Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] How to avoid overlaps between volume labels?
by Cheol Han 07 Jun '12

07 Jun '12

Hi Yuko I think you can use multiple label tags when using mri_label2vol like below: mri_label2vol --subject $subject_name --hemi $hemi --label $label1 --label $label2 --label $label3 --temp $template --o $output --fillthresh 0.3 --proj frac 0 1 0.1 --identity The output volume would have non-zero voxels, marked with three different values. Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea

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FW: misalignment of aseg GM/WM and surface midway between pial and white
by Jeff Eriksen 06 Jun '12

06 Jun '12

I am wondering about how the pial and white surfaces are supposed to match up with the aseg file. I was expecting that when I created a new surface, usinfg mri_surf2surf, halfway between the pial and white surfaces (which I call the cortical ribbon), it would run right down the center of the GM. After creating that surface I converted it to voxel representation with mri_surf2vol. I found that it doesn't match everywhere. Are the pial and white surfaces not based on the aseg segmentation of G&WM? If they are, why the discrepancy? Thanks, -Jeff

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Creating a label from an .mgh file
by Ilia 06 Jun '12

06 Jun '12

Hello, How would one create a label (to be used as an input for "mris_anatomical_stats") based on a a statistical map generated by qdec (for example, the result of a Monte Carlo simulation such as "mc-z.abs.th23.sig.cluster.mgh"). The goal is to obtain average cortical thickness for regions where qdec detected significance. Thank you!!

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Problem with MRISread
by Jürgen Hänggi 06 Jun '12

06 Jun '12

Dear FS expert I try to smooth surface area files with the following command: mri_surf2surf --hemi lh --s MOREA_KG002 --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex But there is an error: srcsubject = MOREA_KG002 srcval = (null) srctype = trgsubject = MOREA_KG002 trgval = lh.area.15.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg Loading source data Reading surface file /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area nquads=9895939, nvertices=399 ERROR: MRISread: file '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more faces than vertices! Probably trying to use a scalar data file as a surface! How to solve the problem? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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error in longitudinal template creation
by Corinna Bauer 06 Jun '12

06 Jun '12

Hi all, I was creating the longitudinal template for a subject when I got this error while on the third time point. Is this a memory problem or is it something else? Thanks, Corinna Resolution: 0 Iteration(single-prec): 1 -- diff. to prev. transform: 0.0425184 Iteration(single-prec): 2mri_robust_template(63717) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 186th slice Cannot allocate memory Darwin killiany-240-97.bumc.bu.edu 11.3.0 Darwin Kernel Version 11.3.0: Thu Jan 12 18:47:41 PST 2012; root:xnu-1699.24.23~1/RELEASE_X86_64 x86_64 recon-all -s 006_S_0498_template exited with ERRORS at Wed Jun 6 15:58:30 EDT 2012

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Re: [Freesurfer] MCSRCH ERROR
by Jeff Thompson 06 Jun '12

06 Jun '12

Hi - Was there ever a solution found for this? I am currently having the same problem. Thanks, Jeff Thompson Can you send us e recon-all.log file? On Aug 8, 2011, at 4:30 AM, "Irwin, William" <WIrwin at memory.ucsf.edu> wrote: > Hi- > > > > I’m at a bit of a loss as to how to address and/or fix these errors. > > > > The native input images are very good quality; the conversion to T1.mgz is fine; the brainmask.mgz is good, a bit of dura remained at the parietal/occipital region (very common); otherwise, the skull stripping is very clean. > > > > The recon-all “finished” but with errors as expected. Processing “continued” to the end, but there is no output except in /mri and /touch. > > > > Doing: #@# Skull Stripping > > > > First under “Computing MAP estimate using 3481 samples...” > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10327.2 tol 0.000010 > > > > Then several of the same under “EM alignment process ...” > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 4 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 5 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 017: -log(p) = 1145822.4 tol 0.000000 > > > > Then again at “Computing MAP estimate using 2772 samples...” > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 7006.0 tol 0.000010 > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 838978.4 tol 0.000000 > > > > Thanks, > > Wil > > > > ____________________________________ > William Irwin | Brain Imaging Coordinator > UCSF | Memory and Aging Center > 350 Parnassus Avenue, Suite 905 > San Francisco CA 94143-1207 > wirwin at memory.ucsf.edu | memory.ucsf.edu > p: 415.476.1680 | f: 415.476.1816 > >

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SNR and voxWM
by Kushal Kapse 06 Jun '12

06 Jun '12

hi doug and fellow FS users, i am going thru the recon_checker.log file to look into anat SNR, mWM, stdWM and voxWM.....the ones with lowest SNR are seemed to be marked with arrow....may i know the reason why some of them have lowest SNR and they are marked with arrow in front of em?..the data is acquired on 3t scanner kk

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acquiring substancia nigra volume
by Zohra Ahmadzai 05 Jun '12

05 Jun '12

The final recon process, autorecon3 - uses "ASegStatsLUT.txt" by default to segment certain subcortical structures listed within this textfile. On the otherhand, FreeSurferColorLUT.txt has labels for more subregions, including the substancia nigra which is a region of interest for a particular project we are doing here. The Aseg. output does not label or calculate the volume of the substancia nigra and I was wondering if there is a way to do this? cheers ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Re: [Freesurfer] freesurfer question
by Douglas Greve 05 Jun '12

05 Jun '12

Hi Tony, you can use bbregister to create the registration file. You might also look at the multi-modal tutorial on our wiki as this goes over the steps that you will need to get and apply the registration. For the 2nd question, you can use mris_anatomical_stats. doug ps. Please send questions to the list instead of me directly. Thanks! On 6/5/12 2:37 PM, Jiang, Zhiguo wrote: > > Hi, Douglas > > Thanks for your comments. I was trying to run mri_vol2surf. But it > asks for a registration file. Would youp lease tell me how to get that > registration file? I figured that must be registering volume file to > subject's T1. (of course in my case, the volume file is already in T1 > space since I drawed them on top of the subject T1 image). > > Another quick question is, once the label is created, is there a quick > command to pull out the thickness values (mean etc ) > > Thanks a lot, > > Best, > > Tony > > Zhiguo Jiang, Ph.D. > > http://pain.loni.ucla.edu > > > IMPORTANT WARNING: This email (and any attachments) is only intended > for the use of the person or entity to which it is addressed, and may > contain information that is privileged and confidential. You, the > recipient, are obligated to maintain it in a safe, secure and > confidential manner. Unauthorized redisclosure or failure to maintain > confidentiality may subject you to federal and state penalties. If you > are not the intended recipient, please immediately notify us by return > email, and delete this message from your computer.

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Re: [Freesurfer] using own average subject
by Schuster, Christina /DZNE 05 Jun '12

05 Jun '12

Hi, many thanks for your help! Unfortunately, I still have some questions: 1) Why would someone only want to display the results on a cohort-specific average, but not use that average for calculation? 2) So if I want to use my cohort-specific average for calcuation of the cortical thickness and I registered all subjects on that, do I then still have to calculate a newnew make_average_subject as it is described on the SurfaceRegAndTemplated page? What is the reason behind that? If I should do it, what flags would mris_preproc need: the --target newnewtemplate and the surfreg newtemplate.sphere.reg? Best wishes, Christina _______________________________________ Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Gesendet: Freitag, 1. Juni 2012 17:44 An: Bruce Fischl Cc: Schuster, Christina /DZNE Betreff: Re: AW: [Freesurfer] using own average subject If all you want to do is display it on your average subject, then you can pass fsaverage to mris_preproc and then just display it on your cohort-specific average. doug On 06/01/2012 11:37 AM, Douglas N Greve wrote: > Hi Christina, if you want to use the registration to your new > template, then you need to run mris_register on each subject to > register to the new template. You can actually do this with surfreg, > something like: > > foreach subject (subj1 subj2) > surfreg --s $subject --t newtemplate --lh > end > > This will create $subject/surf/lh.newtemplate.sphere.reg > > You can then run > > mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ... > > Note that the surfreg cmd above will take about an hour for each subject > > doug > > > > > On 06/01/2012 11:05 AM, Bruce Fischl wrote: >> Hi Christina >> >> you should cc the list so others (Doug!) can answer. The purpose of >> mris_register is to bring your subjects into a common surface-based >> coordinate system. fsaverage lives in that space, but so will the >> average that you make >> >> cheers >> Bruce >> >> >> On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote: >> >>> Hi Bruce, >>> >>> just to be sure that I understood it correctly: >>> >>> I just use make_average_subject to create my template and then I use >>> mris_preproc --target newtemplate and not further --surf-reg >>> specification. >>> Then after mri_glmfit --surf newtemplate ... I have my final results?! >>> >>> So what is the purpose of the mris_register command? >>> >>> Many thanks for your help. >>> Best wishes >>> Christina >>> >>> ________________________________________ >>> Von: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >>> Gesendet: Donnerstag, 31. Mai 2012 20:39 >>> An: Schuster, Christina /DZNE >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Betreff: Re: [Freesurfer] using own average subject >>> >>> Hi Christina, >>> >>> the new template will already be in the same target space as fsaverage >>> since you used the sphere.reg to create it. Just use it as a >>> background for >>> your group results. >>> >>> cheers >>> Bruce >>> >>> On Thu, 31 May 2012, Schuster, >>> Christina /DZNE wrote: >>> >>>> Dear FreeSurfer experts, >>>> >>>> I am trying to create an average subject based on a matched >>>> subsample (2 different scanners, patients and healthy controls). >>>> >>>> I successfully ran make_average_subject receiving a "newtemplate". >>>> Now I am unsure how to proceed: >>>> >>>> As far as I understand it, according to the SurfaceRegAndTemplates >>>> page >>>> (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) >>>> I should use mris_register for each subject from my subsample >>>> receiving ?h.sphere.reg.newtemple files with which I should make >>>> again an average subject, let's call it "newnewtemplate". >>>> >>>> Is that correct? >>>> >>>> Now, if I want to assemble the data into common space using >>>> mris_preproc: what do I need to specify? >>>> Would --target be the newtemplate or newnewtemplate? Do I need to >>>> specifiy the --surf-reg as well? >>>> >>>> >>>> On the other hand, I read in one of your tutorials that I only need >>>> to run make_average_subject receiving a "newtemplate" which I then >>>> specify using mris_preproc as --target and that --surf-reg is not >>>> needed. >>>> >>>> >>>> So what would be the correct way to use my own template for the >>>> group analysis? >>>> >>>> Many thanks for you help! >>>> >>>> Best wishes >>>> Christina >>>> >>>> >>> >>> 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

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