Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

(no subject)
by hankee 07 May '07

07 May '07

Hi, In the ?h.aparc.stats file,the Gray Matter Volume's units is mm,not mm^3. Is it right? Can you tell me the reason,because I want to use this option.Thank you very much! hankee，duhanjian(a)sohu.com 2007-05-05

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ascii and mri_surf2surf??
by David Perlman 07 May '07

07 May '07

Forgive me if I'm simply missing the obvious, but as far as I can tell, mri_surf2surf is not capable of writing output in *any* of the surface formats listed in the Freesurfer surface formats document on the wiki, except .w paint format. Also, mris_convert doesn't accept .w as input; so there's no way at all to get output from mri_surf2surf into ascii format? I'm also confused about why mri_surf2surf only writes out in volume formats like analyze and mgh (other than .w). If there are surface versions of these filetypes, where can I find documentation about those other surface formats, since they're not in the existing surface formats document? Actually, this is all extra confusing because the output of --help for mri_surf2surf conflicts with the documentation on the wiki. The wiki says output can be curv format; the --help says not. It doesn't seem to be possible. Also some of the options have different names in the two locations. Just out of curiosity, why does it work like that? I'd think it would make more sense simply to have it write out in the standard surface formats (surface or curv or ascii)... All I'm trying to do is to subtract one set of curv-format data from another. (I have cortical thickness measures for the same subjects at two different times, and I want to be able to see the changes for individual subjects.) I have successfully registered the time 1 data onto the time 2 surface, and I can visualize it overlaid no problem. But I am struggling to find a way to subtract the aligned data... which seems like it should be easy... which makes me think I'm missing something obvious, but I've been searching through documentation for hours. I can see how to do it with Matlab, using mri_surf2surf to generate .w format output and reading it into Matlab, but I was hoping there would be a more straightforward way... Also, as an aside, the comments for read_wfile.m are actually the comments for write_wfile.m. -- -dave---------------------------------------------------------------- After all, it is not *that* inexpressible. -H.H. The Dalai Lama

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Cortical sheet mask?
by David Perlman 07 May '07

07 May '07

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

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

05 May '07

On May 5, 2007, at 8:37 AM, Gheorghe Postelnicu wrote: > PS: this might take a couple of days, as I can foresee small technical > problems occurring with the resolution increase. Speaking of small technical problems: I manually increased the resolution of brain.mgz and orig.mgz (I read in two different places conflicting statements about which of those two is used as the resolution template) and then ran mris_volmask. It ran for a while and then gave a "malloc failed" error: dyn-120-159:~/data/freesurfer/sp01MULTt1/mri omgoleus$ time mris_volmask --out_root laplaceribbon --label_left_white 3 -- label_right_white 3 --label_left_ribbon 2 --label_right_ribbon 2 sp01MULTt1 CTABreadASCII(/Applications/freesurfer/FreeSurferColorLUT.txt): Line 178: Duplicate structure index 222, was Ectorhinal 197 150 250 255 mris_volmask.bin(10271,0xa000cfc0) malloc: *** vm_allocate (size=536870912) failed (error code=3) mris_volmask.bin(10271,0xa000cfc0) malloc: *** error: can't allocate region mris_volmask.bin(10271,0xa000cfc0) malloc: *** set a breakpoint in szone_error to debug ERROR: In /usr/pubsw/packages/vtk/CVS/src/VTK/Common/ vtkDataArrayTemplate.txx, line 95 vtkFloatArray (0x8cbcaf80): Unable to allocate 134217728 elements of size 4 bytes. Bus error real 15m58.366s user 13m59.934s sys 0m8.270s dyn-120-159:~/data/freesurfer/sp01MULTt1/mri omgoleus$ On a different computer (both Intel Macs) it's been running for a couple of hours, but that computer only has 1 gig of memory and it has been paging like crazy. So I guess I have to wait for the modified code... thanks for the help with this -- -dave---------------------------------------------------------------- After all, it is not *that* inexpressible. -H.H. The Dalai Lama

1 0

glibc version compatability
by Paul Greenberg 05 May '07

05 May '07

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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

2 1

(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 >> > > -- > > > > > > > > > > --

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Freesurfer