Freesurfer

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30096 discussions

Missing ribbon.mgz file
by ye tian 02 Jul '13

02 Jul '13

Dear freesurfers, Recon-all -s subject -autorecon2 returns the following error messages *mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file* mghRead(Path_to_subject/mri/*ribbon.mgz, -1)*: could not open file. Prior to autorecon2, I did recon-all -s subject -autorecon1, which completed without errors. I found a similar problem in the archive, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/030025.html and I will follow the suggestion given. In the same time, does anybody know what is going wrong? Thank you very much! Sincerely, Ye

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Xhemi files can not be downloaded
by Hamza Alshuft 02 Jul '13

02 Jul '13

Dear Freesurfer experts I can not download files required for surface based inter hemispheric registration :http://ftp.nmr.mgh.harvard.edu/fswiki/Xhemi outcome "curl: (78) RETR response: 550" I am currently using Mac version 5.1. Any help please? Thanks, Hamza This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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freesurfer registration problem
by Lijia Wang 02 Jul '13

02 Jul '13

Hi experts, When I'm pre-processing the 4D whole brain BOLD images using "preproc-sess -sf -mni305 -fwhm 5 -fsd bold -per-run" , the results of registration from BOLD images to the MNI305 template are always only a small part of the original images. I tried to use another T1_152 template instead(higher resolution) of the original MNI305 template, then"recon-all", "preproc-sess", but the results still remain the small part. How can I solve this problem? Thanks! Best Regards! Rebecca

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Re: [Freesurfer] Problem with FS-FAST, mkcontrast
by O'Shea,Andrew 02 Jul '13

02 Jul '13

That was my problem Doug, thanks! I used ' sudo ln -s /Applications/MATLAB_R2011b.app/bin/matlab /usr/local/bin ' and it fixed it. -Andrew Message: 9 Date: Mon, 01 Jul 2013 09:46:39 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Problem with FS-FAST, mkcontrast To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <51D1883F.5050103(a)nmr.mgh.harvard.edu<mailto:51D1883F.5050103@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed doyou have matlab installed and in your path? doug On 07/01/2013 08:55 AM, O'Shea,Andrew wrote: Hello, I am trying to work through the FS-FAST tutorial on my data. I am using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make contrast command which I run ' mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 ' I get the following output error: " phhp-jcraggs-mb:Project aoshea$ mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 INFO: Found 1 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 mkcontrast -anadir test -wcond 1.00000000000000000000 -sumconds -o test/pain-v-rest.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile test/pain-v-rest.mat nconds 1, wcond 1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir test -wcond 1.00000000000000000000 -sumconds -o test/pain-v-rest.mat -wdelay 1 -no-octave Mon Jul 1 08:51:02 EDT 2013 " It is not creating a .mat file in the analysis directory. Any suggestions would be greatly appreciated. Thanks! -Andrew _______________________________________________ Freesurfer mailing list Freesurfer(a)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> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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REPOST: Volume ROI statistics
by Garikoitz Lerma-Usabiaga 01 Jul '13

01 Jul '13

Hi again, is it possible to use mri_convert with a register.dat to create a .mgh volume in the registered space? any help would be appreciated... thanks! Gari On Mon, Jul 1, 2013 at 8:45 PM, Garikoitz Lerma-Usabiaga < garikoitz(a)gmail.com> wrote: > Hi, > I want to obtain volume statistics from a ROI in fsaverage. > I have register.dat and a .nii file (the ROI), but I don't now how to get > to the .label. > > The last try has been: > mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/ROI.nii > --o $SUBJECTS_DIR/fsaverage/label/ROI.mgh > --reg > $SUBJECTS_DIR/fsaverage/mri/transforms/my_own_register_created_with_bbregister.dat --targ > fsaverage > > (but it is failing, error: > corRead(): can't open file $SUBJECTS_DIR/fsaverage/COR-.info) > > My next steps were: > cor2label (in fsaverage) > mri_label2label (per every subject) > mri_segstats (per every subject) > > > Is there any simpler method to accomplish the same? Or at least that it > works? > many thanks, > Gari >

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Recon-all -autorecon1: Talairach Failure Detection yet "finished without error"
by ye tian 01 Jul '13

01 Jul '13

Dear freesurfers, After running recon-all -s Subject -autorecon1, I checked the status.log file, it seems to have two contradictory statements: #@# *Talairach Failure Detection* Mon Jul 1 13:00:30 CDT 2013 recon-all -s Barba50527_2 finished *without error* at Mon Jul 1 13:23:15 CDT 2013 When I loaded talairach.xfm into brainmask.mgz, talairach.xfm seems to be fine. I had no idea what is going wrong, so I continued to run autorecon2. Would someone please elucidate? Thank you very much! Sincerely, Ye

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question about format of control points
by Mehul Sampat 01 Jul '13

01 Jul '13

Hi Folks, Once we make control points in tkmedit, they are stored in the file control.dat Are these control points stored in RAS co-ordinate system ? If not what is the co-ordinate system used to store the control points Thanks Mehul

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CUDA Error when runnign freesurfer
by Salil Soman 01 Jul '13

01 Jul '13

Hi, I am running freesurfer 5.3 on an ubuntu 13.04 with a nvidia card and the the CUDA drivers installed. I am getting the following error when I try using the use-cuda command: Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Acquiring CUDA device Using default device ERROR: Unable to acquire a CUDA device! Linux Baldrick 3.5.0-27-generic #46-Ubuntu SMP Mon Mar 25 19:58:17 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux I am running the following freesurfer command: recon-all -i 242.nii.gz -s 242_FS -nuintensitycor-3T -nocanorm -openmp 8 -use-cuda -hippo-subfields -all Any suggestions on how I can fix this problem? Best wishes, Sal

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Re: [Freesurfer] Tracula/ config file error
by Anastasia Yendiki 01 Jul '13

01 Jul '13

That probably means you're not running a C shell. That's fine, can you instead try running trac-all and see if it prints out the value of dcmlist now that you've added that line? I'll repeat my other question: What program are you using to view the text file? On Mon, 1 Jul 2013, Gundran, Andrew wrote: > Whoops. It doesn't read like that every # is a new line along with each "set" > > I did that and the error was > > Line13: syntax error near unexpected token `(' > Line 13: `set subjlist = (freesurfer) > > > -----Original Message----- > From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] > Sent: Monday, July 01, 2013 3:09 PM > To: Gundran, Andrew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Tracula/ config file error > > > What program are you viewing it in? If you add a line at the end of config.txt that says "echo $dcmlist" (without the quotation marks) and then run "source config.txt" on the command line, does it print out "DKI.nii.gz"? > > On Mon, 1 Jul 2013, Gundran, Andrew wrote: > >> It reads like >> >> # Input diffusion DICOMs (file names relative to dcmroot) # If >> original DICOMs don't exist, these can be in other image format # but >> then bvecfile and bvalfile must be specified (see below) # set dcmroot >> = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) >> >> -----Original Message----- >> From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] >> Sent: Monday, July 01, 2013 2:48 PM >> To: Gundran, Andrew >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] Tracula/ config file error >> >> >> Can you see that this is all one line? >> >> # Input diffusion DICOMs (file names relative to dcmroot) # If >> original DICOMs don't exist, these can be in other image format # but >> then bvecfile and bvalfile must be specified (see below) # set dcmroot >> = >> /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz) >> >> >> On Mon, 1 Jul 2013, Gundran, Andrew wrote: >> >>> Yes, the text was saved on a unix system >>> >>> -----Original Message----- >>> From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] >>> Sent: Monday, July 01, 2013 2:34 PM >>> To: Gundran, Andrew >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Tracula/ config file error >>> >>> >>> Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep breath and let it all go. >>> >>> More to the point, when I view the text file that you sent, I see that several of the lines are joined together, so both the dcmroot and dcmlist variables appear commented out. Is this intentional? Was this text file saved on a unix system? >>> >>> a.y >>> >>> On Mon, 1 Jul 2013, Gundran, Andrew wrote: >>> >>>> >>>> I have been trying to run tracula with a config file but keep >>>> getting the same error message when I use the trac-all command for >>>> pre-processing >>>> >>>> "set: Variable name must begin with a letter" >>>> >>>> >>>> >>>> It has become very, very annoying. PLEASE SOMEONE HELP!!! >>>> >>>> >>>> >>>> Andrew >>>> >>>> >>>> >>>> ------ >>>> >>>> # FreeSurfer SUBJECTS_DIR >>>> >>>> # /home/baileype/Desktop/JG005/freesurfer/mri >>>> >>>> # >>>> >>>> setenv SUBJECTS_DIR /home/baileype/Desktop/JG005 >>>> >>>> >>>> >>>> # Output directory where trac-all results will be saved # Default: >>>> Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005 >>>> >>>> >>>> >>>> # Subject IDs >>>> >>>> # >>>> >>>> set subjlist = (freesurfer) >>>> >>>> >>>> >>>> # In case you want to analyze only Huey and Louie # Default: Run >>>> analysis on all subjects # set runlist = (1) >>>> >>>> >>>> >>>> # Input diffusion DICOMs (file names relative to dcmroot) # If >>>> original DICOMs don't exist, these can be in other image format # >>>> but then bvecfile and bvalfile must be specified (see below) # set >>>> dcmroot = >>>> /home/baileype/Desktop/JG005 set dcmlist = (DKI.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 = >>>> /home/baileype/Desktop/JG005/bvecs >>>> >>>> >>>> >>>> # 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 = >>>> /home/baileype/Desktop/JG005/bvals >>>> >>>> >>>> >>>> # Perform registration-based B0-inhomogeneity compensation? >>>> >>>> # Default: 0 (no) >>>> >>>> # >>>> >>>> # set dob0 = 1 >>>> >>>> >>>> >>>> # 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 >>>> >>>> >>>> >>>> # 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 = 0.2 >>>> >>>> >>>> >>>> # Perform diffusion-to-T1 registration by flirt? >>>> >>>> # Default: 0 (no) >>>> >>>> # >>>> >>>> set doregflt = 0 >>>> >>>> >>>> >>>> # Perform diffusion-to-T1 registration by bbregister? >>>> >>>> # Default: 1 (yes) >>>> >>>> # >>>> >>>> set doregbbr = 1 >>>> >>>> >>>> >>>> # Perform registration of T1 to MNI template? >>>> >>>> # Default: 1 (yes) >>>> >>>> # >>>> >>>> set doregmni = 1 >>>> >>>> >>>> >>>> # MNI template >>>> >>>> # Only used if doregmni = 1 >>>> >>>> # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >>>> >>>> # >>>> >>>> # set mnitemp = /path/to/mni_template.nii.gz >>>> >>>> >>>> >>>> # Perform registration of T1 to CVS template? >>>> >>>> # Default: 0 (no) >>>> >>>> # >>>> >>>> # set doregcvs = 0 >>>> >>>> >>>> >>>> # CVS template subject ID >>>> >>>> # Only used if doregcvs = 1 >>>> >>>> # Default: cvs_avg35 >>>> >>>> # >>>> >>>> # set cvstemp = donald >>>> >>>> >>>> >>>> # Parent directory of the CVS template subject # Only used if >>>> doregcvs = 1 # >>>> Default: $FREESURFER_HOME/subjects # # set cvstempdir = >>>> /path/to/cvs/atlases/of/ducks >>>> >>>> >>>> >>>> # 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 >>>> >>>> # It can be a single number for all paths or a different number for >>>> each of the # paths specified in pathlist # Default: 7 for the >>>> forceps major, 6 for the corticospinal tract, >>>> >>>> # 4 for the angular bundle, and 5 for all other paths >>>> >>>> # >>>> >>>> set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 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 >>>> >>>> >>>> >>>> # Number of "sticks" (anisotropic diffusion compartments) in the >>>> bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 >>>> >>>> >>>> >>>> # 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: 7500 # set nsample = 7500 >>>> >>>> >>>> >>>> # Frequency with which MCMC path samples are retained for path >>>> distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 >>>> >>>> >>>> >>>> # Reinitialize path reconstruction? >>>> >>>> # This is an option of last resort, to be used only if one of the >>>> reconstructed # pathway distributions looks like a single curve. >>>> This is a sign that the # initial guess for the pathway was >>>> problematic, perhaps due to poor alignment # between the individual and the atlas. >>>> Setting the reinit parameter to 1 and # rerunning "trac-all -prior" >>>> and "trac-all -path", only for the specific # subjects and pathways >>>> that had this problem, will attempt to reconstruct them # with a different initial guess. >>>> >>>> # Default: 0 (do not reinitialize) >>>> >>>> # >>>> >>>> set reinit = 0 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> 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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manual editing
by Liane Hunter 01 Jul '13

01 Jul '13

I am new to FreeSurfer and have been tasked with running a large number of subjects through the pipeline. I wanted to inquire about the benefits of manually editing the output data at each step as outlined by the manual. Is there anything in the literature regarding the differences, if any, between data that is manually edited vs. not manually edited. Any guidance on this topic would be much appreciated. Thank you. -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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