Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

glmfit flag --frame-mask
by Victor Montal Blancafort 19 Jan '16

19 Jan '16

Dear FS Experts, I have seen few posts about this mri_glmfit flag, and I would like to know how it works. In an older post, ( https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32412.html) Doug suggested to use this flag when only some subjects should be exclude for each vertex (i, e. differnet number of subjects to exclude per vertex). Could anyone give me an insight on how this works? My intention is to perform a GLM analysis of some DTI metric volumes projected into the surface. However, some of the DWI volumes are cutted, so I would like exclude those vertexs where there is no signal (i,e value 0). Will --frame-mask work for this? Any other suggestion? Any help will be very appreciated! Thank you in advance, Victor Montal

2 1

Little cluster after FDR correction
by stdp82＠virgilio.it 19 Jan '16

19 Jan '16

Hi list, I have performed a seed-based fcMRI analysis by FAST.After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file could be also produced when FDR correction is applied? I'm very confused.Please, could you help me because from several days I'm trying to have a solution.Thank you very much for your work.Kind regards. Stefano

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error in selxavg3-sess
by neha hooda 19 Jan '16

19 Jan '16

Hii I am using freesurfer to find the resting state connectivity. I used selxavg3-sess to analyze the data. But it neither terminates nor gives the error. Any help will be appreciated. Regards Neha -------------------------------------------------------------- selxavg3-sess logfile is /home/neha/projectfolder/log/selxavg3-sess-bold-fc.lpccseed.surf.lh-160109152215.log -------------------------------------------------------------- preproc-sess -s sessionid -d /home/neha/projectfolder -a fc.lpccseed.surf.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ NC_2 setenv FREESURFER_HOME /home/NC_2/shubham/freesurfer/freesurfer/ setenv SUBJECTS_DIR /home/neha/AKE01/PA0/ST0/ Linux tapan 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux /home/neha/projectfolder /home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/preproc-sess -s sessionid -d /home/neha/projectfolder -a fc.lpccseed.surf.lh -nolog Sat Jan 9 15:22:16 IST 2016 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain sessionid Template ----------------------------- mktemplate-sess -s sessionid -d /home/neha/projectfolder -fsd bold -nolog -update Session: /home/neha/projectfolder/sessionid ---------------- Sat Jan 9 15:22:16 IST 2016 Detected input format at nii.gz sessionid Update not needed Run: 004 ---------------- Sat Jan 9 15:22:16 IST 2016 sessionid 004 Update not needed Sat Jan 9 15:22:16 IST 2016 mktemplate-sess completed sessionid Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sessionid -d /home/neha/projectfolder -nolog -update ------------------------------------------------ /home/neha/projectfolder/sessionid Sat Jan 9 15:22:16 IST 2016 sessionid Update not needed for session-level mask sessionid Update not needed for run 004 mask sessionid Update not needed for run 004 meanval Sat Jan 9 15:22:16 IST 2016 mkbrainmask-sess done sessionid Registration ----------------------------- register-sess -s sessionid -d /home/neha/projectfolder -fsd bold -dof 6 -per-run -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Sat Jan 9 15:22:16 IST 2016 setenv SUBJECTS_DIR /home/neha/AKE01/PA0/ST0/ cd /home/neha/projectfolder /home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/register-sess -s sessionid -d /home/neha/projectfolder -fsd bold -dof 6 -per-run -nolog -update freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux tapan 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Session: /home/neha/projectfolder/sessionid ---------------- Sat Jan 9 15:22:16 IST 2016 Run: 004 ---------------- Sat Jan 9 15:22:16 IST 2016 Update not needed Sat Jan 9 15:22:16 IST 2016 register-sess completed sessionid MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sessionid -d /home/neha/projectfolder -fsd bold -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /home/neha/projectfolder/sessionid RunList: 004 sessionid 004 Update not needed Sat Jan 9 15:22:16 IST 2016 mc-sess completed SUCCESSFULLY sessionid To MNI305 ----------------------------- rawfunc2tal-sess -fwhm 5 -s sessionid -d /home/neha/projectfolder -fsd bold -nolog -update -subcort-mask -per-run ------------------------------ 1/1 sessionid 1/1 sessionid 004 ---------------- Sat Jan 9 15:22:16 IST 2016 /home/neha/projectfolder/sessionid/bold/004/masks/brain.mni305.2mm.nii.gz does not need updating sessionid 004 Update not needed Sat Jan 9 15:22:16 IST 2016 rawfunc2tal-sess completed ---------------------------------------- Started at Sat Jan 9 15:22:16 IST 2016 Ended at Sat Jan 9 15:22:16 IST 2016 preproc-sess done ------------------------------------------- /home/neha/projectfolder/sessionid Sat Jan 9 15:22:17 IST 2016 anadir = /home/neha/projectfolder/sessionid/bold/fc.lpccseed.surf.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014b (8.4.0.150421) 64-bit (glnxa64) September 15, 2014 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /home/neha/projectfolder >> sxa3cmd = /home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/selxavg3-sess -s sessionid -a fc.lpccseed.surf.lh >> /home/NC_2/shubham/freesurfer/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sessionid ############################### /home/neha/projectfolder/sessionid ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /home/NC_2/shubham/freesurfer/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/NC_2/shubham/freesurfer/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/NC_2/shubham/freesurfer/freesurfer/matlab/MRIread.m ------------------------- outtop = /home/neha/projectfolder Extension format = nii.gz rm: remove regular file `/tmp/tmp9865807.nii'? 0

2 4

still receiving permission denied response
by Jasmin Alves 19 Jan '16

19 Jan '16

Hello, I have already downloaded freesurfer but kept getting a permission denied response to trying any of the freesurfer commands. So I have re-downloaded freesurfer and am on the "testing freesurfer" phase when I still receive the same error -bash: freeview: Permission denied Thanks, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

2 1

Using freesurfer on a partial brain
by Kevin Aquino 19 Jan '16

19 Jan '16

Dear Freesurfer list, I was wondering if anyone here has used freesurfer on anatomical scans acquired on a partial brain? I realise that recon-all and many of the tools are suited for a full brain, but I was wondering if anyone out there has had experience making the tools work for this scenario? Not necessarily the parcellations and the full set-up, but other tools such as segmentation, creating a white and pial surface and topology fixes. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* www.physics.usyd.edu.au/~aquino/ ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

2 1

postoc opportunity in Melbourne, Australia
by Sarah Whittle 19 Jan '16

19 Jan '16

Postdoctoral Research Fellow Position at The University of Melbourne Melbourne Neuropsychiatry Centre, Department of Psychiatry A/Prof Sarah Whittle and Dr. Julian Simmons seek a postdoctoral research fellow to work on a number of longitudinal studies that aim to characterise neurodevelopmental risk/resilience for mental health problems in children and adolescents. A full or part-time position is available; FTE is flexible to accommodate the most suitable applicant. This position is for one year (or longer if part-time), with the possibility of an extension depending on grant funding. Start date is asap. We are looking for a postdoctoral scientist with strong quantitative skills. The successful candidate will primarily be responsible for conducting data analysis for both cross-sectional and longitudinal data spanning a broad range of modalities (e.g., behavioural, neuroimaging, neuroendocrine); assisting the Investigators with data analyses; supervising postgraduate students; and writing scientific papers and presentations. Additional opportunities to work on other ongoing studies are also available. Position qualifications include a PhD in developmental or quantitative psychology, neuroscience, mathematics, or statistics (note that individuals close to completion of their PhD, or appropriately qualified individuals without a PhD may be considered); strong statistical skills and experience with statistical analysis packages (particularly SPSS, Stata, R, and/or MPlus); ability to work independently and in a team environment on multiple tasks and projects and to share expertise through training others. Desired (not required) skills include: Experience with longitudinal statistical analysis; experience with specialized software programs for neuroimaging analysis (FSL, MATLAB, SPM, FreeSurfer); experience with fMRI analysis; experience with neuroendocrine assaying and analysis; experience with structural equation modelling. Excellent scientific writing skills are also desired. Please send a letter of research interests, a CV, and contact information for three references to Sarah Whittle (swhittle(a)unimelb.edu.au<mailto:swhittle@unimelb.edu.au>) and Julian Simmons (jgs(a)unimelb.edu.au<mailto:jgs@unimelb.edu.au>). Applications will be considered on a rolling basis until the position is filled.

1 0

(no subject)
by Jasmin Alves 19 Jan '16

19 Jan '16

Hello, I recently downloaded freesurfer on my mac with a Yosemite operating system. The application itself appears to work, however I am not able to use the command line to do any of the testing free surfer commands, as I keep getting a access denied. I have attached a screenshot. Your help would be very useful. Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

4 10

cortical and subcortical masks
by Nayyereh Ghazi 19 Jan '16

19 Jan '16

DearExperts,Iwant to create some cortical and subcortical masks to use as seed regions infsl’s Probtrackx and have faced some questions that ask you help me with them. Toextract subcortical regions I have used the below commands (e.g. for thalamus_r): {mri_label2vol \ --seg $SUBJECT_DIR/${subject}/mri/aparc+aseg.mgz \ --fillthresh 0 > /dev/null \ --identity \ --temp $SUBJECT_DIR/${subject}/mri/orig.mgz \ --o ${datadir}/aparc+aseg.nii.gz \ mri_binarize --i ${datadir}/aparc+aseg.nii.gz--match 49 --o ${datadir}/thalamus_r.nii.gz} I noticed that the number of voxels of the created masks inthis way are different from which is written in aseg.stats file. Could youplease explain the reason and the way to make these numbers as close as possible. For cortical regions I used both the above and below commands(e.g. for rh.superiortemporal):{mri_annotation2label --subject ${subject} \ --hemi rh \ --annotation$SUBJECTS_DIR/${subject}/label/rh.aparc.annot \ --outdir $SUBJECTS_DIR/${subject}/label\ --surface white mri_label2vol \ --label $SUBJECTS_DIR/${subject}/label/rh.superiortemporal.label\ --temp $SUBJECT_DIR/${subject}/mri/orig.mgz \ --identity \ --o ${datadir}/rh.superiortemporal.nii.gz\ --fillthresh 0> /dev/null}Again I have noticed differences in number of voxels of theresults from two methods for cortical regions and also a difference fromaparc.stats’s numbers. My final goal in to use the masks in probtrackx to findthe connections between subcortical structures and corticalregions in temporal lobe and I wonder which method is more accurate to create cortical masks. Also I want to know using which atlas is better for my purpose, aparc+aseg or aparc.a2009s+aseg. Your help is greatly appreciated. Wishes,Nayyereh

1 0

QDEC. Error in Analyze: command failed: mri_glmfit
by BAUTISTA-PERPINYA Maximilià 18 Jan '16

18 Jan '16

Hi there experts, I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the following error: --------------------------------------------------------------------------------------------------------------- ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 137 Checking inputs nframestot = 137 Allocing output Done allocing nframes = 137 Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh gdfReadHeader: reading /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 LeftAmygdala 1502.65 189.974 Class Means of each Continuous Variable 1 diagnosisBPD 1497.7548 2 diagnosisCCP 1540.8923 3 diagnosisNPC 1488.5490 INFO: gd2mtx_method is dods Reading source surface /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf fsaverage lh --------------------------------------------------------------------------------------------------------------- Any recommendations? Any help is much appreciated :) Best, Max

3 3

error dwi2tensor
by Sanne Oostermeijer 18 Jan '16

18 Jan '16

Dear Freesurfer,experts, I am fairly new at DTI analysis. I have put together a script to pre-process my DTI data (attached). I have been able to succesfully run this for one of my datasets (T3) however, when I try to run the same script for my other set (T4), I get many errors popping up (see screenshot). The first part runs fine for T4; module 0 for mrconvert and 1 for eddy correction. As far as I know images from T4 are essentially the same from T3. I hope someone knows where the error comes from or can poijt me in the right direction. Thank you, Kind regards, Sanne

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