Freesurfer

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glibc version compatability
by Paul Greenberg 05 May '07

05 May '07

2 1

Re: [Freesurfer] Cortical sheet mask?
by David Perlman 05 May '07

05 May '07

That sounds great, of course! Is mris_volmask a new script? It doesn't seem to be present in my installation, which I downloaded last week. Where can I get that program? When I fed a higher-resolution volume as template to mri_surf2vol with --fillribbon, it actually worked just fine, except for the same graininess bug mentioned. So if there's already a bug fix version of mri_surf2vol available I'd sure like to have it now so I can try it out. It is probably sufficient for my current needs. Where can I get the new mri_surf2vol? Thanks so much for your help... On May 5, 2007, at 8:37 AM, Gheorghe Postelnicu wrote: > It can do that, although this is not supported currently. > > Also, the current binary for the ribbon generation is called > mris_volmask. > > I think the best thing to do to satisfy your request is to introduce a > new parameter for voxel scaling. This would be applied to the template > voxel size (which is now by default orig.mgz). > > How would that sound? > > PS: this might take a couple of days, as I can foresee small technical > problems occurring with the resolution increase. > > On 5/5/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi David, >> >> there are two issues here. One is a known bug in which the ribbon >> isn't >> filled properly. This has been fixed by Gheorghe Postelnicu and >> Nick can >> post you a new version. The resolution is a different issue. >> Gheorghe: will >> your code handle generating higher resolution versions of the ribbon? >> >> thanks, >> Bruce >> >> >> On Sat, 5 May 2007, David Perlman wrote: >> >> > Is there a way to re-do the generation of the ribbon but >> generate it with a >> > smaller voxel size? I've already had success resampling the >> T1.mgz to 0.25mm >> > and using it as a template for mri_surf2vol with --mkmask and -- >> fillribbon, >> > but the problem is that only projects out from the vertices, so >> the resulting >> > ribbon is sparse and thready, and doesn't fill the whole >> cortical ribbon. >> > (Likewise the ?h.ribbon.mgz file seems to be missing a lot of >> voxels in its >> > interior.) >> > >> > Ideally what I want is to be able to overlay the surfaces onto a >> volume of my >> > chosen resolution, and then fill the voxels between the >> surface. I've been >> > looking at matlab code, and found this program: >> > http://tinyurl.com/2bbyap >> > surface2volume.m which allegedly does what I want, but it >> doesn't actually >> > seem to work right when I try it: I get only a few scattered >> voxels filled. >> > >> > Does anyone have any idea of how to do this? Any help is greatly >> > appreciated! >> > >> > >> > On May 3, 2007, at 10:31 AM, Bruce Fischl wrote: >> > >> >> Hi David, >> >> >> >> we do generate such a thing called ?h.ribbon.mgz, but note that >> once you go >> >> back into the volume the topology is no longer preserved. >> >> >> >> cheers, >> >> Bruce >> >> On Thu, 3 May 2007, David Perlman wrote: >> >> >> >>> I'm new to freesurfer, so I'm hoping this question isn't too >> obvious. >> >>> I've searched the mailing list archives and the wiki but >> haven't found any >> >>> leads. >> >>> >> >>> I'm wondering if there's a way to generate a volume >> representation of the >> >>> cortical sheet, based on the data from the white surface and >> the pial >> >>> surface, so that the sheet will be guaranteed to have good >> topology, as >> >>> well as retaining the proper thickness at each point? It >> seems like all >> >>> the information for this is there already since we have the >> two surfaces, >> >>> but I don't know how to go about figuring out how to convert >> it into >> >>> volume data. >> >>> >> >>> Here's a small image that might help give an idea of what I need: >> >>> http://brainimaging.waisman.wisc.edu/~perlman/corticalsheet.png >> >>> >> >>> >> >>> In case you're curious, the reason I want this is because >> we're trying to >> >>> test the novel method for cortical thickness measurement given in >> >>> "Three-Dimensional Mapping of Cortical Thickness Using Laplace's >> >>> Equation", Jones, Buchbinder and Aharon, Human Brain Mapping >> >>> 11:12-32(2000). >> >>> >> >>> -- >> >>> - >> dave---------------------------------------------------------------- >> >>> After all, it is not *that* inexpressible. >> >>> -H.H. The Dalai Lama >> >>> >> >>> >> >>> >> >>> _______________________________________________ >> >>> Freesurfer mailing list >> >>> Freesurfer(a)nmr.mgh.harvard.edu >> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>> >> >>> >> >>> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > -- >> > - >> dave---------------------------------------------------------------- >> > Science arose from poetry... when times change the two can meet >> again >> > on a higher level as friends. -Göthe >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > > > > -- > Gheorghe Postelnicu, PhD > MGH, Harvard Medical School -- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe

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(no subject)
by hankee 05 May '07

05 May '07

Hi, How many parts consisted of the occipital lobe in freesurfer's ?h.aparc.stats file and what the name of this parts in this file? Thank you! hankee，duhanjian(a)sohu.com 2007-05-05

2 1

problem of group analysis
by Wang, Xin 04 May '07

04 May '07

Hello, Group I have a question about mri_glmfit. I can not run this commend on my data. An error "MatrixReadTxT: could not scan value [1] [2] file exists ERROR: loading C age.mat" appeared. I do not know what is wrong. The only warning I saw is "ERROR: cound not find volume $SUBJECTS_DIR/average/surf/../mri/orig. Does it exist?" when I ran mri_surf2surf. I am doing group comparison of cortical thickness on 2X2 data. The following is my fsgd.txt and *.mat. GroupDescriptorFile 1 Title thick vs group Class group1 Class group2 Variables age Input APL02R700 group1 48 Input APN02G650 group1 35 Input APN02G700 group2 35 Input APN03L700 group2 30 DefaultVariable age age.mat: -1, 1, 0 If anyone know what is wrong in my analysis, please help. Thank you in advance, Xin

3 3

Re: [Freesurfer] symbolic links
by skloeppe＠uke.uni-hamburg.de 04 May '07

04 May '07

Thanks Doug, I checked all the limits. This shouldn't be the problem. The descriptor limit is indeed 1024. I am using freesurfer-Linux-centos4-stable-pub-v3.0.3 It would be great if you could make the fix available for this version. Regards, Stefan > Stephan, > > You can find out how many open files are allowed by a process by typing: > > limit > > and look for the 'descriptors' setting. If that is less than 102, then > that is likely your problem, and you could try changing the line to: > > limit descriptors 128 > > If your current descriptors default is some number much greater (like > 1024), then the problem is something else. > > Which freesurfer distribution are you using? If the problem is indeed > the 'too many open descriptors' problem, there was a bug that was fixed > to address this (but hasnt yet made to the public distribution), and I > could post the binaries for your platform. > > Nick > > > > On Thu, 2007-05-03 at 17:26 +0000, skloeppe(a)uke.uni-hamburg.de wrote: > > Hi Doug, > > > > Thanks for your swift reply. > > When I run your version I always received the error: > > > > "limit: descriptors: Can't remove limit" > > > > I then deleted the following line in your code: > > > > "limit descriptors unlimited " > > > > That helped but after 88 subjects I always get on error message now: > > "88 of 102: reading > > /mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797.mgz... > > mghRead: encountered error executing: 'zcat > > /mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797. > > mgz',frame -1 > > mri_average: > > MRIread(/mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797.mgz) > > failed" > > > > I am wondering if it might be related to the line I deleted as the one > > above the deleted one reads > > > > # increase number of allowable open files to maximum: > > > > Many thanks, > > > > Stefan > > > > > > > > > > > > > > > > > > > > > > > > > > Copy these into your freesurfer bin > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… > > > > > > then run with --no-link > > > > > > doug > > > > > > skloeppe(a)uke.uni-hamburg.de wrote: > > > > > > >Hi Doug, > > > > > > > >I am also running FS on a virtual machine and encoutered the same problem > > > >with the symbolic links that is described below. When I run the > > > >make_average_subject script only data for the right hemisphere is created. > > > >Then it seems to stop with the message: > > > > > > > >ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not > > > >supported > > > > > > > >I was wondering if you have modified the script to allow a copy instead of > > > >a link. Will symbolic links be used later in the group analysis steps > > as well? > > > > > > > >Many thanks, > > > > > > > >Stefan > > > > > > > > > > > > > > > >Re: [Freesurfer] symbolic links > > > > > > > >Doug Greve > > > >Fri, 01 Dec 2006 09:25:04 -0800 > > > >I don't think recon-all uses any sym links. I can mod the average subj > > > >script to copy instead of link. > > > > > > > >[EMAIL PROTECTED] wrote: > > > > > > > > > > > >Hi Doug, > > > > > > > > > > > > while trying to expand the volume of my virtual machine to be able to > > > >create symbolic links I started wondering if the way I preprocessed my > > > >data with recon_all might be affected somehow by the fact symbolic links > > > >were not supported (the data was located on a mounted drive). The only > > > >error message regarding this came during the make_average_subject part... > > > > > > > > Is there any way to use freesurfer avoiding the creation of symbolic > > > >links? > > > > > > > >many thanks > > > >bogdan > > > > > > > >_______________________________________________ > > > >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 > > > >[EMAIL PROTECTED] > > > > > > > >Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > > > > >In order to help us help you, please follow the steps in: > > > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > In order to help us help you, please follow the steps in: > > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf Körperschaft des öffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jörg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus

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RE: [Freesurfer] ROI of SI cortex
by Rahul Desikan 03 May '07

03 May '07

Hi Xin, Within the *h.aparc.annot files for each subject, there should be individual label files for *h.precentral.label and *h.postcentral.label. If you take a look at your *h.aparc.stats, there should be a value for the thickness and volume. You can, of course, take this *h.aparc.stats file and upload it into matlab, spss or any other stats package and do statistics on these values. Best, rahul On Mon, 30 Apr 2007, Wang, Xin wrote: > Dear Rahul > The SI is primary somatosensory cortex (or postcentral gyrus) and MI is primary motor cortex (or precentral gyrus). I want to compare the thickness and volume of these two areas from left side to right side. > Thank you, > > Xin > > ________________________________ > > From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] > Sent: Mon 4/30/2007 3:52 PM > To: Wang, Xin > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] ROI of SI cortex > > > > Hi Xin, > > What exactly do SI and MI cortices refer to? > > rahul > > On Mon, 30 Apr 2007, Wang, Xin wrote: > >> Hello, group >> I need to compare thickness of left v.s. the right SI and MI cortices. I saw some matlab tools for comparsion of left and right hippocampus in Lundervold.pdf. I could not find similar tools in the matlab folder of Freesurfer stable release 3.0.5 that I just installed. Could anybody kindly tell me the tools I could use for my study? >> Thank you in advance. >> Xin Wang >> > > -- > > > > > > > > > > --

3 2

functional overlay values
by abel cruz vadell 03 May '07

03 May '07

Hi everyone Could I divide the values of a functional overlay volume by a known constant in tkmedit or using any other function of freeSurfer? thanks abel ____________________________________________________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

2 1

Re: [Freesurfer] symbolic links
by skloeppe＠uke.uni-hamburg.de 03 May '07

03 May '07

Hi Doug, Thanks for your swift reply. When I run your version I always received the error: "limit: descriptors: Can't remove limit" I then deleted the following line in your code: "limit descriptors unlimited " That helped but after 88 subjects I always get on error message now: "88 of 102: reading /mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797.mgz... mghRead: encountered error executing: 'zcat /mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797. mgz',frame -1 mri_average: MRIread(/mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797.mgz) failed" I am wondering if it might be related to the line I deleted as the one above the deleted one reads # increase number of allowable open files to maximum: Many thanks, Stefan > > Copy these into your freesurfer bin > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… > > then run with --no-link > > doug > > skloeppe(a)uke.uni-hamburg.de wrote: > > >Hi Doug, > > > >I am also running FS on a virtual machine and encoutered the same problem > >with the symbolic links that is described below. When I run the > >make_average_subject script only data for the right hemisphere is created. > >Then it seems to stop with the message: > > > >ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not > >supported > > > >I was wondering if you have modified the script to allow a copy instead of > >a link. Will symbolic links be used later in the group analysis steps as well? > > > >Many thanks, > > > >Stefan > > > > > > > >Re: [Freesurfer] symbolic links > > > >Doug Greve > >Fri, 01 Dec 2006 09:25:04 -0800 > >I don't think recon-all uses any sym links. I can mod the average subj > >script to copy instead of link. > > > >[EMAIL PROTECTED] wrote: > > > > > >Hi Doug, > > > > > > while trying to expand the volume of my virtual machine to be able to > >create symbolic links I started wondering if the way I preprocessed my > >data with recon_all might be affected somehow by the fact symbolic links > >were not supported (the data was located on a mounted drive). The only > >error message regarding this came during the make_average_subject part... > > > > Is there any way to use freesurfer avoiding the creation of symbolic > >links? > > > >many thanks > >bogdan > > > >_______________________________________________ > >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 > >[EMAIL PROTECTED] > > > >Phone Number: 617-724-2358 Fax: 617-726-7422 > > > >In order to help us help you, please follow the steps in: > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf Körperschaft des öffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jörg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus

2 1

scan res
by Kirk, Gregory 02 May '07

02 May '07

Hi, If I did a good job looking through the maillist archive the use of scans with resolution less than 1mm is not handled automatically yet, i.e. have to manually normalize ( divide ) quantities so the numbers are correct. Since we can only get a tiny bit less than 1mm ( 0.9mm ) for patient scans it seems best ( for me ) to just do 1mm is my reading correct ? Is there a fix in near future that would make it worth to wait a month or two to start processing a new study ? thank you Greg.

2 1

setting up freesurfer on supercomputer
by Paul Greenberg 02 May '07

02 May '07

Hi all, I've installed freesurfer 3.0.5 SuSE linux version, on a supercomputer, modified the setup .csh file and am getting the following errors. mri_convert: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory I've included the following information in case it helps. Typing: which mri_convert /gpfs/pagreenb/SuSEfreesurfer5_Apr8/bin//mri_convert Typing: ldd mri_convert mri_convert: ./mri_convert: /lib/libc.so.6: version `GLIBC_2.3' not found (required by ./mri_convert) libgsl.so.0 => /gpfs/pagreenb/SuSEfreesurfer5_Apr8/lib/gsl/lib/libgsl.so.0 (0x40018000) libgslcblas.so.0 => /gpfs/pagreenb/SuSEfreesurfer5_Apr8/lib/gsl/lib/libgslcblas.so.0 (0x40174000) libjpeg.so.62 => not found libtiff.so.3 => not found libz.so.1 => /lib/libz.so.1 (0x401a8000) libm.so.6 => /lib/libm.so.6 (0x401b8000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x401e0000) libc.so.6 => /lib/libc.so.6 (0x40214000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) Thanks in advance, Paul

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