Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

mri_fill problem
by Shay Ohayon 07 Jun '12

07 Jun '12

Hi, I am having problem getting mri_fill to run on one of my volumes (it did work with another monkey, so I assume I am running things right). I am using v5.0 (but it also happens on 5.1). The input is a monkey wm file with specified coordinates for the corpus callosum. The error I get is: "could not find corpus callosum" (see full log below). The input volume is available for download here <http://tsaolab.caltech.edu/sites/default/files/wm.mgz>( http://tsaolab.caltech.edu/sites/default/files/wm.mgz) Any takers? I tried various different coordinates and all of them fail. A hint may be this statement: "find_cutting_plane:seed point not in structure! Searching neighborhood..." which I don't fully understand as the point given is inside a connected component... Many thanks, Shay Tsao Lab Caltech --------------------------- reading input volume...done. searching for cutting planes...INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 1400) area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill: could not find corpus callosum /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill /space/data/shayo/cooked/test2/mri/wm.nii /space/data/shayo/cooked/test2/mri/filled.nii -CV 128 117 91: Signal 124

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loading surface in freeview
by Kushal Kapse 07 Jun '12

07 Jun '12

hi doug n fellow fs users, whenever we try to load a fsaverage surface in freeview, it shows me following message: "Surface does not contain valid volume geometry information. It may not align with volumes and other surfaces" this message is limited only to fsaverage surfaces..... was just wondering if this is something to be worried about for further group analysis in qdec?.....any words on how to fix/avoid this message to reappear??? please let us know thanks kk

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Creating DMPFC ROIs in Freesurfer
by Wu, Paula (NIH/NIMH) [F] 07 Jun '12

07 Jun '12

I was wondering whether anyone here has used Freesurfer to create ROIs for the Dorsomedial Prefrontal Cortex, or if anyone knows citations of articles that have. Thanks, Paula Paula Wu Postbaccalaureate Intramural Research Training Associate Section on Functional Imaging Methods Laboratory of Brain and Cognition National Institute of Mental Health (301) 451-9582 wup2(a)mail.nih.gov<mailto:wup2@mail.nih.gov>

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fsgd
by Marie Schneider 07 Jun '12

07 Jun '12

Dear FreeSurfer experts, I am trying to start mris_preproc, but unfortunately it doesn't find my created fsgd file. I saved it in the foulder where you can find all subjects data. Shall I save it somewhere else? Thanks for your help, best Marie

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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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Freesurfer June 2012