Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

Tracula AD weighted average
by Cat Chong 18 Jul '14

18 Jul '14

Dear Anastasia, Another quick question: We found significant differences in two subject groups for the AD_AVG as well as the AD_AVG_Weight, which is stated as the "weighted average over the entire path distribution'. Could you tell me how the average weight is calculated and why it would be better to use than the AD_AVG perhaps? Thank you very much, Cat

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Re: [Freesurfer] recon-all ERROR, no idea why
by Remy Wahnoun 18 Jul '14

18 Jul '14

Thanks Douglas, I definitely appreciate your help. Here is what it Spit out, *Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University *www.NeuralControl.net <http://www.neuralcontrol.net/>* set echo = 1 ; set debug = 1 ; set debug = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 11 != 0 ) set flag = $argv[1] ; shift ; set flag = --n shift switch ( $flag ) switch ( --n ) if ( $#argv == 0 ) goto arg1err ; if ( 10 == 0 ) goto arg1err set nIters = $argv[1] ; shift ; set nIters = 1 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 9 != 0 ) set flag = $argv[1] ; shift ; set flag = --proto-iters shift switch ( $flag ) switch ( --proto-iters ) if ( $#argv == 0 ) goto arg1err ; if ( 8 == 0 ) goto arg1err set nProtoIters = $argv[1] ; shift ; set nProtoIters = 1000 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 7 != 0 ) set flag = $argv[1] ; shift ; set flag = --distance shift switch ( $flag ) switch ( --distance ) if ( $#argv == 0 ) goto arg1err ; if ( 6 == 0 ) goto arg1err set Distance = $argv[1] ; shift ; set Distance = 50 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; shift ; set flag = --no-rescale shift switch ( $flag ) switch ( --no-rescale ) set DoRescale = 0 ; set DoRescale = 0 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 ) set flag = $argv[1] ; shift ; set flag = --i shift switch ( $flag ) switch ( --i ) if ( $#argv == 0 ) goto arg1err ; if ( 3 == 0 ) goto arg1err set InVol = $argv[1] ; shift ; set InVol = orig.mgz shift breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = --o shift switch ( $flag ) switch ( --o ) if ( $#argv == 0 ) goto arg1err ; if ( 1 == 0 ) goto arg1err set OutVol = $argv[1] ; shift ; set OutVol = orig_nu.mgz shift breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#InVol == 0 ) then if ( 1 == 0 ) then if ( ! -e $InVol ) then if ( ! -e orig.mgz ) then if ( $#OutVol == 0 ) then if ( 1 == 0 ) then goto check_params_return ; goto check_params_return set OutDir = `dirname $OutVol` ; set OutDir = `dirname $OutVol` dirname orig_nu.mgz mkdir -p $OutDir ; mkdir -p . if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log set LF = ./mri_nu_correct.mni.log if ( -e $LF ) mv $LF $LF.bak if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak pwd | tee -a $LF pwd tee -a ./mri_nu_correct.mni.log /media/sf_Imagery/FreeSurfer/xx/mri which mri_nu_correct.mni | tee -a $LF which mri_nu_correct.mni tee -a ./mri_nu_correct.mni.log /usr/local/freesurfer/bin/mri_nu_correct.mni echo $cmdargs | tee -a $LF echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz tee -a ./mri_nu_correct.mni.log --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz echo "nIters $nIters" | tee -a $LF echo nIters 1 tee -a ./mri_nu_correct.mni.log nIters 1 echo $VERSION | tee -a $LF tee -a ./mri_nu_correct.mni.log echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ uname -a | tee -a $LF uname -a tee -a ./mri_nu_correct.mni.log Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux date | tee -a $LF date tee -a ./mri_nu_correct.mni.log Mon Jun 23 15:32:45 EDT 2014 nu_correct -version | tee -a $LF nu_correct -version tee -a ./mri_nu_correct.mni.log Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$ if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745 set tmpdir = ./tmp.mri_nu_correct.mni.1745 mkdir -p $tmpdir mkdir -p ./tmp.mri_nu_correct.mni.1745 echo "tmpdir is $tmpdir" | tee -a $LF echo tmpdir is ./tmp.mri_nu_correct.mni.1745 tee -a ./mri_nu_correct.mni.log tmpdir is ./tmp.mri_nu_correct.mni.1745 set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc ) if ( $UseFloat ) set cmd = ( $cmd -odt float ) if ( 1 ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float ) pwd | & tee -a $LF pwd tee -a ./mri_nu_correct.mni.log /media/sf_Imagery/FreeSurfer/xx/mri echo $cmd | & tee -a $LF echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float tee -a ./mri_nu_correct.mni.log mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float $cmd | & tee -a $LF mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float tee -a ./mri_nu_correct.mni.log mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=25.00, TE=5.36, TI=0.00, flip angle=30.00 i_ras = (-1, 1.49012e-08, 0) j_ras = (0, 0, -1) k_ras = (-1.30385e-08, 1, -5.96046e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc... if ( $status ) then if ( 0 ) then @ nthIter = 1 ; @ nthIter = 1 while ( $nthIter < = $nIters ) while ( 1 < = 1 ) echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log echo "--------------------------------------------------------" | & tee -a $LF echo -------------------------------------------------------- tee -a ./mri_nu_correct.mni.log -------------------------------------------------------- echo "Iteration $nthIter `date`" | & tee -a $LF echo Iteration 1 `date` tee -a ./mri_nu_correct.mni.log date Iteration 1 Mon Jun 23 15:32:49 EDT 2014 @ m = $nthIter - 1 @ m = 1 - 1 set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc $tmpdir/nu${nthIter}.mnc ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ; set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ) if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ; if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ; if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop ) if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ; if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ; if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm ) echo $cmd | & tee -a $LF echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 tee -a ./mri_nu_correct.mni.log nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 $cmd | & tee -a $LF nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 tee -a ./mri_nu_correct.mni.log [fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] [2014-06-23 15:32:49] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) if ( $status ) then if ( 0 ) then rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu0.imp @ nthIter = $nthIter + 1 ; @ nthIter = 1 + 1 echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log end end while ( $nthIter < = $nIters ) while ( 2 < = 1 ) echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log set numnc = $tmpdir/nu$nIters.mnc set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc if ( $DoRescale ) then if ( 0 ) then if ( ! -e $numnc ) then if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then echo "ERROR: file $numnc does not exist!" | & tee -a $LF echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! tee -a ./mri_nu_correct.mni.log ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! exit 1 ; exit 1 ------------------------------ This transmission, including any attachments, is for the sole use of the intended recipient (s) and may contain information that is confidential, proprietary, legally privileged, or otherwise protected by law from disclosure. Any unauthorized review, use, copying, disclosure, or distribution is prohibited. If you are not the intended recipient, or the person responsible for delivering this to an addressee, you should notify the sender immediately by telephone or by reply e-mail, and destroy all copies of the original message.

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Tracula trac-all -stat flag -stat unrecognized
by Cat Chong 18 Jul '14

18 Jul '14

Hello Anastasia, I have just converted pathstas.overall.txt files to a table for group analyses. Now, I am trying to convert pathstats.byvoxel.txt files to a table for group analyses using the command: trac-all -stat -c I am receiving the error message: ERROR: flag -stat unrecognized I am working on a mac using bash script using Freesurfer version 5.3 Do you have any ideas? Cheers, Cat

2 2

transforming Base surfaces to Cross space
by prasser 18 Jul '14

18 Jul '14

Dear All, For longitudinal data sets, is there a way that the lh.pial surface from the Base can be transformed into the brainmask.mgz space of a Cross so that it can be viewed with tkmedit on the Cross brainmask.mgz? Thanks, Paul

2 2

Group differences in pc1 (longitudinal stage2)
by Tudor Popescu 18 Jul '14

18 Jul '14

Dear FS list, (dear Martin!) I have a longitudinal design, 3 groups, 2 timepoints, and I created three different QDEC tables (two groups at a time) in order to be able to compare each pair of groups in terms of percentage change from pre to post (what's referred to as "pc1" in the first stage of the two-stage-model). I look at thickness, area and lGI as dependent variables. Group is a categorical factor of interest, gender as the other categorical factor (not interested in its effect), and age as (continuous) nuisance. I'm interested in the contrast "Does the average ..., accounting for gender, differ between G1 and G2?" Say that, for some analysis (e.g. group 1 vs group 2, thickness, LH) I get a certain cluster that survives the MonteCarlo Null-Z correction. If the cluster is redish, I take it to mean that group 1 has a higher signed value of pc1 than group 2, and vice-versa if the cluster is blueish. However, because pc1 is (I think) a signed statistic, i.e. is negative for thickness decrease and positive for thickness increase, this makes me unsure how to interpret the stage2 (cross-sectional) result. As I understand it, having a significant red cluster in the group comparison can mean either of these 3 scenarios: 1. Both groups have pc1>0 2. G1 has pc1>0 and G2 has pc1<0 3. Both groups have pc1<0 ..but that the pc1 of G1 is always greater, as a signed number, than that of G2, since that is what defines the cluster. The problem is that, when I run the same analysis but keeping only subjects of one group in at one time, i.e. for each group separately and looking at the contrast "Does the average ... differ from zero?", in most cases I don't get the same cluster that appeared in the group comparison. My question is therefore: can a cluster appearing in the between-groups analysis be trusted if the same (or similar) cluster does *not *appear in each of the two within-groups (one-sample test) analyses? And if the latter analysis produces null results but the former does have sig clusters, does it still make sense to look at the sign of each group's mean pc1 in order to find the effect of the longitudinal treatment (atrophy or increase), even if that group in fact did not have a pc1 that was significantly different from zero? Many thanks for your help! Tudor

2 1

Spatial smoothing in Matlab
by Reza Rajimehr 18 Jul '14

18 Jul '14

Hi, For a simulation purpose, I want to load a surface into Matlab, assign a random value (taken from a normal distribution) to each vertex, do spatial smoothing on the surface with a given FWHM (e.g. 5mm), then do some computations with the smoothed values. I am wondering if there is a Matlab code that I can use for surface smoothing, similar to what FS-FAST preprocessing does in Freesurfer version 5 and above. Thanks, Reza ***************** Reza Rajimehr, MD Postdoctoral Research Fellow McGovern Institute for Brain Research Massachusetts Institute of Technology (MIT) NMR Martinos Center Massachusetts General Hospital (MGH) Harvard University *****************

3 2

retinotopic mapping using selxavg3-sess
by Alan Lee 18 Jul '14

18 Jul '14

Hello freesurferers, I ran this command (33333 is my subject name): selxavg3-sess -a Retinotopy.33333.lh -s 33333 and got this error message: # ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy bet.fsl /tmp/mkbrainmask_14781/in.nii /tmp/mkbrainmask_14781/brain -m -f 0.1 /usr/lib/fsl/5.0/bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory It seems that something is wrong with the file libfslvtkio.so, or perhaps some path problem (I've manually set $FSLDIR to /usr/lib/fsl/5.0/). Any feedback would be greatly appreciated. Below are the versions of software I'm using: Linux debian 3.2.0-4-486 #1 Debian 3.2.57-3+deb7u1 i686 GNU/Linux (run in virtualbox with a Windows 8 Host) FSL 5.0.6 freesurfer-Linux-centos4-stable-pub-v5.3.0 Many thanks, Alan -- Alan Lee sites.google.com/site/alanlflee/

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Re: [Freesurfer] Spatial smoothing in Matlab
by Reza Rajimehr 18 Jul '14

18 Jul '14

Thanks Doug! I need to do this procedure 100 times, so I have to automate it. Do you have an example C-shell script for this? Or is there a way to call mri_surf2surf inside a "for loop" of Matlab? Thanks, Reza not that I know of. When I have to do this, I save the data to a file, then call mri_surf2surf with a system call, then load the result back into matlab.

1 0

Re: [Freesurfer] mri_convert
by Douglas Greve 18 Jul '14

18 Jul '14

You can use mri_convert to change the orientation in the header. If you run mri_convert without options it will give you lots of documentation doug On 7/18/14 9:17 AM, Fan, Qiuyun wrote: > Hi Doug, > > I think I figured it out. It's the angulation of the image plane. ImageOreintation (should have been axial slices) reads "0.99995101907245\0.00923454555106\-0.0035612672513\-0.0089978930043\0.69829945291611\-0.7157491962821", and was thus identified as coronal. So, nothing went wrong with mri_convert. > > As a follow up question, although technically, there's nothing wrong with it, it does look confusing intuitively. I'm wondering if there's a way to fool the nifti to label it as LPS at all? > > Thanks a lot! > > Best, > > Qiuyun > ________________________________________ > From: Fan, Qiuyun > Sent: Thursday, July 03, 2014 4:19 PM > To: Douglas N Greve > Subject: mri_convert > > Hi, Doug, > > I found an error when using mri_convert to convert image from dicom to nifti. I have one odd subject, whose orientation labels were wrong. The dicom-info-dump looks the same as the other subjects, and the images look fine too. > > If you have a chance to take a look at the images, here's the path to the "odd" subject:/autofs/cluster/hcps/data_preproc/HCPS_017/dcm/diff_1k/ > > An example of a "good" subject can be found here: /autofs/cluster/hcps/data_preproc/HCPS_015/dcm/diff_1k/ > > BTW, I'm using /usr/local/freesurfer/stable5_3_0. > > Please let me know if you need more information from me. > > Thanks a lot! > > Best, > > Qiuyun > >

1 0

Errors in Mapping of Brodmann Areas
by pfannmoelj＠uni-greifswald.de 18 Jul '14

18 Jul '14

Dear Experts, I am working with freesurfer 5.3 on Mac OSX. I applied recon-all to a data set. This has been done with the same data on a Linux system with Freesurfer 5.3 without any problems. Everything works fine on the Mac except of the labelling of Brodmann Areas. On the Mac the regions are not created as a single areal with a border at the outline. Instead they consist of an outside border and several small regions inside the label. I already tried to create the Brodmann Areas by myself using the command: mri_label2label --srclabel /.../subjects/fsaverage/label/lh.BA3b.label --srcsubject fsaverage --trglabel lh.BA3b.test.label --trgsubject subjid --regmethod surface --hemi lh This does not change the result. I attached a screen shot of the label in fsaverage and one of my subjects. Any help is highly appreciated. Regards pfannmoe

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Freesurfer July 2014