Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

longitudinal pipeline surface error
by Mihaela Stefan 06 Apr '16

06 Apr '16

Dear FreeSurfers, We are doing a longitudinal analysis with three time points (MRI1, MRI2, MRI3). All the subjects were processed well except for one. The MRI3.long of that subject has very bad surfaces (see attachment - I am also attaching the log file). The cross, the template and the first two long runs were reconned well, though. We can't figure out why this third run is so bad. As a note, we processed all the cross runs on an Ubuntu machine but we ran the longitudinal pipeline on a computer cluster (both with freesurfer v5.3). We ran the long twice for that subject thinking that the pipeline crashed somehow the first time. However, the results were the same. Any help would be appreciated. Thanks! Mihaela

2 7

Tracula problems (creating symbolic link)
by Efrat Kliper 05 Apr '16

05 Apr '16

Dear Freesurfer experts, I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has already been completed in Freesurfer 5.1) in order to run some new functions of Tracula (I have also installed the latest Tracula update (tracula.update.centos4_x86_64.5.3.2014_05_26). I am using: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 I encountered two problems: 1. When I run the initial code of Tracula: trac-all –prep code: /home/fsl/ usr/local/freesurfer/bin/trac-all -prep -c /mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt Subject TB_480 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux *I am getting the following message:* ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz ln: creating symbolic link `/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to `/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not supported 2. If I run the trac-all –bedp command of Tracula (on already trac-all data which was preproc on Freesurfer version 5.1. /home/fsl /usr/local/freesurfer/bin/trac-all -bedp -c /home/fsl/Desktop/xxx.txt Subject TB_201 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux *I am getting the following message:* Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /mnt/hgfs/linux_share/subjects/TB_201/dmri subjectdir is /mnt/hgfs/linux_share/subjects/TB_201/dmri /mnt/hgfs/linux_share/subjects/TB_201/dmri/data not found I am guessing those problems are from the same source. Do you have any suggestions on how can I resolve these issues? Is there a way to overcome the "ln" command and to create this data file without it? (I have also tried to run it from local OS linux and not from shared folder. Many thanks, Efrat

2 3

Mismatch in dimensions using mri_label2vol
by Afzal, Afsana 01 Apr '16

01 Apr '16

Hi, I'm using mri_label2vol with the parameters below but the output .nii volume has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension mismatch is causing issues in our gPPI pipeline. How can I generate a .nii output file with the 27307x1x6 dimension? mri_label2vol --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from preproc step) --label label_name.label --o label_name.nii --identity Thanks, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

3 6

Longitudinal TRACULA - Error in path reconstruction
by Emad Ahmadi 01 Apr '16

01 Apr '16

Hi Anastasia, I hope you’re enjoying your evening! I’m doing longitudinal TRACULA analysis on two subjects, each having two time points. I have already taken the steps of longitudinal recon-all and trac-all -prep & -bedp. Now I’m trying to do trac-all -path, but it gives me an error that I cannot recognize. I would greatly appreciate your help. I’ve attached the log files and the config file. Thank you so much, Emad Emad Ahmadi, MD ----------------------------------------------- Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

2 3

bbregister problems with PET data
by Adam Martersteck 31 Mar '16

31 Mar '16

Hi Freesurfer team, I’m encountering a problem using bbregister on PET data: -- When I attempt to register a PET volume to T1-space the asymmetric tracer uptake of the PET throws off proper registration. (Treating the PET as a T1 because of the non-specific white matter uptake > grey matter signal). -- You can really see the bbregister mis-registration in this gif here: https://goo.gl/iM6yrT -- It (expectedly) attempts to find the best match between signal intensities on both the left and right surfaces, but is inherently biased by the asymmetric uptake shifts the entire volume to the right. -- Are there any suggestions for dealing with asymmetric scans like this? Stick with just a simple FLIRT? It doesn't seem to do that great a job for everyone. Cutting left and right hemispheres apart and register separately? Using Martin’s new robust register for multi-modal data? Any suggestions on the parameters of ROBENT? Thanks, Adam

3 4

ERROR running mkcontrast
by Joseph Dien 31 Mar '16

31 Mar '16

Hi, I ran into an odd problem which I was able to fix but wanted to let others know about. This is OS X 10.11.4 with Matlab 2016a and FreeSurfer 5.3. I got the following error when I ran mkcontrast using batch files that previously worked fine: /private/var/folders/wt/vj5q34fs20x50sh_6rcrtkn80000gn/T/Cleanup At Startup/sh.h4SI0w: No such file or directory. ERROR running mkcontrast Looking into the directories in question, I found that while there was no directory named 'Cleanup At Startup’ inside the T directory, there was such a directory inside ‘vj5q34fs20x50sh_6rcrtkn80000gn’. I’m guessing some version update changed the location of this directory. I went into T and performed the following command: mkdir 'Cleanup At Startup' after doing so, everything worked again. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07(a)mac.com Cell Phone: 202-297-8117 http://joedien.com

1 0

Surface-based PET maps
by Alshikho, Mohamad J. 31 Mar '16

31 Mar '16

Hi Doug, In order to run surface based analysis on PET maps, I used the following steps: 1. Co-registering SUVR to T1 bbregister --s name --mov suvr.nii --bold --init-fsl --reg reg.dat --o suvr_T1.mgh 2. Concatenate SUVR maps mris_preproc --target fsaverage --hemi lh --iv subject1/suvr/suvr_T1.mgh subject1/suvr/reg.dat --iv subject2/suvr/suvr_T1.mgh subject2/suvr/reg.dat --iv ... --projfrac 0.5 --out lh.suvr.mgh 3. Smoothing(sm) mri_surf2surf --hemi lh --s fsaverage --fwhm 10 --cortex --sval lh.suvr.mgh --tval lh.suvr.sm10.mgh 4.Group analysis (GLM) mri_glmfit--y lh.suvr.sm10.mgh --fsgd fsgd.txt --C X.mtx --surf fsaverage lh --cortex --glmdir lh.suvr 5. Correction for multiple comparisons ( Cluster -wise) mri_glmfit-sim --glmdir lh.suvr --cache 1.3 neg --cwp 0.05 --2spaces # Cache 1.3 ( P<0.05) * In a second analysis for the same set of data, I replaced the first step ( co registration) by the following command line: spmregister --s name --mov suvr.nii --reg reg.dat --o suvr_T1.mgh I got the results as attached ( figure1 using bbregister and figure 2 using SPM register) Kindly, 1. Where this difference came from? In other words, should I expect such like difference between "bbregister" and "spmregister" ? 2. For co registration which command do you recommend "bbregister" or "spmregister" ? Best, Mohamad

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Fwd: 5 year Post Doctoral Fellowship in South Korea - Korean Genome and Epidemiology Study
by Douglas N Greve 31 Mar '16

31 Mar '16

FYI -------- Original message -------- From: "Thomas,Robert" <rthomas1(a)bidmc.harvard.edu> Date: 03/30/2016 5:52 AM (GMT+05:30) To: all(a)nmr.mgh.harvard.edu Cc: Chol Shin <chol-shin(a)hanmail.net> Subject: 5 year Post Doctoral Fellowship in South Korea - Korean Genome and Epidemiology Study A 5-year Post-Doctoral Fellowship is available in South Korea, at the Korean Genome and Epidemiology Study, with the center at Ansan Hospital, about 45 minutes outside Seoul. Those with a PhD is the general area of neuroimaging are encouraged to apply. The support is US $ 70,000/ year, with direct additional support for accommodation. The program is funded by the Korean Government. Agreeing to the full 5 years is necessary, no partial support is possible. The KoGES has been in existence since 2001, and has biannual health exams. Rich demographic and cardiovascular information is collected, GWAS is available. Brain MRI (structural, DTI), sleep (including polysomnography) and detailed cognition evaluations were initiated in 2008, and is now in the second cycle. The Fellowship will focus on the brain-sleep-heart interface, a major role for the Fellow will be oversight and aiding the analysis of MRI data, currently obtained at 1.5 T but to move to 3T during the course of the award. High productivity will be expected, and evidence of prior first author publications will be desirable. The awardee will also work with investigators from Harvard (MGH Martinos Center, Beth Israel Deaconess Medical Center) and Boston University-Framingham Heart Study, and can be expected to have substantial freedom to pursue cutting edge analysis techniques in the neuroimaging and Big Data / “omics” realm. Decisions will be made by the end of April. Prospective candidates will need to travel to Seoul for a meeting with Dr. Chol Shin, the Principal Investigator of KoGES, in April; travel costs are covered. Interested individuals should send their NIH style biosketch to Chol Shin, M.D. chol-shin(a)hanmail.net <mailto:chol-shin@hanmail.net> and Robert Thomas, M.D. rthomas1(a)bidmc.harvard.edu <mailto:rthomas1@bidmc.harvard.edu> ------------------------------------------------------------------------ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

1 0

Re: [Freesurfer] DODS vs DOSS for correlation analysis
by Cassandra Wannan 31 Mar '16

31 Mar '16

Hi Doug, I'm using version 5.3. I had read about the bug but the release notes for 5.3 didn't mention not using DOSS in Qdec, so I thought the issue must have been resolved. If not, I'll let my colleagues know as I believe some of them are still using DOSS in Qdec. Cheers, Cassie

2 1

Summer School course 'Genetics for Imagers', 8 August - 12 August in Nijmegen, The Netherlands
by Marten.Onnink＠radboudumc.nl 31 Mar '16

31 Mar '16

Dear Freesurfer users, I would like to promote our Radboud Summer School in Nijmegen (The Netherlands) which might be interesting for FSL imaging people that would like to expand their knowledge in the genetics area. This intensive one-week (8 August - 12 August 2016) course covers various aspects of genetics analyses of neuroimaging data. More info here: http://www.ru.nl/radboudsummerschool/courses/brain-behaviour/vm-more-course… Cheers! Marten Marten Onnink, Msc Radboud University Medical Center Nijmegen Department of Human Genetics (855) | PO Box 9101 | 6500 HB Nijmegen | The Netherlands T +3124 36 10981| Email: Marten.Onnink(a)radboudumc.nl<mailto:Marten.Onnink@radboudumc.nl> Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Freesurfer March 2016