Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Subgroup analysis
by Mahinda Yogarajah 29 Nov '12

29 Nov '12

Hi, I think (hope) i am finally getting to grips with how to analyse things but wanted to check one last thing. Say I have 1 factor with 3 levels (3 groups of subjects) and 2 covariates (age and icv). My design matrix would include: Regressor 1 - ones for subject in Gp 1, 0 otherwise, codes intercept/mean for gp 1 Regressor 2 - ones for subject in Gp 2, 0 otherwise, codes intercept/mean for gp 2 Regressor 3 - ones for subject in Gp 3, 0 otherwise, codes intercept/mean for gp 3 Regressor 4 - age for subjects in Gp 1, 0 otherwise, codes age slope for gp 1 Regressor 5- age for subjects in Gp 2, 0 otherwise, codes age slope for gp 2 Regressor 6 - age for subjects in Gp 3, 0 otherwise, codes age slope for gp 3 Regressor 7 - icv for subjects in Gp 1, 0 otherwise, codes icv slope for gp 1 Regressor 8 - icv for subjects in Gp 2, 0 otherwise, codes icv slope for gp 2 Regressor 9 - icv for subjects in Gp 3, 0 otherwise, codes icv slope for gp 3 In terms of contrast would the following be correct: 1.5 0.5 -1.5 0 0 0 0 0 0 - to look for linear change in dependent variable across groups after correcting for age and icv 0 0 0 1.5 0.5 -1.5 0 0 0 - to look for linear change in age slope against dependent variable across groups while correcting for icv ie whether age-dependent measure correlations get stronger/weaker across gps Thanks Mahinda

2 1

functional ROI analysis
by Susan Alice McLaughlin 29 Nov '12

29 Nov '12

Hi, I am hoping do a surface-based functional ROI analysis on subject-specific ROIs that are both defined structurally and are masked by an all/nothing functional contrast. func2roi-sess seems perfect for this except that my data are not in an FS-FAST data/analysis structure, but are instead pre-processed and preliminarily analyzed using FSL and mapped to the surface using reg-feat2anat. Is there any way to pass my original analysis into func2roi-sess? I tried using: func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis 1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG -maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz -maskthreshold 2 -s 1012 -d but get "ERROR: cannot find any sessions." Or is there another tool more appropriate for what I am trying to do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on fsaverage in tksurfer and morphed to each subject using label_2_label) are in .label format and are on the surface. Thanks in advance for and advice or suggestions. Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 29 Nov '12

29 Nov '12

Hi Doug, Thank you for reply. yes all 4 are in bold separately. I tried -run-wise with selxavg3-sess, but it failed with the following msg: Saving X matrix to /media/local_home/zhouw4/EM0220/analysis/retinotopy/SUBJ01/bold/rtopy.self.lh/pr001/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 254) XCond = cond(XtX); I attach the mat file in the email. I am thinking that the error is similar as that I only put polar or eccen session in bold folder. Thank you for looking into it. Best Wei ________________ But all four runs into a single bold folder, then try running selxavg3-sess with the -run-wise option. This will create separate run analysis in the output directory. I have not tried it with retinotopy before, so get back to me if it fails. doug On 11/26/2012 05:53 PM, Zhou, Wei wrote: > Hi Doug, > I think I didnt explain clearly last time. > Here's the thing: > I have four runs: 2 eccen and 2 polars. I followed the > processhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyA… > and I hope to view the result of an individual session, e.g. one polar, > which could display the activations with different angles. What should I do > after all the analysis is done? Or I should run a retinotopy analysis > different from the link above. > Thank you in advance. > Best > Wei > ---- > Hi Wei, do you have both polar and eccentricity? It looks like you only > have polar. > doug > On 11/19/2012 01:39 PM, Zhou, Wei wrote: > > Please find the Xtmp.mat in the attachment.Thank you, Doug. > > Best > > Wei > > ---- > > Can you send me the Xtmp.mat file? > > dloug > > > > On 11/16/2012 01:01 PM, Zhou, Wei wrote: > > > Hi Doug, > > > > > > It seems the previous fieldsign-sess problem is due to that I stored > > > data on one server while freesurfer is on the other server. > > > But when I put the data and freesurfer on the same server and run the > > > retinotopy analysis again, it reported fail msg for "selxavg3-ses" : > > > -- > > > ntptot = 80, nX = 27, DOF = 53 > > > Saving X matrix to > > > > > > > > /media/local_home/zhouw4/testf/retinotopy/SUBJ01/bold/rtopy.self.lh/Xtmp.mat > > > Error using svd > > > Input to SVD must not contain NaN or Inf. > > > > > > Error in cond (line 39) > > > s = svd(A); > > > > > > Error in fast_selxavg3 (line 254) > > > XCond = cond(XtX); > > > --- > > > I checked Xtmp.mat. There is NaN in Xn and XtX. > > > My rtopy par is: eccen and pos. > > > > > > Would you please give me some idea about this error? > > > > > > Best > > > Wei > > > > > > >> > > > Try using this version > > > > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fieldsign-sess > > > > > > doug > > > > > > On 11/01/2012 11:47 AM, Zhou, Wei wrote: > > > > Hi Doug, > > > > > > > > The subject name for structural is "SUBJ1" when I did recon-all, > > which > > > > is also the content of file "subjectname". My dir structures of > > > > "structural" and "retinotopy" are the same as > > > > http://www.alivelearn.net/?p=65 . "SUBJ1" is stored under > > > > "structural". if I set SUBJECTS_DIR as "....../structural", > > > > $SUBJECT_DIR/SUBJ1 does exist, then still I get the same error > > msg. > > > > > > > > The following is the log file: > > > > > > > > fieldsign-sess log file $Id: fieldsign-sess,v 1.2 2010/05/04 > > 22:00:18 > > > > greve Exp $ Thu Nov 1 10:36:52 CDT 2012 Linux rii-appserv-02 > > > > 2.6.32-279.11.1.el6.x86_64 #1 SMP Sat Sep 22 07:10:26 EDT 2012 > > x86_64 > > > > x86_64 x86_64 GNU/Linux /media/users/zhouw4/testf/retinotopy > > > > /usr/local/freesurfer/fsfast/bin/fieldsign-sess -a rtopy.self.lh > > > > -occip -s SUBJ1 uid=20120(zhouw4) gid=22000(rii_users) > > > > groups=22000(rii_users),21100(rii_appservers),23000(domain^users) > > > > context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 > > > > > > > > Best > > > > Wei > > > > > > > > > > > > >What is the name of FreeSurfer subject? This is not necessarily > > the > > > > same>> > > > > >as SUBJ01 in your command line below. That is the session (which > > may > > > or > > > > >may not be the same as the "subject name"). What ever the > > subjectname > > > > is, does SUBJECT_DIR/subject exist? > > > > On 10/31/2012 03:07 PM, Zhou, Wei wrote: > > > > > > > > > > Hi, Doug > > > > > > > > > > Thank you for your reply. I have tried exporting > > SUBJECTS_DIR to > > > the > > > > > directory of upper fold, retinotopy or SUBJ01 But none of > > them > > > works. > > > > > Still the same error msg. > > > > > > > > > > So what should SUBJECTS_DIR be exported to for this > > analysis? > > > > > > > > > > Best > > > > > > > > > > Wei > > > > > > > > > > > > > > > > > > > > >Hi Wei, this is a bug in the error msg. It is trying to > > say that > > > your > > > > > >source subject is not in the $SUBJECTS_DIR. > > > > > >doug > > > > > > > > > > >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > > > > > > Dear freesurfers, > > > > > > > > > > > > I am trying retinotopy analysis in freesurfer. For > > > > "fieldsign-sess", I > > > > > > encounter the following problem when I type > > "fieldsign-sess > > > -a > > > > > > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess > > -a > > > > rtopy.self.lh > > > > > > -occip -sf sessid": > > > > > > > > > > > > > > > > > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > > > > > > *subject: Undefined variable.* > > > > > > > > > > > > my structure of retinotopy fold is : > > > > > > retinotopy > > > > > > | |--sessid > > > > > > |--SUBJ01 > > > > > > |--subjectname > > > > > > > > > > > > |--bold > > > > > > |--001 > > > > > > |--f.nii > > > > > > |--rtopy.par| > > > > > > > > > > > > I really appreciate it if you could give me some > > idea about > > > that > > > > > > problem. Thanks a lot in advance. > > > > > > > > > > > > Best > > > > > > Wei Zhou > > > > > > Medical Physics Ph.D. Student > > > > > > Diagnostic Imaging Track > > > > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > > > > > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > 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 > > > > > gr...(a)nmr.mgh.harvard.edu > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > Best > > > > Wei Zhou > > > > Medical Physics Ph.D. Student > > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > Best > > > Wei Zhou > > > > > > > > > > > > _______________________________________________ > > > 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 > > gr...(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Best > > Wei Zhou

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Re: [Freesurfer] spline_smooth (please reply, no answer from email-list)
by Douglas N Greve 29 Nov '12

29 Nov '12

Hi Negar, I cannot reproduce this error. I'm not sure how to proceed, but here are three possibilities: 1. Is this a virtual machine? If so, do you have a real machine you can run it on? 2. You only have 2G of memory on your machine. Can you increase that or run it on a machine with more? 3. There is an outside chance it could be an MNI version issue. Run nu_estimate_np_and_em and look at the version (should be 1.10) doug On 11/27/2012 03:31 PM, Negar Memarian wrote: > Hi Doug, > > Thanks very much for your reply. I checked the org.mgz and it looks > okay, so as you advised I uploaded the subject to FileDrop for you to > see. I also uploaded the recon-all log file so you can see where > exactly the error occurs. > > Many thanks and looking forward to hear from you, > Negar > > On Tue, Nov 27, 2012 at 9:42 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Negar, sorry about the delay. The first thing to do is to look > at the orig.mgz to see if there is anything funny going on, maybe > most of the image is dark with one very bright spot or some other > distortion. If that looks ok, please tar up the subject and drop > it to me at our file drop (url at thenend of this email). > doug > > > On 11/26/2012 09:10 PM, Negar Memarian wrote: > > Hello Dr. Greve, > I'm not sure if my questions actually get posted on the > FreeSurfer email list or not, as I have never received a > reply. I really need help with the following issue and would > appreciate if you or your colleagues please advise: > **I've checked similar posts on the email-list and still could > not find an answer to my question. I'd really appreciate your > attention and feedback: > recon-all -autorecon1 crashes for me in one of the steps > before skull stripping with an error like this: > Done spline_smooth: posixio.c:210: px_pgin: Assertion `*posp== > ((off_t)(-1)) || *posp== lseek(nciop->fd, 0, 1)' failed. > nu_estimate_np_and_em: crashed while running > spline_smooth(termination status=6) > nu_correct: crashed while running > nu_estimate_np_and_em(termination status=65280) > ERROR: nu_correct > Linux FreeSurfer2.6.28-11-generic #42-UbuntuSMPFri Apr 17 > 01:57:59 UTC2009 i686GNU/Linux > recon-all -s BT501_FSexited with ERRORS at Mon Nov 26 15:26:10 > EST2012 > I made sure that I have the newest version of FreeSurfer, the > environment variables MNI_DATAPATH and MNI_PERL5LIB and > PERL5LIB exist and I ran $FREESURFER_HOME/bin/fixup_mni_paths > as well. But unfortunately I still face the same problem. I > also tried the process for a different subject, but the same > error. Does anyone have any idea how I can fix this? I have > attached the recon-all.log file. > I'd really appreciate your help. > Negar > Negar Memarian, MASc, PhD > NSERC Postdoctoral Fellow > Department of Neurology > David Geffen School of Medicine at UCLA > > > -- > 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 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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voxel number estimation kvlQuantifyPosteriorProbabilityImages
by lorenzo pasquini 29 Nov '12

29 Nov '12

Dear freesurfer users, I have a question regarding the kvlQuantifyPosteriorProbabilityImages command to quantify hippocampal subfield volumes. Are all voxels with a probability value bigger than 0 counted? Or is the command applying any threshold for the estimation? I have transformed the subfield .mgz images in .nii images. The number of voxels with a probability bigger than 0 in the nii images do not correspond to the estimations extracted with the kvlQuantifyPosteriorProbabilityImages command. Thank you! yours, Lorenzo Pasquini Can. Ph. D., Medical Life Science and Technology (Technische Universität Muenchen) Neuroimaging Lab, Neuroradiology Klinikum r. d. Isar (Technische Universität) 81675 München Tel.: 0049 (0) 89 4140-7666

1 0

What provides mri_annot2aparc?
by Chris McNorgan 28 Nov '12

28 Nov '12

Hello all, I've posted this question on the cmtk-users google group as well. In that forum there was an author who had been working on applying the Lausanne 2008 parcellation scheme to a functional data analysis. After running the connectomemapper toolkit to subdivide the Freesurfer parcellation into smaller ROIs, nodes along the white-matter/pial boundary are assigned to one of ~1000 1.5cm^2 ROIs. The next step is to propagate these ROI assignments outwards to the gray matter surface, and the solution entails running mri_annot2aparc on the cmtk .annot files according to the thread posted at: https://groups.google.com/forum/#!topic/cmtk-users/rjaVwDdhQOo The problem I am having is that I have been unable to find any executable or script named mri_annot2aparc anywhere in my filesystem, nor have I been able to find any clues online as to what package provides this resource. Does anyone have any insight? Thanks, Chris

2 1

FW: TRACULA some fiber volumes being too small
by Fernando Ventrice 28 Nov '12

28 Nov '12

Dear Freesurfer/Tracula users, Finally I could successfully test Tracula and I think it is amazing what it can do automatically. These are the commands I used: export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source $FREESURFER_HOME/SetUpFreeSurfer.sh source /etc/fsl/fsl.sh export FSLPARALLEL=condor trac-all -prep -c /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice trac-all -bedp -c /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice # "trac-all -bedp" gave some errors so I used bedpostx directly: bedpostx /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri trac-all -path -c /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice freeview -tv /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz -v /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz & All finished without errors, but there seems to be a problem with CC Forceps Mayor volume, which gave very small values. Is this OK or I made some mistake? First I tested with some patient and other fiber tracks also gave very small volumes. I attached some pictures and the dmrirc and trac-all log files. Best, Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar

3 6

preproc-sess and option -mni305-1mm results in an error
by Jörg Pfannmöller 28 Nov '12

28 Nov '12

Hi, if I apply the following command: preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force The preprocessing runs into trouble at the following point mri_vol2vol done mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem? Cheers Joerg

2 4

optseq2 using dependent trials
by Danielle Miller 28 Nov '12

28 Nov '12

Hi Freesurfer, I have a paradigm in which the conditions are dependent on each other. That is, trials (e.g., congruent or incongruent) are linked to each other in that I want an equal number of trials to follow each other (e.g., congruent- congruent, congruent- incongruent, incongruent-congruent, incongruent-incongruent). When trying optseq2, it of courses randomizes the presentation, and I do not get equal presentations of the "pairs" of trials. Is there a way to jitter dependent trials using optseq? If not, do you have any suggestions on how to address this issue? Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

2 1

Info extraction hippocampus
by Andrea Tateo 28 Nov '12

28 Nov '12

Hello FS experts, I would like to extract from head's MRI a bunary image showing only hippocampus. I used command: ############### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-all -s SUBJECT_name -autorecon-all mri_extract_label aseg.mgz 17 53 hippocampi.mgz ############# This command spends more then 12 computing houres. I would like to spend less computing time. Is there any procedure? thanks All the best Andre Tateo

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