Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30133 discussions

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.

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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.

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freeview error
by charujing 04 Jan '14

04 Jan '14

5 6

LGI computation problem
by Chong-Yaw Wee 04 Jan '14

04 Jan '14

Hi all, I am trying to compute LGI index using freesurfer. However i got the following error message: *Improper assignment with rectangular empty matrix.Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2));Error in mesh_vertex_nearest (line 29)nearestIndex = dsearchn(vertices,points);Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step);* Following is the information of my system: *Linux distribution: Linux bass-comp1.cs.unc.edu <http://bass-comp1.cs.unc.edu> 2.6.32-431.1.2.el6.x86_64 #1 SMP Sun Nov 24 09:37:37 EST 2013 x86_64 x86_64 x86_64 GNU/LinuxSUBJECTS_DIR: /home/user_name/software/freesurfer/subjectsCurrent working directory: /server_name/user_name/data/Surface/Command used: recon-all -s subj_folder -localGI* *Matlab version: R2013b (8.2.0.701) 64-bit (glnxa64)* I suspect this error is caused by the Matlab and i have tried the method described in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032203.html to solve it. Unfortunately, i doesn't work for me. Any suggestions to solve it? Thanks, wee

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freeview error {Disarmed}
by Rujing Zha 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. Rujing Zha Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: 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 . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button "configure overlay". Then freeview were suspended. The CPU ran "100%",and memory ran "23%". There was nothing to do but terminated it manually in the command console by "ctrl + c". I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is "NVIDIA GeForce 8600 GT", and CPU is "Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz", and RAM is 2.00G. Thanks Bruce and others. All the best. 2014-01-03 Rujing Zha

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possible to run freeview using other versions of libjpeg.so.62?
by Salil Soman 03 Jan '14

03 Jan '14

Hi, My cluster environment is setup to use libjpeg turbo on ubuntu 13.04 (ends up with libjpeg.so.8.0.2 in the /usr/lib/x86_64-linux-gnu/ directory). Is it possible to use this version of libjpeg to run freeview (it currently complaints that it cannot find libjpeg.so.62)? If so, can anyone provide info on what symbolic links or environment variables I need to create to do this? Thank you. Salil

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possible to run freeview using other versions of libjpeg other than libjpeg.so.62?
by Salil Soman 03 Jan '14

03 Jan '14

Hi, My cluster environment is setup to use libjpeg turbo on ubuntu 13.04 (ends up with libjpeg.so.8.0.2 in the /usr/lib/x86_64-linux-gnu/ directory). Is there a way to get freeview to work with a different version of libjpeg (e.g. by making a symbolic link from libjpeg.so.62 to the libjpeg.so.8.0.2 file)? Thanks, -Sal

1 0

Mac Download
by Shazia Dharssi 03 Jan '14

03 Jan '14

Hi FreeSurfer, I was wondering which installation I should use if I am running iOS 10.9.1 Mavericks? Thanks, Shazia

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