Freesurfer June 2011

freesurfer@nmr.mgh.harvard.edu

118 participants
168 discussions

cvs template missing in 5.1
by Martin Kavec 15 Jun '11

15 Jun '11

Hi, I did a fresh download and install of the FS-5.1.0 for CentOS_x86_64 and I am not finding the cvs_avg35 template in $FREESURFER_HOME/subjects. Plus the cvs settings text file is not there either. In contrast Mac distribution has it. Is there any problem with cvs on CentOS_x86_64 platform? Thanks, Martin

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Adding tracts to Tracula!
by Seán Froudist Walsh 15 Jun '11

15 Jun '11

Hi FreeSurfing Gurus, I would like to add some new tracts to the Tracula pipeline using my own regions of interest. What would be the best way to do this? All the best and many thanks in advance, Seán

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mri_label2label problem
by Righart, Ruthger Dr. 15 Jun '11

15 Jun '11

Dear Freesurfers, I am using mri_label2label in Fs v5.0.0 to map a label between subjects. I have some problems in that the target label shows little holes while the location of the target label seems to correspond rather well with the source label. Checking these holes backward to the source subject using the function tools/send to subject in tksurfer ... brings the saved point in the source label. I think this problem has been reported in the list before (see copy below) but unfortunately I do not find a solution that removes the holes. In my case I see this now and then both for ROIs that I drew myself in tksurfer but also pre-defined ROIs that were already there (e.g., rh.G_and_S_cingul-Mid-Ant.label). What might go wrong here? I am using --regmethod surface and trgsurf white. I wondered further how one may check how well mri_label2label worked for each subject. Is there a way to test that source and target labels have the same location in terms of for example gyri and sulci? Are there cases that mri_label2label cannot work? Thank you very much for your help, any suggestions appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany Ruthger.Righart(a)med.uni-muenchen.de http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15125.html Re: [Freesurfer] Mri_label2label problem? Douglas N Greve Tue, 21 Sep 2010 06:47:09 -0700 what does the original label look like? Can you convert one of the predefined labels (eg, lh.V1.label) to see if the same thing happens? doug Pye, Brandon (NIH/NIMH) [F] wrote: > Hey guys, > > We are using mri_label2label to convert a label created from a cluster (using > mri_surfcluster) from an average subject to each individual subject. We have > 6 individual labels that we are converting. All of the analysis is done > using surface data. I use the command in the generalized form listed below: > > Mri_label2label -srcsubject fsaverage -srclabel cluster1.label -trg subject > Subject -trglabel Subject_cluster1.label -regmethod surface -hemi lh > > 5 of the 6 labels transfer well, but a 6th label translated to the correct > anatomical location, but the number of labeled vertices is greatly reduced > after the translation. This problem persists across all subjects. There > doesn't appear to be much interior to the label, just a lot of the outline of > the label (i.e. If the outline of the label is yellow and the interior is > blue, I see a lot of yellow and not much blue, as if there are a bunch of > small "islands"). The region on them most inferior part of the lateral > surface approximately where the temporal and occipital lobes meet. > > Any ideas what might be going on? > > Thanks, > --------------------------------------------------------------------- > Brandon Pye > Post-Baccalaureate IRTA > Laboratory of Brain and Cognition, NIMH/NIH/DHHS > Building 10, Room 4C214 > 10 Center Dr MSC 1366 > Bethesda, MD 20892 > Phone: (301) 402-3893 > Fax: (301) 402-0921 > brandon....(a)nih.gov > >

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mri_ca_register error
by Vanessa Lim 14 Jun '11

14 Jun '11

Hi, I am getting the same error. I did set the environment to an external drive with LOTS of space. When I run it though I did notice it repeats the subject path which is the external drive but then says actual path ~/apps/freesurfer/subjects - this doesn't have much space cause it's a virtualbox and I don't know how to make it bigger. But the error below seems to be pointing to the right directory /home/...Desktop etc. > > GCAMwrite(transforms/talairach.m3z): gzip encountered error. > writing output transformation to transforms/talairach.m3z... > mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed > ERROR: mri_ca_register with non-zero status 252 > but continuing despite the error > #-------------------------------------- > #@# CA Reg Inv Thu May 26 12:42:11 EDT 2011 > /home/virtualuser/Desktop/freeSurfer/CG2/mri > > mri_ca_register -invert-and-save transforms/talairach.m3z > > Loading, Inverting, Saving, Exiting ... > Reading transforms/talairach.m3z > ERROR: cannot find or read transforms/talairach.m3z > ERROR: mri_ca_register with non-zero status 0 > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux > > Cheers, > Vanessa

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error in *recon-all -all -s* and *qdec*
by Sophy Zhu 14 Jun '11

14 Jun '11

Hello, Freesurfers, When I use *recon-all -all -s ...* there exists the error *mris_volmask.bin: error while loading shared libraries: /usr/local/freesurfer//lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: cannot restore segment prot after reloc: Permission denied* Would you please tell me how to solve it? Another problem is that I cannot use the *qdec*, does this error come from my installation of freesurfer? Thanks a lot Sophy

2 1

Talairach Transformation failed on Freesurfer 5.1
by Yiyu Chou 14 Jun '11

14 Jun '11

Dear Freesurfer users, I got different transformation matrices (shown below) when running ver 5.0 and ver 5.1 on the same subject - ver 5.0 was doing great but ver 5.1 failed: I would appreciate it if you can give me some advice. Yi-Yu Chou ------------------------------------------------------------------------------------------------------------------------- ver 5.0 1.09499812 -0.07903829 -0.05864276 3.68856287 -0.00531462 1.04585004 0.30695227 -12.39152050 0.05851136 -0.39031574 1.20183659 13.30094814 ver 5.1 1.128152 -0.008014 -0.149835 2.440697 1.389055 4.761067 -3.739542 -67.997681 -0.828629 -2.725178 3.870089 46.025513

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trac-all - bedp errors
by Deryk S. Beal, Ph.D. 14 Jun '11

14 Jun '11

Dear Tracula Users I completed trac-all -prep -c without difficulty or errors. However, without any changes to my director structure or my Tracula config file I am receiving the following errors when running trac-all -bedp -c. I will copy and past my config file contents below the error messages. Please advise. trac-all -bedp -c /media/5424CE1A24CDFECC/UofT/data/Tracula/tracula_config.txt -debug INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects INFO: Diffusion root is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer ln -sf /usr/local/freesurfer/subjects/C001/dlabel/diff/anat_brain_mask.bbr.nii.gz /usr/local/freesurfer/subjects/C001/dmri/nodif_brain_mask.nii.gz ln -sf /usr/local/freesurfer/subjects/C001/dmri/dwi.nii.gz /usr/local/freesurfer/subjects/C001/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri subjectdir is /usr/local/freesurfer/subjects/C001/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x53: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected CONFIG FILE CONTENTS: # # dmrirc.example # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. # # Original Author: Anastasia Yendiki # CVS Revision Info: # $Author: ayendiki $ # $Date: 2011/05/24 06:47:12 $ # $Revision: 1.3.2.3 $ # # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH" # # Terms and conditions for use, reproduction, distribution and contribution # are found in the 'FreeSurfer Software License Agreement' contained # in the file 'LICENSE' found in the FreeSurfer distribution, and here: # # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense # # Reporting: freesurfer(a)nmr.mgh.harvard.edu # # # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /usr/local/freesurfer/subjects # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /usr/local/freesurfer/subjects # Subject IDs # set subjlist = (C001 C002 C003 C004 C005 C006 C007 C008 C009 C010 C011 S001 S002 S003 S004 S005 S006 S007 S008 S009 S010 S011) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # 2 3 4 5 6 7 8 9 10 11) #12 13 14 15 16 17 18 19 20 21 22) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile, bvalfile, and nb0 must be specified (see below) # set dcmroot = /media/5424CE1A24CDFECC/UofT/data/Tracula set dcmlist = (C001_merged.nii.gz \ C002_merged.nii.gz \ C003_merged.nii.gz C004_merged.nii.gz \ C005_merged.nii.gz \ C006_merged.nii.gz \ C007_merged.nii.gz \ C008_merged.nii.gz \ C009_merged.nii.gz \ C010_merged.nii.gz \ C011_merged.nii.gz \ S001_merged.nii.gz \ S002_merged.nii.gz \ S003_merged.nii.gz \ S004_merged.nii.gz \ S005_merged.nii.gz \ S006_merged.nii.gz \ S007_merged.nii.gz \ S008_merged.nii.gz \ S009_merged.nii.gz \ S010_merged.nii.gz \ S011_merged.nii.gz) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bvecfile = /media/5424CE1A24CDFECC/UofT/data/Tracula/bvecs.txt # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /media/5424CE1A24CDFECC/UofT/data/Tracula/bvals.txt # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 2 # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # set dob0 = 0 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm) # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.3 # Perform diffusion-to-T1 registration by flirt? # Default: 1 (yes) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 0 (no) # set doregbbr = 1 # MNI template (the only option for inter-subject registration in this version) # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # set mnitemp = /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # Number of path control points # Default: 5 # set ncpts = 5 # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Use long (more descriptive) directory hierarchy for saving path distributions? # By default, paths distributions are saved directly under $subjectname/dpath # Default: 0 (no) # set dopathsubdirs = 0 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 5000 # set nsample = 5000 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO Speech-Language Pathologist C.I.H.R. Post Doctoral Research Fellow Department of Cognitive and Neural Systems Speech Laboratory Boston University, 677 Beacon Street, Boston, MA 02215 dsbeal(a)bu.edu http://blogs.bu.edu/dsbeal/about/ ************************************************************************* This email may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by others is strictly prohibited. If you have received this email in error, please contact the sender and delete all copies. Opinions, conclusions or other information expressed or contained in this email are not given or endorsed by the sender unless otherwise affirmed independently by the sender. On Fri, Jun 10, 2011 at 3:28 PM, Deryk S. Beal, Ph.D. <dsbeal(a)bu.edu> wrote: > Hi Anastasia > > If I have T1 data available in my FS subject directory and I have > > Use brain mask extracted from T1 image instead of low-b diffusion image? > # Has no effect if there is no T1 data > # Default: 1 (yes) > # > set usemaskanat = 1 > > then will the B0 brain mask we spoke of below be used? > > Deryk > > > On Fri, Jun 10, 2011 at 10:46 AM, Anastasia Yendiki < > ayendiki(a)nmr.mgh.harvard.edu> wrote: > >> >> Hi Deryk - This variable is only used to average lowb images to create a >> mask, so in your case you can set it to 2 and it'll just use the first 2 >> volumes from your nii file. Sorry for the confusion! >> >> a.y >> >> >> On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote: >> >> Dear Tracula Users >>> >>> Does Tracula assume that the number of B0 scans, specified in Step 7.3 of >>> the config file tutorial (below), are the first X number of volumes in >>> the >>> 4Dnii.gz file or will the Tracula routines know from the bvals file where >>> the B0 scans are ordered in the file? For example, I have two runs of 16 >>> directions + 2 B0s each for each of my subjects. I have merged the two >>> runs >>> together and the resulting file has the volumes ordered such that the >>> bvals >>> are entered into Tracula as follows: >>> >>> 0 >>> 0 >>> 1000 >>> 1000 >>> 1000 >>> etc >>> 0 >>> 0 >>> 1000 >>> 1000 >>> 1000 >>> etc >>> >>> My question pertains to the following part of the Tracula config file: >>> >>> Step7.3: Specifying Number Of low-b Images The last step to set up if not >>> using original DICOMs would be to specify the number of low-b images with >>> the following variable: >>> >>> set nb0 = *No. of low-b images* >>> Thank you in advance for your help. >>> Cheers, >>> Deryk >>> >>> Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO >>> Speech-Language Pathologist >>> C.I.H.R. Post Doctoral Research Fellow >>> Department of Cognitive and Neural Systems Speech Laboratory >>> Boston University, 677 Beacon Street, Boston, MA 02215 >>> dsbeal(a)bu.edu >>> http://blogs.bu.edu/dsbeal/about/ >>> ************************************************************************* >>> This email may contain confidential and/or privileged information for the >>> sole use of the intended recipient. Any review or distribution by others >>> is >>> strictly prohibited. If you have received this email in error, please >>> contact the sender and delete all copies. Opinions, conclusions or other >>> information expressed or contained in this email are not given or >>> endorsed >>> by the sender unless otherwise affirmed independently by the sender. >>> >>> >>> >> >> 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. >> > >

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Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz
by Douglas N Greve 14 Jun '11

14 Jun '11

that's weird. I'm not sure what to do. The log says that it is creating T1.mgz and not t1.mgz. Can you try this: cd $SUBJECTS_DIR/subject/mri mri_normalize -g 1 nu.mgz T1.mgz this should create T1.mgz and not t1.mgz doug tulu wrote: > Dear FS experts and Prof. Douglas N Greve, > Here is log file. I work on other machine under CentOS 5 and FS 4.5 version > but I copy the result from this machine to other machine and find it only > have t1.mgz rather than T1.mgz. > I guess is the language system problem ? > Finally I use a short matlab script to change t1.mgz name as T1.mgz. > > Thanks in advance > Best > JLH > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Monday, June 13, 2011 11:01 PM > To: tulu(a)ms36.hinet.net > Cc: freesurfer > Subject: Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz > > Do you mean your individual subject after running through FS has a file > called t1.mgz and not T1.mgz? Something is definitely wrong there. Can > you send the log file? > doug > > tulu(a)ms36.hinet.net wrote: > >> Dear FS experts, >> I use FS5.1 and previous data run on other machine. When I try to >> make_average_subjects program, I get error message that it can not get >> T1.mgz data from subject folder. When I check my dataset, actually it >> has t1.mgz rather than T1.mgz. how could I change the setting from >> T1.mgz to t1.mgz >> thanks help >> JLH >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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 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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Adding a new measure to the design tab
by Jeanette Berberich 14 Jun '11

14 Jun '11

Hi, So I'm trying to add new measures, after having run recon-all -qcache, to my design tab drop-down menu and it doesn't seem to be working. I was a little confused about the .Qdecrc file. I put a file named qdec.Qdecrc file inside my $SUBJECTS_DIR/qdec/ and i also have a qdec.fsgd file in the same place. I'm not sure what else to do to get my new measurements to show up. Thank you so much, Jeanette

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Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation
by Seán Froudist Walsh 14 Jun '11

14 Jun '11

Hi Balaji, fslswapdim (a command line program which comes as part of fsl) should solve your orientation problems. If you have fsl installed (which you should do!) then typing fslswapdim input_volume_name -x output_volume_name into the terminal should swap RAS to LAS and vice versa. Or you can just type in fslswapdim into the terminal to get help. Best of luck! Sean

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Freesurfer June 2011