Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

Analysis using a custom template
by Cathy Scanlon 05 Nov '09

05 Nov '09

Hi, I have a question regarding group analysis using a custom template. I have created a custom template using mris_make_template as described http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates I then registered all my study subjects (that have previously been run through recon-all) to this new template using mris_register and named the spherical registration ?h.sphere.reg for each subject. I want to conduct a group analysis of cortical thickness. So my question is do I need to rerun autorecon3 or any subset of it (e.g. ?h.avg_curv) that might affect my analysis or creation of the 'average subject'? All the best, Cathy

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multiple recon-all processes
by Ahmed, F, Me <fahmed＠sun.ac.za> 05 Nov '09

05 Nov '09

Hello, I know that FS can run multiple recon-all processes at one time, but I wanted to know how exactly one can do that. Is it just a matter of opening a terminal window for each recon-all process you wish to run? Thanks, Fatima

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RES: Single subject vs. group
by Pedro Paulo de Magalhaes Oliveira Jr 05 Nov '09

05 Nov '09

Our group published a paper with single subject vs group. The paper you can find in FreeSurfer's website article list: search by polymicrogiria If you want to discuss the results we published send me an e-mail. -----Msg original----- De: Tricia Merkley Enviado: 05/11/2009 00:15:17 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] Single subject vs. group Hi, I've seen similar questions posted to the list, but I haven't been able to find an answer. So sorry if this is a repeat. Is it possible (or even advisable) to create a map comparing cortical thickness for a single subject against a group? If so, how is the best way to go about doing that? Would I need to use z-score transformations? I would appreciate any suggestions for this. Thanks, Tricia Merkley

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Single subject vs. group
by Tricia Merkley 04 Nov '09

04 Nov '09

Hi, I've seen similar questions posted to the list, but I haven't been able to find an answer. So sorry if this is a repeat. Is it possible (or even advisable) to create a map comparing cortical thickness for a single subject against a group? If so, how is the best way to go about doing that? Would I need to use z-score transformations? I would appreciate any suggestions for this. Thanks, Tricia Merkley

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question about preproc-sess
by 卯野賢太 04 Nov '09

04 Nov '09

Hi,Freesurfers I'm practicing freesufer analysis with tutorial data set. I downloaded all data and I adhere to hierarchy. Now I'm in preprocess session. But I get the following message in that shell every few seconds. I'm a beginner of freesurfer,so please tell me about solvent on this problem. Kenta [root@localhost fsfast-tut_2]# ls fb1-analysis-study fb1-raw fbph1-101 fbph1-104 fbph1-106 fb1-preproc-study fb1-raw-study fbph1-103 fbph1-105 [root@localhost fsfast-tut_2]# setenv SUBJECTS_DIR $PWD [root@localhost fsfast-tut_2]# ls fb1-analysis-study fb1-raw fbph1-101 fbph1-104 fbph1-106 fb1-preproc-study fb1-raw-study fbph1-103 fbph1-105 [root@localhost fsfast-tut_2]# mkdir -p my-study [root@localhost fsfast-tut_2]# ls fb1-analysis-study fb1-raw fbph1-101 fbph1-104 fbph1-106 fb1-preproc-study fb1-raw-study fbph1-103 fbph1-105 my-study [root@localhost fsfast-tut_2]# cd my-study/ [root@localhost my-study]# ls [root@localhost my-study]# mkdir -p mgh-101.1/bold [root@localhost my-study]# mkdir -p mgh-101.1/bold/003 [root@localhost my-study]# mkdir -p mgh-101.1/bold/005 [root@localhost my-study]# mkdir -p mgh-101.1/bold/007 [root@localhost my-study]# mkdir -p mgh-101.1/bold/010 [root@localhost my-study]# cp ../fb1-raw/f.mgh-101.1-r003. nii mgh-101.1/bold/003/f.nii [root@localhost my-study]# cp ../fb1-raw/f.mgh-101.1-r005.nii mgh-101.1/bold/005/f.nii [root@localhost my-study]# cp ../fb1-raw/f.mgh-101.1-r007.nii mgh-101.1/bold/007/f.nii [root@localhost my-study]# cp ../fb1-raw/f.mgh-101.1-r010.nii mgh-101.1/bold/010/f.nii [root@localhost my-study]# cd $SUBJECTS_DIR/my-study/ [root@localhost my-study]# echo fbph1-101 > mgh-101.1/subjectname [root@localhost my-study]# preproc-sess -s mgh-101.1 -fwhm 5 -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- instem f mc 1 f fmc stc 0 fmc sm 1 fmc fmcsm5 mask 1 brain mgh-101.1 MC ----------------------------- 2009年 11月 2日月曜日 19:54:41 JST /usr/local/freesurfer/fsfast-tut_2/my-study mc-sess -fstem f -fmcstem fmc -s mgh-101.1 -d /usr/local/freesurfer/fsfast-tut_2/my-study -fsd bold -new -update -no-inorm ---------------------------------------- Logfile is /usr/local/freesurfer/fsfast-tut_2/my-study/log/mc-mgh-101.1-bold.log ------------------------------------------- /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1 RunList: 003 005 007 010 Targ Stem is 003/f ------- ************************** ----------- ------- Motion Correcting Run 003 ----------- ------- ************************** ----------- sess = mgh-101.1 2009年 11月 2日月曜日 19:54:42 JST mc-afni2 --i 003/f.nii --t 003/f.nii --frame 0 --o 003/fmc.nii --mcdat 003/fmc.mcdat /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1/bold mri_info --nframes --o /tmp/mriinfo.7888 003/f.nii log file is 003/fmc.nii.mclog mcdat file is 003/fmc.mcdat tmp dir is 003/tmp.mc-afni2.7888 #@# -------------------------------- /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1/bold mri_convert 003/f.nii 003/tmp.mc-afni2.7888/tempvol.nii.gz --nskip 0 --ndrop 84 -odt float mri_convert 003/f.nii 003/tmp.mc-afni2.7888/tempvol.nii.gz --nskip 0 --ndrop 84 -odt float nskip = 0 ndrop = 84 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 003/f.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9973, -0.0712038, 0.0179835) j_ras = (0.0625429, -0.951817, -0.300222) k_ras = (0.038494, -0.298286, 0.9537) changing data type from 4 to 3 (noscale = 0)... Dropping last 84 frames writing to 003/tmp.mc-afni2.7888/tempvol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1/bold mri_convert 003/f.nii 003/tmp.mc-afni2.7888/invol.nii.gz -odt float mri_convert 003/f.nii 003/tmp.mc-afni2.7888/invol.nii.gz -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 003/f.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9973, -0.0712038, 0.0179835) j_ras = (0.0625429, -0.951817, -0.300222) k_ras = (0.038494, -0.298286, 0.9537) changing data type from 4 to 3 (noscale = 0)... writing to 003/tmp.mc-afni2.7888/invol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/fsfast-tut_2/my-study/mgh-101.1/bold 3dvolreg -verbose -dfile 003/fmc.mcdat -base 003/tmp.mc-afni2.7888/tempvol.nii.gz -prefix 003/tmp.mc-afni2.7888/outvol.nii.gz 003/tmp.mc-afni2.7888/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [32-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 003/tmp.mc-afni2.7888/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:003/tmp.mc-afni2.7888/tempvol.nii.gz is 17.858507 degrees from plumb. ++ Reading in base dataset 003/tmp.mc-afni2.7888/tempvol.nii.gz ++ Oblique dataset:003/tmp.mc-afni2.7888/invol.nii.gz is 17.858507 degrees from plumb. ++ Reading input dataset 003/tmp.mc-afni2.7888/invol.nii.gz ++ Edging: x=3 y=3 z=2 ++ Creating mask for -maxdisp + Automask has 35321 voxels + 5274 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 85 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84.. ++ CPU time for realignment=3.03 s [=0.0356 s/sub-brick] ++ Min : roll=-0.058 pitch=-0.007 yaw=-0.048 dS=-0.054 dL=-0.105 dP=-0.106 ++ Mean: roll=-0.007 pitch=+0.094 yaw=-0.023 dS=+0.145 dL=-0.029 dP=-0.026 ++ Max : roll=+0.062 pitch=+0.333 yaw=+0.016 dS=+0.318 dL=+0.121 dP=+0.017 ++ Max displacements (mm) for each sub-brick: 0.00 0.06 0.04 0.06 0.08 0.11 0.16 0.15 0.17 0.14 0.23 0.32 0.38 0.44 0.25 0.28 0.37 0.37 0.39 0.28 0.30 0.58 0.18 0.31 0.29 0.29 0.27 0.26 0.25 0.30 0.29 0.27 0.64 0.31 0.17 0.22 0.30 0.31 0.33 0.38 0.38 0.35 0.17 0.17 0.35 0.41 0.39 0.36 0.36 0.41 0.39 0.39 0.39 0.46 0.36 0.42 0.40 0.39 0.38 0.39 0.38 0.41 0.38 0.30 0.33 0.36 0.35 0.37 0.38 0.38 0.39 0.38 0.38 0.38 0.37 0.36 0.34 0.35 0.33 0.34 0.34 0.37 0.36 0.37 0.33 ++ Max displacement in automask = 0.64 (mm) at sub-brick 32 ++ Wrote dataset to disk in 003/tmp.mc-afni2.7888/outvol.nii.gz Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out

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pial error...
by Gonzalo Rojas 04 Nov '09

04 Nov '09

Hi: How can I correct a pial boundary error such as that appears in the image ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 1

tkmedit File menu option in gray...
by Gonzalo Rojas 04 Nov '09

04 Nov '09

Hi: Why the options "Save Manin Volume" and "Save Main Volume as" in TkMedit' "File" menu appears in gray (disabled) ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

3 2

Freesurfer installation on Ubuntu
by Miguel Burgaleta 04 Nov '09

04 Nov '09

Hello FS experts, I am trying to install FS on Ubuntu 9.04. I am testing the installation as suggested in your website, and found the following message when attempting to start the qdec application: *********************************************************************************************************** qdec.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory *********************************************************************************************************** I am new to Linux as well, so I would really appreciate step-by-step instructions to solve this issue. Thanks in advance for your time, Miguel

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convert inflated surface to mnc
by Feng-Xian Yan 04 Nov '09

04 Nov '09

Hi, Thank you for your responses before. Now, I want to convert the inflated surface of fsaverage to the .mnc file which file I want to do the template for spm. What command do I type to obtain .mnc file? Thank you in advance! Feng-Xian

2 1

Skull Stripping Free surfer
by Ribes Delphine 04 Nov '09

04 Nov '09

Dear Users, I've just started using FreeSurfer. I would like to use it for skull-stripping. I've created a batch file to process all my subjects. and I am basically using the command line: recon-all -autorecon1 -skullstrip -s subj1 I would like to know if there is a way to only do skull-stripping and not doing the Talairach Transform and then INU correction? I would like to have the skulll-stripp volume in the same space coordinate as originally? Otherwise, I am doing skull-stripping of T1 weighted images of normal elderly subejcts. Is there any specific recommandation for skull-stripping parameters? Thanks a lot, Delphine

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