Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

Re: [Freesurfer] tracula: bvec-error
by Robby De Pauw 05 Sep '14

05 Sep '14

Hi Anastasia, I’m using this version of tracula. trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp I’ve attached the log-file you requested. Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

3 3

Re: [Freesurfer] problems with tracula pre-processing (bvecs)
by Michele Cavallari 04 Sep '14

04 Sep '14

Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp <bakk.hbg(a)googlemail.com> wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 9

problems with tracula pre-processing (bvecs)
by Michele Cavallari 04 Sep '14

04 Sep '14

Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help.

4 3

FreeSurfer NVIDIA card drivers with CentOS 6.5
by raij＠nmr.mgh.harvard.edu 04 Sep '14

04 Sep '14

Hi, Is there a FreeSurfer/MNE (maybe even FSL, TrackVis) recommendation to use the "noveau" drivers that come with CentOS 6.5 or would it be better to go with the proprietary drivers from NVIDIA? I would imagine that since FS 5.3 does not use GPU for analysis, this is mainly relevant for visualization (freeview etc) requiring 3D rendering of volumes, surfaces, and tractography results simultaneously. In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here. Thanks! Tommi --- Tommi Raij, MD, PhD

3 5

Re: [Freesurfer] trac-all -prep error field map error
by Eileen Moore 04 Sep '14

04 Sep '14

Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example? As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map. I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file). Thanks, Eileen. > ------------------------------ > > Message: 10 > Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1407170411110.12767(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Eileen - All image formats that mri_convert (and thus any freesurfer > program) can read will do, you don't need dicom. Try giving trac-all the > phase difference maps you have and let's see what happens. > > Best, > a.y > > On Wed, 16 Jul 2014, Eileen Moore wrote: > > > Hi Anastasia, > > > > OK - our imaging physicists had developed a wrapper script around > epidewarp > > which takes our dicom images and converts them into the phase difference > map > > (it is based on the script that was authored by Doug Greve for the fBIRN > > consortium). It looks like the tracula script requires dicom images. Is > > there a way for me to do epidewarp manually and then follow through with > the > > remaining steps using trac-all? > > > > Thanks, > > Eileen. > > > > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > Message-ID: > > <alpine.LRH.2.03.1407141119560.23459(a)nmr.mgh.harvard.edu> > > Content-Type: text/plain; charset="utf-8" > > > > > > Hi Eileen - That step is run with the program epidewarp.fsl, > > which you can > > run on the command line to see the available options. The input > > phase map > > volume is expected to have either 2 frames (2 separate phase > > maps) or 1 > > frame (the difference phase map). This error from trac-all means > > that it > > found that your input phase map has something other than 1 or 2 > > frames, so > > it doesn't know how to handle it. > > > > Hope this helps, > > a.y > > > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > > I'm tyring to > > > run tracula on some? images acquired from a GE scanner. I am > > running into > > > problems when I try to perform the registration-based > > B0-inhomogeneity > > > compensation, getting an error in the terminal output: "ERROR: > > Unrecognized > > > format of phase map". However, trac-all -prep runs fine when I > > skip the > > > B0-inhomogeneity compensation step. Is there something else I > > need to do to > > > use field map correction? > > > > > > I've attached the trac-all.log and a copy of the terminal > > output. > > > > > > Thanks, > > > Eileen. > > > > > > > > > > > > > > > > > > > >

2 1

Tracula - May update version
by Peggy Skelly 04 Sep '14

04 Sep '14

I have a few questions about the May 2014 update to Tracula: 1. Between the 2013-12-04 trac-all version 1.53 and 2014-05-26 trac-all version 1.56, the longitudinal stream now uses the aparc+aseg.mgz from the *.long.* directories, and all output is saved there, too. Are the <subj_tp>.long.<subj_base>/dlabel/anat and anatorig transformed into the base space like other images from the longitudinal recon-all, or are they in the original space of the timepoint T1 image? 2. Are there any changes to the bedpostX step, other than using a different mask? I've already run bedpostx in the Dec 2013 version (with lowb_brain_mask). Can the results be used with the new version by moving the <subj>/dmri.bedpostX directory to <subj_tp>.long.base/dmri.bedpostX? 2a. (Maybe pertains to both versions) The link to .../dmri/nodif_brain_mask.nii.gz seems to be made during the -prep stage using .../dlabel/diff/aparc+aseg_mask.bbr.nii.gz or lowb_brain_mask.nii.gz depending on usemaskanat's value in the dmrirc file. The bedpost stage seems to use the target file as its mask no matter what usemaskanat is in the dmrirc file used when calling trac-all -bedp. (I'm trying to use aparc+aseg_mask for -prep and -path, but lowb_brain_mask for -bedp in anticipation of using the bedpostx output for other seed-base tracking in FSL.) 3. May 2014 version: trac-all -prep -notensor fails when it gets to computing the priors because dmri_train includes the --fa flag and the dtifit_FA.nii.gz is not present. Running trac-all -prior without a computed FA also fails the same way. I could compute the tensor, but thought I would save some time. I didn't realize computing the priors would use it. Does it improve the accuracy? Thanks, Peggy

2 1

Change in the location/path and the name of subject
by Reza Rajimehr 01 Sep '14

01 Sep '14

Hi, I have got anatomicals of a subject from someone else. The anatomicals have been processed, and the surfaces have been reconstructed. The path to these files in my machine is obviously different from the path where data have been analyzed. I also want to change the name of the subject and give a name based on a convention that I have for my other subjects. Would the change in the location and name of the subject be problematic later on when I want to work with the anatomical data or use them during the functional data analysis? (re-processing of the anatomicals is not an option, since these are monkey data with heavy amounts of manual editings) Thanks, Reza

3 2

license file problem solved
by Philipp G. Sämann 30 Aug '14

30 Aug '14

Hi all, the license file problem I have described earlier today could be solved by following earlier hints on a workaround, mainly in the following two contributions: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29404.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29433.html It turned out to be the same problem: by an update of the SuSe system (from an old system 11.x to 13.x), the libcrypt.so.1 tool could not be used any more. Copying an old version (of an old SuSe system) to the freesurfer/lib folder, linking it and adding the folder to the LD_LIBRARY_PATH worked out... I think the problem should be pointed out in the installation instructions. The error message (I am not a sys admin...) that the license file is not valid was very misleading. Best wishes, Philipp I am stuck with a license error in that freesurfer (after a simple recon-all call for segmentation) continues to interrupt the process soon after starting it, see complete copy of the error log file below. I have freshly installed Freesurfer FROM SCRATCH and applied for a new licence file which lies at the appropriate location. What does "INVALID LICENSE FILE" actually indicate, how can the file be invalid? What can be done and why does the programm run absolutely smoothly on another Linux-64-bit system?? vG Philipp Sat Aug 30 17:17:48 CEST 2014 /net/PE1/raid1/enigma-mdd/data/WG_989 /net/PE1/raid1/enigma-mdd/freesurfer/bin/recon-all -subjid WG_989 -all -hippo-subfields subjid WG_989 setenv SUBJECTS_DIR /net/PE1/raid1/enigma-mdd/data FREESURFER_HOME /net/PE1/raid1/enigma-mdd/freesurfer Actual FREESURFER_HOME /net/PE1/raid1/enigma-mdd/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux PE3 3.11.6-4-desktop #1 SMP PREEMPT Wed Oct 30 18:04:56 UTC 2013 (e6d4a27) x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 2066987 maxlocks unlimited maxsignal 2066987 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 264665936 263134184 1531752 0 194912 255250340 -/+ buffers/cache: 7688932 256977004 Swap: 20972820 4929156 16043664 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /net/PE1/raid1/enigma-mdd/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /net/PE1/raid1/enigma-mdd/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Sat Aug 30 17:17:53 CEST 2014 Found 1 runs /net/PE1/raid1/enigma-mdd/data/WG_989/mri//001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /net/PE1/raid1/enigma-mdd/data/WG_989/mri//001.mgz /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz /net/PE1/raid1/enigma-mdd/data/WG_989 mri_convert /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz /net/PE1/raid1/enigma-mdd/data/WG_989/mri/orig.mgz --conform mri_convert /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz /net/PE1/raid1/enigma-mdd/data/WG_989/mri/orig.mgz --conform -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /net/PE1/raid1/enigma-mdd/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz... Linux PE3 3.11.6-4-desktop #1 SMP PREEMPT Wed Oct 30 18:04:56 UTC 2013 (e6d4a27) x86_64 x86_64 x86_64 GNU/Linux recon-all -s WG_989 exited with ERRORS at Sat Aug 30 17:17:57 CEST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Max-Planck-Institut für Psychiatrie AG Kernspintomographie Kraepelinstr. 2-10 80804 München Tel. 089-30622-413 Fax 089-30622-520

1 0

Group cortical thickness QDEC help
by Taylor North 30 Aug '14

30 Aug '14

Hello, I am having some troubles using QDEC to analyze the thickness changes in my group study and I was hoping someone may be able to give me a hand. The steps I have done are as follows: I am working on a study looking at 40 subjects scanned at two time points (base and 6 months after). I have followed all the steps for longitudinal processing for each subject (cross,base, and longitudinals) and made edits where they were necessary to the base. I then entered all 40 subjects into a QDEC table as follows fsid fsid-base time gender age crosstpN1 base1 0 female 20 crosstpN2 base1 6 female 20 .......... continues for rest of the subjects then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and then transformed the longitudinal QDEC table into a QDEC table which looks like: fsid time gender age Base1 3 female 20 .......... continues for the rest of the subjects. I then followed the QDEC steps outlined In the group tutorial. (import cross sectional table, generate stats data table, import aseg volume, set longitudinal dependent variables and pick continuous variable. 1) the first problem I am having is that when I go to process the longitudinal group results through QDEC it makes me pick a continuous variable when I just want to analyze the dependent variable The symmetrized percent change. So I have tried picking different continuous variables ( such as age or importing rhcortex volume etc...) with choosing symmetrized percent change as the dependent variable. No matter what continuous variable I pick the question: ``does the average symmetrized percent change differ from zero"? always comes up, the problem is depending on what continuous variable I pick the results change. Is there a way to just look at the longitudinal thickness changes across a group alone, because I first want to look at the atrophy across the whole group over 6 months and then compare the differences in atrophy against the diagnosed and non diagnosed group. 2) another thing I don't quite understand is it seems like the longitudinal qdec tables are made with the cross of the subjects under fsid, but why wouldn't you use the longitudinals under the fsid for the longitudinal table instead? Also it seems like in the cross sectional qdec table the base is the subject being analyzed under fsid, which also doesn't make sense to me because in the tutorial it says base should not be used directly for analysis. thanks for the help! Taylor

1 1

mri_watershed: really bad skull stripping
by Úrsula Pérez Ramírez 30 Aug '14

30 Aug '14

Hello, I’m new with FreeSurfer and I’m getting a really bad skull stripping (almost nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerably. I have tried with a subject from the tutorial dataset and it’s OK. What can be the problem? Thank you very much! Úrsula

3 6

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2014