Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

glmfit and surfcluster
by j janssen 09 Oct '08

09 Oct '08

Hi, version 4.0.5. after: mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh --glmdir stats/newperm_lh/ i got an csd file (attached), "stats/newperm_lh and --glmdir stats/newperm_lh/" were ignored (as expected). i want to use this .csd file to inspect clusters: mri_surfcluster --in qdec/N83_only_boys.mgh --csd stats/perm_lh-diff-1-2.txt.csd --cwsig stats/cluster_map.mgh --sum qdec/summary.txt which gives the following output (summary.txt is attached): ******************** # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ # $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $ # CreationTime 2008/10/08-08:52:02-GMT # cmdline mri_surfcluster --in qdec/N83_only_boys.mgh --csd stats/perm_lh-diff-1-2.txt.csd --cwsig stats/cluster_map.mgh --sum q dec/summary.txt # cwd /home/neuro/joost/redes/maranon/freesurfer # sysname Linux # hostname fedoraneuro.lim.local # machine x86_64 # FixVertexAreaFlag = 1 # # Input qdec/N83_only_boys.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /home/neuro/joost/redes/maranon/freesurfer # Minimum Threshold 1.3 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 1.300000 # CSD nreps 1000 # CSD simtype perm # CSD contrast diff-1-2.txt # CSD confint 90.000000 # Overall max 4.37947 at vertex 3484 # Overall min 1.58841e-06 at vertex 136280 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 4.379 3484 98860.55 -34.7 11.5 -6.9 0.00100 0.00000 0.00200 155267 [neuro@fedoraneuro qdec]$ cd .. [neuro@fedoraneuro freesurfer]$ mri_surfcluster --in qdec/N83_only_boys.mgh --csd stats/perm_lh-diff-1-2.txt.csd --cwsig stats/cluster_map.mgh --sum qdec/summary.txt thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = lh srcid = qdec/N83_only_boys.mgh paint srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 1.3 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 sumfile = qdec/summary.txt subjectsdir = /home/neuro/joost/redes/maranon/freesurfer FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /home/neuro/joost/redes/maranon/freesurfer/fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white.avg.area.mgh Done reading source surface Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 4.37947 at vertex 3484 overall min = 1.58841e-06 at vertex 136280 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=1.300000 (1.300000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 1 clusters Max cluster size 98860.554688 INFO: fixing MNI talairach coordinates Saving cluster pval stats/cluster_map.mgh ************************ - the cluster size seems way to big. your thoughts? - for visualizing the cluster i thought: loading the --cwsig file (cluster_map.mgh) as an overlay on the (inflated) surface of fsaverage and then configure the overlay to set the minimal threshold to 1.3. your thoughts? thanks! -joost On Tue, Oct 7, 2008 at 7:37 PM, Pratap Kunwar <pkunwar(a)nmr.mgh.harvard.edu>wrote: > > Hi, > > You have a continuous variable "age" in your fsgd file. As far as i know, > permutation can't have continuous variables. > > Try mc-z that should work. > > pratap > > > Hi, > > > > using version 4.0.5 > > > > i ran the command: > > mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf > > fsaverage lh --C qdec/diff-1-2.txt --glmdir stats/ > > > > it worked. > > > > then i did: > > > > mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf > > fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh > > --glmdir stats/newperm_lh/ > > > > output: > > > > gdfReadHeader: reading qdec/qdec.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 Age 15.4819 > > Class Means of each Continuous Variable > > 1 control 15.0882 > > 2 patient 15.7551 > > INFO: gd2mtx_method is doss > > Reading source surface > > /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white > > reading group avg surface area 822 cm^2 from file > > Reading in average area > > > /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white.avg.area.mgh > > simbase stats/perm_lh > > Number of vertices 163842 > > Number of faces 327680 > > Total area 65416.648438 > > AvgVtxArea 0.399267 > > AvgVtxDist 0.721953 > > StdVtxDist 0.195470 > > > > $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ > > cwd /home/neuro/joost/redes/maranon/freesurfer > > cmdline mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss > > --surf fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 > > stats/perm_lh > > --glmdir stats/ > > sysname Linux > > hostname fedoraneuro.lim.local > > machine x86_64 > > user neuro > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh > > logyflag 0 > > usedti 0 > > FSGD qdec/qdec.fsgd > > glmdir stats/ > > DoFFx 0 > > Loading y from > > /home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh > > Matrix condition is 404.504 > > search space = 82220 > > ERROR: design matrix is not orthogonal, cannot be used with permutation. > > If this something you really want to do, run with --perm-force > > > > mri_info N83_only_boys.mgh gives 83 frames. > > > > what´s wrong with my design matrix? > > > > thanks! > > -joost > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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[Fwd: Re: [Freesurfer] A methodological question]
by Michael Harms 09 Oct '08

09 Oct '08

I'm trying to post this again to the list, since the papers attached (in response to a post from Pedro) may be of interest to others, but they appear to have not been distributed to the overall list in my previous reply to Pedro. Does the list server perhaps reject certain posts based on number or size of attachments? cheers, Mike H. -------- Forwarded Message -------- From: Michael Harms <mharms(a)conte.wustl.edu> To: Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] A methodological question Date: Fri, 03 Oct 2008 13:29:29 -0500 Hi Pedro, Attached are 4 papers that I'm aware of that explicitly compare aspects of FS to other approaches (Lee 2006; Tae 2008; Pengas 2008; Ju 2005) Those particularly interested in TICV should take a look at the Pengas paper (which is timely, given the recent discussion on the list regarding the reliability of the "eTIV" measure). cheers, Mike H. On Fri, 2008-10-03 at 13:50 -0200, Pedro Paulo de Magalhães Oliveira Junior wrote: > Some weeks ago,I have posted here a compilation of the main papers > that describe FreeSurfer implementation. > > > I was wondering if someone has researched in comparison between > FreeSurfer methodology and other ones. (For instance: > doi:10.1016/j.neuroimage.2004.12.056) > > > Best Regards > > > PPJ > > -- > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Voxel-wise analysis of subcortical strucutures
by Juergen Haenggi 09 Oct '08

09 Oct '08

Dear FS experts I am wondering whether it is possible to do an voxel-wise analysis on the subcortical segmentations similar to a voxel-based morphometry (VBM) in SPM or FSL. Because there is no .mgz file that encodes the probability that a particular voxel belongs to a particular tissue type (GM or WM) in the mri folder of the subject, I guess that it is not possible (yet), right? Any advise is appreciated Regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Problem tkmedit after recon-all -long
by Juergen Haenggi 09 Oct '08

09 Oct '08

Dear FS experts I have processed longitudinal data with recon-all -long of three patients with atrophy in the caudate nucleus. When I produce a figure from time point 1 and one figure from time point 2 in order to visualize the atrophy, the figures look different due the different orientations of the two images in native space. How can I reorient the two T1.mgz images and the aseg and the surfaces in a way that the AC-PC plane is horizontal in the native space in order to produce figures that show both images at the same plane. Is there any option that can be used with tkmedit to accomplish this? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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tksurfer display tcl error & FS training
by Derin Cobia 08 Oct '08

08 Oct '08

Two questions: 1. We installed the latest version of 32-bit FS on several workstations running CentOS 5.1 in our lab. However, once we ran the CentOS updates (~280 of them through up2date), tkmedit now fails to open and tksurfer exhibits behavior exactly as described in this message from the mail archive: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07570.html Having attempted to troubleshoot it I discovered that a blt lib was missing, but even with re-installation of this tksurfer continues to not display correctly. I believe it's a tcl problem, but I don't understand why performing incremental updates to CentOS would break FS. More importantly, I'm not sure which of the updates does "the breaking" so I can just avoid it. Any ideas? 2. We are in the process of training new research assistants in how to use FS. Typically we have approached this in a more qualitative way by working side-by-side with them to guide their edits and processing. I was wondering if there is a quantitative way of comparing their work that you (or others) have used when training "new recruits" in FS. Maybe something like was done in the Han et al (2006) paper, such as compare their thickness (or other) maps with someone we know does well with manual interventions? In essence, we're trying to think of a rigorous way to train new people in FS, thanks! -Derin

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qcache commands
by Mishkin Derakhshan 08 Oct '08

08 Oct '08

Hi, I am trying to understand what happens when you run the recon-all -qcache command I noticed these three commands get run: mris_preproc --s tester2 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh mri_surf2surf --hemi lh --srcsubject tester2 --surfreg sphere.reg --sval /lab1/FreeSurfer/4.0.5/ms-mni/testing/tester2/surf/lh.thickness --sfmt curv --trgsubject fsaverage --tval ./tmp.mris_preproc.12176/tester2.1.mgh --noreshape mri_concat ./tmp.mris_preproc.12176/tester2.1.mgh --o lh.thickness.fsaverage.mgh My questions are: 1. Am I right to assume that the first command (mris_preproc) is just a wrapper script that calls the 2nd and 3rd commands? 2a. In the case above, does the 3rd command (mri_concat) simply copy the contents of tester2.1.mgh into lh.thickness.fsaverage.mgh. 2b. Is there a case when mri_concat will actually concat more than one thing into lh.thickness.fsaverage.mgh? thanks, mishkin

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Re: [Freesurfer] qdec.table.dat error
by Mishkin Derakhshan 08 Oct '08

08 Oct '08

Hi Nick, I tried unalias -a and then runnig qdec but it didn't work either. I think the problem is with bash vs. sh in ubuntu (possible all debian systems). ie. /bin/sh is not the same as /bin/bash so not all bash commands will work. I did this: sudo mv /bin/sh /bin/sh.bak sudo ln -s /bin/bash /bin/sh and then it worked. I'm hoping this doesn't have repercussion for my other programs though. thanks, mishkin On Tue, Oct 7, 2008 at 11:20 PM, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > yes, this sounds like a tough one. the VerifySubjects routine that > produces that error message just runs the 'ls' command on that subject > directory name, so that is why i asked. if you run the 'ls' command on > '/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester', does it return a correct > response? ie a non-zero status? > > what does 'which ls' say? possibly it is aliased to something that is > causing a problem. > > does qdec work despite the error? the code is setup to just print the > error, but continue anyway. if the subject doesnt exist, it will fail > downstream (during mri_glmfit). > > i'll try to think of other things. > > nick > > > On Tue, 2008-10-07 at 21:26 -0400, Mishkin Derakhshan wrote: >> Hi Nick, >> Yes I've checked most of the obvious things I could think of. >> The directories all exist, permissions on all files are 775, i will >> try 777 but don't suspect that will make a difference. >> My env variables seem to be set properly as well. >> >> opus[/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester]$ . >> /lab1/FreeSurfer/4.0.5/quarantine/SetUpFreeSurfer.sh >> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /lab1/FreeSurfer/4.0.5/quarantine >> FSFAST_HOME /lab1/FreeSurfer/4.0.5/quarantine/fsfast >> FSF_OUTPUT_FORMAT nii >> SUBJECTS_DIR /lab1/FreeSurfer/4.0.5/ms-mni/testing/ >> MNI_DIR /lab1/FreeSurfer/4.0.5/quarantine/mni >> >> I get the same error when trying to load the tutorial qdec.table.dat as well. >> >> My analysis is stuck at this point so any help is greatly appreciated. >> >> thanks, >> mishkin >> >> >> On Tue, Oct 7, 2008 at 7:27 PM, Nick Schmansky >> <nicks(a)nmr.mgh.harvard.edu> wrote: >> > Mishkin, >> > >> > Does this directory exist? >> > >> > /lab1/FreeSurfer/4.0.5/ms-mni/testing/tester >> > >> > The error message you are seeing is checking for the existence of that >> > directory. >> > >> > Nick >> > >> > >> > On Tue, 2008-10-07 at 14:30 -0400, Mishkin Derakhshan wrote: >> >> Hi, >> >> When I try to load a qdec.table.dat I always get the same error: >> >> >> >> sh: Syntax error: Bad fd number >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in >> >> SUBJECTS_DIR >> >> >> >> I've tried digging around through the archives and still can't seem to >> >> find a solution for this problem. >> >> I've tried tcsh and the bash shell. >> >> Here is a bit more information and my qdec.table.dat is attached. Any >> >> ideas on how to get qdec up and running would be very useful. >> >> thanks, >> >> mishkin >> >> >> >> >> >> FREESURFER_HOME: /lab1/FreeSurfer/4.0.5/quarantine >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 >> >> Debian version: lenny/sid >> >> Kernel info: Linux 2.6.24-18-generic x86_64 >> >> >> >> opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> qdec & >> >> opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> >> >> Reading /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/tkUtils.tcl >> >> >> >> Using /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/fsgdfPlot.tcl >> >> >> >> Loading data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat... >> >> Setting SUBJECTS_DIR to '/lab1/FreeSurfer/4.0.5/ms-mni/testing' >> >> Number of columns: 4 >> >> fsid column: 1 >> >> Number of factors: 3 >> >> Number of subjects: 2 >> >> Reading discrete factor levels from config file >> >> /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/gender.levels...'Male','Female', >> >> done. >> >> >> >> Data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat loaded. >> >> SUBJECTS_DIR is '/lab1/FreeSurfer/4.0.5/ms-mni/testing' >> >> sh: Syntax error: Bad fd number >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in >> >> SUBJECTS_DIR >> >> sh: Syntax error: Bad fd number >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester2' in >> >> SUBJECTS_DIR >> >> Error loading the data table. >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> >> > >

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legacy option
by R D 08 Oct '08

08 Oct '08

Hello, I have some surfaces created by freesufer in 2006. Spherical registration was not done at that time, which needs to be done. I ran recon-all with -legacy, but it crashed due to disk space problems. Now it doesn't run either with or without -legacy option. When -legacy is specified, it says "this is not a legacy analysis. It once was, but it has been fixed." Without -legacy, it asks for some files such as filled.mgz and aseg.mgz that are not present. Is there a way to 'reset' the analysis (e.g., change a flag somewhere) so it can start over with -legacy? thanks, Rutvik

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Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats
by bell0368＠umn.edu 08 Oct '08

08 Oct '08

I was wondering how the calculations of the wm volume were performed as well. The six values below are volume values from aseg I believe. I assume mris_wm_volume does more than sub-divide these regions into the wm parcellations, but probably also includes partial volume estimations along the wm/gm surface, is this correct? I basically have the same question for the gm volume values in aparc.stats; do they include partial volume calculations from the gm/pial and gm/white borders? Which binary is used to create these values for gm in aparc.stats... is it mri_segstats (with --pv)? I was assuming it would be an mris (surface) calculation as well. I am asking because if you use tkmedit to view the ?h.surface files and load the aparc+aseg or wmparc segmentation volumes in also, the surfaces and the segmentations don't seem to line up. Is there a way to create a segmentation volume that includes partial-volumed voxels at the gray/white and gray/pial boundries? Thanks for your help. Chris Bell the interior voxels are only included in the volume if they are one of the following in the aseg.mgz: case Left_Cerebral_Cortex: case Right_Cerebral_Cortex: case Left_Cerebral_White_Matter: case Right_Cerebral_White_Matter: case Left_WM_hypointensities: case Right_WM_hypointensities: cheers, Bruce On Tue, 15 Jul 2008, Marin Richardson wrote: OK, so aparc.stats is better for cortical gray matter. I want to look at the parcellated white matter volumes as well - is the only/best option to use the wm volumes from wmparc.stats? Also, when using mris_wm_volume to calculate total white matter, I saw the result defined as the volume within the white matter surface minus non-WM structures? Can you tell me which regions are and are not included? Marin Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>> It is better to use the aparc as it is derived from surface measurements, which have sub-voxel resolution. The wmparc.stats are generated by counting 1mm^3 voxels. doug Marin Richardson wrote: Hi all, I noticed that the gray volumes for parcellated cortical regions in wmparc.stats are different from those for the same region in aparc.stats (e.g. ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = 9466 in lh.aparc.stats). Why are the values different and which one is a better measure to use? Thanks, Marin

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Can Optseq produced mixed blocked/event-related design?
by BumSeok Jeong 08 Oct '08

08 Oct '08

Dear Freesurfer expert, I'd like to make mixed blocked/event-related design using Optseq. (15sec fixed block - 15sec condition 1 block - fixed block - 15sec condition2 block ....) This below command does not seem to produce what I want. optseq2 --ntp 129 --tr 1.5 --tprescan -9 --psdwin -1.5 21 1.5 --nsearch 10000 --ev Condition1 3 15 --ev Condition2 3 15 --ev fix 15 6 --nkeep 2 --o test Any comment will be appreciated. thanks, Bumseok

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