Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

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

1 0

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

2 1

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

1 0

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

4 7

Using clusters as ROIs
by Dankner, Nathan (NIH/NIMH) [F] 03 Nov '09

03 Nov '09

Hello all, I have recently run a cluster correction on some data, and was hoping to use these clusters as ROIs and pull stats from them. What is the best way to do so? Thank you in advance for your help, Nathan

1 0

orientation problem resulting in talairach failure
by Dominic Brendon Dwyer 02 Nov '09

02 Nov '09

Dear Freesurfer developers, I have a few analyse images which are oriented incorrectly that are part of a larger dataset. When viewed in tkmedit, what is supposed to be coronal is actually displayed as axial and the sagittal is flipped. In these cases the Talairach transform fails spectacularly. To try and fix the problem I used mri_info to determine the orientation information of my good files (LSA) and of the ones that aren't working (LAS), then used mri_convert with the --in_orientation and out_orientation flags to change the dimensions in analyse format. The analyze images look fine in MRIcro and the orig.mgz looks fine in tkmedit, but yet again the Talairach fails in the same way. I've also tried this by reorienting the images using MRIcro but this has the same result. When you view the analyze images using GWRaw MRI viewer http://www.wideman-one.com/gw/brain/orientation/orientterms.htm (supposed to read the image file without header information), they look the same, but I'm a bit unsure of this program. I'm really at a bit of a loss to try and fix this problem now so any help or suggestions would be really appreciated! Many thanks, Dominic Melbourne Neuropsychiatry Centre

2 3

Between-Groups Analysis Question
by Derek Huffman 02 Nov '09

02 Nov '09

Hello FreeSurfer Team, I am in the process of running a between-groups analysis in FreeSurfer (Two groups: younger adults, older adults). We are analyzing areas of cortical thickness that are important for memory recall. I am able to perform between groups analysis in the QDEC that shows where the correlation between thickness and memory differs between the two groups, and we have found some promising results. The next step is to find areas of thickness that correlate with memory recall across both groups independently (as just looking at all subjects together could be driven by one group or the other). I am wondering if there is a way to find areas that show significant results for both groups, essentially finding an intersection point between the two groups where the correlation is significant for both. Thank you, Derek

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Freesurfer November 2009