Freesurfer

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19 participants
30088 discussions

Dura, manual editing, mri_gcut
by roger.jou＠yale.edu 12 Apr '11

12 Apr '11

Hi all, Sorry for the newbie questions, but I was wondering if there were any general guidelines on how much remaining DURA MATER and ARACHNOID MATER is acceptable after running autorecon1. In general, should dura be completely removed and arachnoid be left as is? Also, is mri_gcut run automatically as part of autorecon1? If so, how would I rerun mri_gcut to help remove more dura and/or arachnoid? Finally, is manual editing recommended for removing remaining dura and/or arachnoid? If so, should I strive to remove absolutely all of it? Thanks you all in advance! Roger

2 1

bbregister
by Saad Ramadan 12 Apr '11

12 Apr '11

Hi freesurfer-ers: when you run something like: *bbregister --s MySubject --t1 --mov t1_svs.nii --init-fsl --reg t1.reg.dat* ** I expect to generate a file "t1.reg.dat". bbregister is exiting normally with no error message. Where is this file? I cannot find it. Thanks in advance. Saad

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Error downloading old version of freesurfer
by Rune Eikeland 12 Apr '11

12 Apr '11

Hi, When I try to download an old version of freesurfer (4.3.1) from http://www.freesurfer.net/pub/dist/freesurfer/4.3.1/ I get the following error message: The connection was reset The connection to the server was reset while the page was loading. I get the same error message with all versions of 4.3.1. Will it be possible for someone to fix these links? Alternatively, is it possible to download this version for Leopard/Mac from some other location? Best regards, Rune

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unable to dload freesurfer old versions
by Nikhil Pratap Singh 11 Apr '11

11 Apr '11

Hi, I was trying to download freesurfer realease 4.3 from the archives but unable to do so. Is the website down? freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0-full.tar.gz <http://www.freesurfer.net/pub/dist/freesurfer/4.3.0/freesurfer-Linux-centos…> Best, Nikhil

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Re: [Freesurfer] functional ROI analysis problem
by Katie Bettencourt 11 Apr '11

11 Apr '11

Ok, I ran that and a couple questions. I ran it on 2 different subjects and got the exact same value, is that expected? Do I need to run it for each subject? Also, do I need to do this for event-related designs as well, or just block designs? I tried to run it on another analysis I did, an event-related one, but got this error: ??? Error using ==> times Matrix dimensions must agree. Katie > On Mon, Apr 11, 2011 at 12:22 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> You can run it anytime after the analysis. The 'X' file below is >> an actual file that is there (X.mat). The value that you get out >> of this procedure should be used to multiply the values you get >> out of roisummary-sess. >> >> >> doug >> >> >> >> Katie Bettencourt wrote: >> >> I'm working with Yaoda Xu. Thanks for the percent signal >> change fix, but I"m a little >> confused by what you wrote. When do I run that? after running >> roisummary-sess? Or after the analysis is run? >> >> >> Also, is the load('X' a placeholder where I need to put >> load('filename')? or will it just work as is? Obviously I >> change the session and analysis in the cd line. And is >> that a flat scale factor for all conditions for that >> subject? >> >> Katie >> >> On Fri, Apr 8, 2011 at 10:59 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >> >> btw, I notice that you have a harvard email now (was BU). >> who are >> you working with there? >> doug >> >> Katie Bettencourt wrote: >> >> Hi all, >> >> I'm doing ROI analysis on functional data with an >> anatomical >> label, and while the activity looks strong and robust in >> tksurfer, the % signal changes I am getting are very >> low (and >> much lower than we've previously found), and I'm not sure >> what's going on. >> >> I'm running Freesurfer 4.5 on red hat linux. >> >> The design is a blocked design with 4 non-null conditions, >> baseline is fixation. Attached is a picture of the >> activity I >> get for 2 subjects for on of the conditions vs fixation >> (baseline) at a p<0.05 threshold with the ROI outlined in >> black as well as the output from roisummary-sess for >> these two >> subjects in that roi. I calculate % signal change based of >> the output from roisummary-sess, dividing each condition by >> the baseline in that file and then multiplying by 100. % >> signal changes are listed below, along with all >> commands run. >> >> % signal change: >> 110222SKJ_connected 110222SP_connected >> 0.000988998467052 0.000533852720367 >> 0.00105349836708 0.000556814127695 >> 0.000408499366826 0.000327200054419 >> 0.000440749316839 0.000436266739225 >> >> commands: >> mkanalysis-sess -analysis connect -TR 2 -paradigm >> connect.dat >> -designtype blocked -funcstem fmc -motioncor -runlistfile >> connect_runs.txt -inorm -tpexclude tpexclude.dat >> -nconditions >> 4 -timewindow 20 -gammafit 2.25 1.25 -noautostimdur >> >> mkcontrast-sess -analysis connect -contrast >> connected_vs_unconnected -a 1 -c 2 >> mkcontrast-sess -analysis connect -contrast >> connected_vs_noise >> -a 1 -c 3 >> mkcontrast-sess -analysis connect -contrast >> connected_vs_phase >> -a 1 -c 4 >> mkcontrast-sess -analysis connect -contrast >> connected_vs_fix >> -a 1 -c 0 >> mkcontrast-sess -analysis connect -contrast >> unconnected_vs_noise -a 2 -c 3 >> mkcontrast-sess -analysis connect -contrast >> unconnected_vs_phase -a 2 -c 4 >> mkcontrast-sess -analysis connect -contrast >> unconnected_vs_fix >> -a 2 -c 0 >> mkcontrast-sess -analysis connect -contrast >> noise_vs_phase -a >> 3 -c 4 >> mkcontrast-sess -analysis connect -contrast >> noise_vs_fix -a 3 -c 0 >> mkcontrast-sess -analysis connect -contrast >> shape_vs_noise -a >> 1 -a 2 -c 3 >> mkcontrast-sess -analysis connect -contrast >> shape_vs_phase -a >> 2 -a 1 -c 4 >> mkcontrast-sess -analysis connect -contrast >> shape_vs_noisephase -a 2 -a 1 -c 3 -c 4 >> mkcontrast-sess -analysis connect -contrast act_vs_fix >> -a 2 -a >> 1 -a 3 -a 4 -c 0 >> >> selxavg3-sess -sf connect-sess -df connect.dir >> -analysis connect >> >> #run ROIs >> setenv anal connect >> foreach roi ( infIPS supIPS loc ) >> foreach h (lh rh) >> func2roi-sess -roidef ${roi}-${anal}-${h} -analysis $anal >> -anatlabel ips_loc/${roi}-${h} -sf connect-sess -df >> connect.dir >> roisummary-sess -sumfile ips-rois/${anal}_${roi}-${h}.dat >> -roidef ${roi}-${anal}-${h} -analysis ${anal} -sf >> connect-sess >> -df connect.dir >> python roi_reader.py -r ${roi} -a ${anal} -z ${h} -f >> ips-rois -c 4 >> end >> end >> >> Thanks, >> >> Katie >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> >> The information in this e-mail is intended only for the >> person to >> whom it is >> addressed. If you believe this e-mail was sent to you in >> error and >> the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was >> sent to >> you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >

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Fwd: bbregister bug? with init-spm option--flips left and right
by Tyler Seibert 11 Apr '11

11 Apr '11

Screenshot2 attached ---------- Forwarded message ---------- From: Tyler Seibert <tseibert(a)ucsd.edu> Date: Thu, Mar 17, 2011 at 4:02 PM Subject: bbregister bug? with init-spm option--flips left and right To: freesurfer(a)nmr.mgh.harvard.edu Hello, I hope this is the correct email list--this is my first time posting (just subscribed). I have been using bbregister to calculate a tranformation matrix between a T2 image (T2brain.nii.gz) and the subject's T1.mgz for subsequent use with mri_vol2surf. I have found that the init-fsl option frequently gives very poor registrations (e.g., registered T2 is rotated 30+ degrees from T1). The init-spm option seemed to be working great. However, upon close inspection, I became suspicious this option was actually flipping the T2 so that the left hemisphere became right and vice versa. I am using FreeSurfer version 4.5 and have spm8 referenced in my matlab path. I used a directory ~/bbreg_test in my home directory for the test (linux), which consisted simply of running bbregister with init-fsl and init-spm options. The attached log file (log.txt) contains the commands I used. The terminal output from each test was saved in text files as well, also attached. I have also attached two screenshots of the tkregister2 output for these tests. In each screenshot the far left image is the registered T2 using init-spm, and the far right image is the registered T2 using init-fsl. As the init-fsl version is clearly wrong, the middle image in each screenshot is the init-fsl output again, but manually rotated several degrees to the left to better emphasize the mirror-image relationship between the init-spm (far left) and init-fsl (middle and far right) output images. Please let me know if there is anything further you need from me to investigate this or if there is any insight you can give me as far as how to avoid this error. I noticed at line 209 of the spm_test.txt log file there is a message stating that RAS coordinate system is assumed (see below, where I have copied lines 208-213 for convenience). This may very well be the problem, as the T2brain.nii.gz volume is in LAS, according to mri_info output. However, I do not see where I can override this RAS assumption. >> >> >> >> >> >> >> >> >> /home/tylers/apps/spm8/spm_coreg.m > >> >> >> >> >> INFO: Assuming RAS coordinate system > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using > /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/refvol.spmregister.img > as the target image > >> using > /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/movvol.spmregister.img > as the source image > >> >> >> >> >> >> >> >> >> >> >> >> >> >> > Thank you, -- Tyler Seibert Dept. of Bioengineering Medical Scientist Training Program University of California, San Diego -- Tyler Seibert Dept. of Bioengineering Medical Scientist Training Program University of California, San Diego

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selxavg3 can't find image that exists
by Scott Burns 11 Apr '11

11 Apr '11

Freesurfers -- Here's the output of my terminal... kerryave:functionals $ cd /cluster/kuperberg/SemPrMM/MRI/functionals/ kerryave:functionals $ rm /cluster/kuperberg/SemPrMM/MRI/functionals/ya24/scripts/atlloc_fs-stats.log kerryave:functionals $ selxavg3-sess -analysis ya.ATLLoc.spm.sm8.lh -s ya24 -d /cluster/kuperberg/SemPrMM/MRI/functionals/ -svres -nolog Surface data fsaverage lh -------------------------------------------------------------- selxavg3-sess logfile is /dev/null -------------------------------------------------------------- ------------------------------------------- /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 Fri Apr 8 16:47:17 EDT 2011 anadir = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh ERROR: cannot find /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz kerryave:functionals $ ls -l ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz -rw-rw-r-- 1 sburns lingua 83660305 Apr 7 07:56 ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz Does anyone know what's going on? Here's my analysis.info for that analysis... kerryave:functionals $ cd ya.ATLLoc.spm.sm8.lh/ kerryave:ya.ATLLoc.spm.sm8.lh $ cat analysis.info # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5_0_0/fsfast/bin/mkanalysis-sess -analysis ya.ATLLoc.spm.sm8.lh -fsd ATLLoc -rlf rlf -p atlloc.par -spmhrf 0 -refeventdur 2 -event-related -TR 2 -nconditions 4 -mcextreg -hpf 128 -funcstem fmcpr.odd.sm8.fsaverage.lh.nii.gz -surface fsaverage lh -force # DATE Fri Apr 8 08:31:01 EDT 2011 analysis ya.ATLLoc.spm.sm8.lh mcstem fmcpr funcstem fmcpr.odd.sm8.fsaverage.lh.nii.gz fsd ATLLoc runlistfile rlf TR 2 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 0 RawSTC none inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 128 nconditions 4 parname atlloc.par RefEventDur 2 timewindow 40.000000 prestim 0 TER 0.050000 spmhrf 0 stimulusdelay 0 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 nuisreg mcprextreg 3 Thanks for the help. Scott Burns Kuperberg Lab Martinos Center for Biomedical Imaging sburns(a)nmr.mgh.harvard.edu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

4 5

distance between two points along cortical surface
by Fariba Sharifian 11 Apr '11

11 Apr '11

Hi, How should I have the distance between two points in mm? If I use the ?h.sphere, as all the spherical surfaces are normalized to have 100 radius. so the geodesic distances should not be the real distance in mm? Fariba __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology

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distance between two points along cortical surface
by Fariba Sharifian 11 Apr '11

11 Apr '11

1 0

recommende pc and cuda
by Knut J Bjuland 09 Apr '11

09 Apr '11

Hi I am in the process of acquiring a new computer to run freesurfer on. I am currently think about buying a PC with a geforce 4X0 and a Tesla card along with a two screen setup running either Ubuntu or Redhat Linux enterprise 6.0. I think the PC should be a core i7 with 6 core and above 12 gigs byte of ram. What kind of tesla card is recommend for using with Freesurfer? Will Freesurfer 5.1 also support cuda 4.0. Knut J

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