Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

How to do a surface-based group analysis with single-subject SPM5 contrast images
by Johannes Klackl 06 Aug '07

06 Aug '07

Dear all, I'm currently trying to conduct a surface-based group analysis using 1st level contrast images from SPM5. I wanted to ask if somebody could tell me if what I'm doing is OK. I would relly appreciate your help! I will now describe the procedure: The functionals of each subject were realigned and unwarped using SPM5 preprocessing commands and then entered into an SPM 1st level designs. Additionally, of course, cortical models from all subjects were created using Freesurfer. I used spmregister to realign the contrast images (con_0001.img) with the Freesurfer anatomicals. spmregister --s v01 --mov ../f2/auS1_v01_06LOC_x001.img --reg v01_register.dat Then I used mri_vol2surf (with the resulting registration file from spmregister) to bring the volumetric information from the contrast images onto each subject's individual surface. mri_vol2surf --hemi lh --src con_0001.img --src_type analyze --srcreg v01_register.dat --out lh.con_0001.mgh --out_type mgh --projfrac 0.5 --noreshape After that, I used mri_surf2surf with ico as the target to bring all the functionals from the individual subject surface onto a common surface. mri_surf2surf --hemi lh --srcsubject v01 --srcsurfval lh.con_0001.mgh --src_type mgh --trgsubject ico --trgicoorder 7 --trgsurfval lh.ico.con_0001.mgh --trg_type mgh I was thinking about smoothing here, but I didn't do this yet. Then, I used mri_concat to concatenate the functionals from all subjects into one file and mri_glmfit to do the statistics. Thanks, Johannes Klackl, University of Salzburg

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Re: [Freesurfer] Fake thickness map 2
by Inês Souta 06 Aug '07

06 Aug '07

And after creating the mgh volume, how can I read it? Is it possible to open it in tksurfer? Should I load it as an overlay? I've used one of my already pre-processed subjects, created a 'vol' with the same number of vertices of one of the hemisferes, and saved the output of save_mgh file as an rh.thickness.mgh file. However, when I don't seem to be able to open it in tksurfer... Thanks Ines 2007/8/6, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > > they don't matter. For a real volume they would be the ras2vox transform > and the mr parameters. For your purposes they can be any 4x4 and you can > leave the mri_parms one out (it will detect and fill it in with zeros). > > Send these to the list so other people can answer! > > Bruce > On > Mon, 6 Aug 2007, Inês Souta wrote: > > > Hi again, > > > > I still don't understand what all the input objects of save_mgh function > > stand for. 'vol' is the vector of thickness values, 'fname' is the name > of > > the output .mgh file, and what about M and <mr_parms>? What do they > stand > > for and how should I define them? > > > > Thanks again, > > > > Ines > > > > 2007/7/31, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > >> > >> Hi Ines, > >> > >> use the mgh route. The "vol" is actually the vector of thickness > values, > >> with one entry per vertex on the surface. > >> > >> cheers, > >> Bruce > >> On Tue, 31 Jul 2007, Inês Souta > >> wrote: > >> > >>> Hello, > >>> > >>> I was trying to create a cortical thickness map with constant values > in > >>> order to perform some tests. At first I tried using mris_convert. I > >>> converted my thickness file into ascii: > >>> > >>> mris_convert lh.thickness lh.thickess.asc > >>> > >>> then I used matlab to change all the values in the last column to 2,0. > I > >>> tried to convert the ascii file back to surface file by doing > >>> > >>> mris_convert lh.thicness.asc lh.thickness > >>> > >>> but I got "Segmentation fault". How can I convert may ascii file into > a > >>> surface one? > >>> > >>> After failling to acomplish this, I tried using the save_mgh and > >> load_mgh > >>> file, nevertheless I'm not quite sure which input values are needed. > >> Where > >>> can I put my fake values in the save_mgh file? And what is "vol"? > >>> > >>> Thanks, > >>> > >>> Ines > >>> > >

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Fake thickness map 2
by Inês Souta 06 Aug '07

06 Aug '07

---------- Forwarded message ---------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: 06/08/2007 14:23 Subject: Re: [Freesurfer] Fake thickness map 2 To: Inês Souta <ines.souta(a)gmail.com> they don't matter. For a real volume they would be the ras2vox transform and the mr parameters. For your purposes they can be any 4x4 and you can leave the mri_parms one out (it will detect and fill it in with zeros). Send these to the list so other people can answer! Bruce On Mon, 6 Aug 2007, Inês Souta wrote: > Hi again, > > I still don't understand what all the input objects of save_mgh function > stand for. 'vol' is the vector of thickness values, 'fname' is the name of > the output .mgh file, and what about M and <mr_parms>? What do they stand > for and how should I define them? > > Thanks again, > > Ines > > 2007/7/31, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >> >> Hi Ines, >> >> use the mgh route. The "vol" is actually the vector of thickness values, >> with one entry per vertex on the surface. >> >> cheers, >> Bruce >> On Tue, 31 Jul 2007, Inês Souta >> wrote: >> >>> Hello, >>> >>> I was trying to create a cortical thickness map with constant values in >>> order to perform some tests. At first I tried using mris_convert. I >>> converted my thickness file into ascii: >>> >>> mris_convert lh.thickness lh.thickess.asc >>> >>> then I used matlab to change all the values in the last column to 2,0. I >>> tried to convert the ascii file back to surface file by doing >>> >>> mris_convert lh.thicness.asc lh.thickness >>> >>> but I got "Segmentation fault". How can I convert may ascii file into a >>> surface one? >>> >>> After failling to acomplish this, I tried using the save_mgh and >> load_mgh >>> file, nevertheless I'm not quite sure which input values are needed. >> Where >>> can I put my fake values in the save_mgh file? And what is "vol"? >>> >>> Thanks, >>> >>> Ines >>> >

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Re: [Freesurfer] show the results
by Bruce Fischl 03 Aug '07

03 Aug '07

look in /Users/lning/subjects/MGH_Ruphert/mri and /Users/lning/subjects/MGH_Ruphert/surf and see if there is any processed data there On Fri, 3 Aug 2007, Ning Liu wrote: > I think so. It is someone's data. He had created the surfers. I just wanted > to have a look at it. > > On 8/3/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> >> did you run recon-all on this subject? >> >> On Fri, 3 Aug 2007, Ning Liu wrote: >> >>> I copied some subjects' data to my computer, but i cannot run the surfer >>> >>> here is the command line: >>> >>> tksurfer MGH_Ruphert lh inflated >>> >>> screen output >>> >>> surfer: current subjects dir: /Users/lning/subjects >>> surfer: not in "scripts" dir ==> using cwd for session root >>> surfer: session root data dir ($session) set to: >>> surfer: /Users/lning/subjects/MGH_Ruphert >>> surfer: ### Could not find anatomical header information >>> >>> >> > > > >

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starting midway in the pipeline
by Brianna Schuyler 03 Aug '07

03 Aug '07

Hello, I would really like to use a freesurfer surface to display non-human primate data that I have already put into a standard space and segmented, but I am having trouble finding information on how to skip many of the initial steps to this point. Also, I have seen references to a "-monkey" option for some steps, but I haven't been able to find any documentation on that either. Thanks for any help, Brianna Schuyler

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/usr/lib/libstdc++.so.5 is missing I have /usr/lib/libstdc++.so.6
by Keith Sudheimer 03 Aug '07

03 Aug '07

I am running a Fedor Core 4 machine and have installed the CentOS 4 version of freesurfer. I can run tkmedit and tksurfer. However, I am running into trouble running trhough recon-all -s 004FSC -autorecon1 When I get to Nu Intensity Correction (mri_nu_correct.mni) on iteration1, during volume stats calculations, I get a missing file error in /usr/lib/libstdc++.so.5 in /usr/lib/ I do have a /usr/lib/libstdc++.so.6 but no libstdc++.so.5 any advice or tips would be greatly appreciated. Thank you. Keith Sudheimer Department of Psychiatry Neuroscience Program University of Michigan ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Growing spots
by Troy Mcan 02 Aug '07

02 Aug '07

Hi,I have a group of talairach coordinates on a brain that I would like to grow to a specified amount (e.g. 8 mm radius). Is there a function in freesurfer that allows me to do this? Also, some of the points are far away from the main group, but I would like to have them all connected. Is there a blur filter or an equivalent that I can use to accomplish this?Thank you! _________________________________________________________________ Recharge--play some free games. Win cool prizes too! http://club.live.com/home.aspx?icid=CLUB_wlmailtextlink

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writing surface file
by Marie Schaer 02 Aug '07

02 Aug '07

Hello everybody, I would like to write a surface in freesurfer format from a matlab triangular mesh (e.g. list of 67120 vertices associated with 134236 faces). To read the freesurfer surfaces, I usually use the very useful bioelectromagnetism toolbox by Darren Weber, but I am not able to find out why the freesurfer_write_surface function (attached to this mail) do not work with my mesh. It indeed seems to write a surface of adequate size (2.3MB), but when I try to visualize it, tkmedit respond: "(null): vertex 0 x coordinate 282617032931096509022208.000000 ! " Does someone has any hints on that or an available matlab script to write a freesurfer surface? Many thanks for your help, Marie Schaer

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RE: [Freesurfer] Ubuntu, Xeon 64bit multi-core, and freesurfer
by Nicolas Cherbuin 01 Aug '07

01 Aug '07

Thanks for your response Nick! Would you be able to also give us an update on when the next release is going to be available and whether it will include white matter parcellation? I need to reprocess a fairly large number of scans and I would prefer if it includes the latest bells and whistles. Regards, Nic -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tuesday, 31 July 2007 12:07 PM To: Nicolas Cherbuin Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Ubuntu, Xeon 64bit multi-core, and freesurfer Nic, Concerning Ubuntu and Freesurfer, we have not used that OS directly ourselves, but I believe people on the list have used Ubuntu and Freesurfer. I think there were some library issues, but nothing that was a show-stopper or overly difficult to fix. We have many Xeon dual core machines in use here, so Freesurfer should run fine on that. Your plan run a recon-all on each processor is fine. Nick On Mon, 2007-07-30 at 11:24 +1000, Nicolas Cherbuin wrote: > Hi, > > > > I am about to order new hardware that will be used to process scans > with freesurfer but also for processing with other packages. Has > anyone had experience with the combination of Xeon quad-core > processors, Ubuntu, and Freesurfer? And if yes are there any issues I > should be aware of? > > > > To my knowledge one Freesurfer process cannot run in parallel on > multiple processors but I intend to process multiple scans > simultaneously, hence the selection of a multi-core architecture. If > somebody has some experience of the difference between 2.33 GHZ, 2.66 > GHZ, and core-duo 3.00 GHZ I would also be interested to hear about > it. > > > > Thanks > > > > Nic > > > > > > ***************************************** > > > > Nicolas Cherbuin > > > Centre for Mental Health Research > Australian National University > Canberra > ACT 0200 > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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measurement of cortical thickness
by T. Song 01 Aug '07

01 Aug '07

Hi All: I am trying to measure the cortical thickness of specific ROI. I got a ROI, and are able to save it to a label file. Should I use mris_thickness to measure the thickness? If so, how do I get the thickness file, using mri_label2vol? Thanks in advance! Tao

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Freesurfer