is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX >> 650 and setup the NVIDIA driver. Freesurfer version is >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has >> 2G memory and 4 processors. >> I need help to fix it. >> If anyone have viewed sample data or other data(*.inflated, >> *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by >> freeview just as above, would you please tell me some information? The >> information I need is Freesurer version, Centos version(desktop or >> others) and something in CentOS setup, graphic card version and its >> driver, memory size. >> Thanks very much, doug, brucen and others. >> Any reply will be highly appreciated. >> All the best. >> Rujing Zha >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > 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.

1 0

freeview error
by charujing 04 Jan '14

04 Jan '14

Dear Ruopeng, Thanks for your help, Ruopeng.I learned the groupanalysis by manu ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this command on your tutorial data (buckner data). Would you please tell me where my hardware setup is inappropriate? Thanks. All the best. 2014-01-01 charujing

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Freesurfer January 2014