Freesurfer January 2008

freesurfer@nmr.mgh.harvard.edu

54 participants
69 discussions

Analysis question
by Corey Keller 10 Jan '08

10 Jan '08

> > Hi, > > I have a quick and hopefully simple question. The picture on the left > is an individual fmri mean functional display. To get it I used > > Tksurfer-sess -hemi rh -aparc -s PROZ06004 -analysis simple_v_complex -c > simple_v_complex while in /space/multnomah/3/users/gow/PROZ06/fMRI > > The picture is "splotchy" whereas the second picture which is the average > of all subjects for this same analysis and contrast is smooth and cleaner. > In order to display the averaged data I used > > Tksurfer fsaverage rh inflated -annot aparc -overlay > group-analysis/simple_v_complex/rh.meanfunc.nii -fthresh 2 while in the > same directory > I'm trying to get the individual subjects to look like the smooth averaged output. Can you help me with this? Thanks so much. > Best, > Corey > > -------------------- > Corey Keller > Epilepsy Unit > Clinical Research Coordinator > Massachusetts General Hospital > Wang 735, 55 Fruit Street > Boston, MA 02114 > Phone 802.578.6292 > Email cjkeller(a)partners.org > ckeller(a)nmr.mgh.harvard.edu >

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evaluating schedules with optseq2
by rhdesai＠mcw.edu 10 Jan '08

10 Jan '08

Hello, I am trying to find the cost for a schedule with optseq2. As a start, I am just using a .par file generated by optseq2 itself (from a previous search). There are two problems: (1) The --i option does not seem to work at all. It always gives the error that --nosearch option requires an input file (no matter which file you specify with --i) (2) the --in option takes the input file, but gives a bus error, as shown below. Version: $Id: optseq2.c,v 2.12 2006/12/29 02:09:11 nicks Exp $ MacOSX Tiger 10.4.11 thanks, Rutvik --------- % ./optseq2 --in optseq_out_run1-001.par --ntp 160 --tr 2 --psdwin 0 12 --polyfit 2 --nosearch --ev M 2 9 --ev L 2 9 --ev A 2 9 --ev P 2 9 --ev N 2 9 --ev F 2 6 --evc 1 -1 0 0 0 0 --evc 1 0 -1 0 0 0 --evc 0 1 -1 0 0 0 --cost vrfavg --o optseq_eval optseq2 $Id: optseq2.c,v 2.12 2006/12/29 02:09:11 nicks Exp $ NoSearch = 1 nKeep = 1 PctUpdate = 10.000000 nCB1Opt = 0 seed = -1 Ntp = 160 TR = 2 TPreScan = 0 PSD Window = 0 12 2 nEvTypes = 6 EvNo Label Duration nRepsNom 1 M 2.000 9 2 L 2.000 9 3 A 2.000 9 4 P 2.000 9 5 N 2.000 9 6 F 2.000 6 PctVarEvReps = 0 VarEvRepsPerCond = 0 PolyOrder = 2 tNullMax = -1 tNullMin = 0 outstem = optseq_eval nInFiles: 1 0 infile = optseq_out_run1-001.par AR1 = 0 No refractory penalty Cost = vrfavg OutStem = optseq_eval Summary File = optseq_eval.sum nTaskAvgs = 36 C Contrast Matrix ---------------------- 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; ================== ---------------------- 0 0 0.0 3.83588 0.639127 0.5103 3.83588 0.0714353 3.72409 3.93012 0.206034 0 0 outstem = optseq_eval Bus error

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Re: [Freesurfer] Memory problems
by Juergen Haenggi 10 Jan '08

10 Jan '08

Hi Doug I tried to make that file executable (as root I typed chmod a+x make_average_volume) but it did not work. The file I found under the URL you send me is a text file and it is not compiled. Please can you give me any hint to make the new version of make_average_volume executable. Is there a compiled version that is already executable? Thanks a lot in advance Best regards Juergen On 4.1.2008 23:06 Uhr, "Doug Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > You may have to make it executable > > Juergen Haenggi wrote: >> >> Hi Doug >> >> Thanks for the new version, but the following error occurred: >> >> Cleaning up >> ----------------------- >> rm -r ./tmp.mris_preproc.9682 >> Fri Jan 4 21:36:04 CET 2008 >> mris_preproc done >> --------------------------------------------------- >> >> >> >> Fri Jan 4 21:36:04 CET 2008 >> make_average_surface done >> >> make_average_volume --subjects SNPs_Vp01 SNPs_Vp02 SNPs_Vp03 SNPs_Vp04 >> SNPs_Vp05 SNPs_Vp06 SNPs_Vp07 SNPs_Vp08 SNPs_Vp09 SNPs_Vp10 SNPs_Vp11 >> SNPs_Vp12 SNPs_Vp13 SNPs_Vp14 SNPs_Vp15 SNPs_Vp16 SNPs_Vp17 SNPs_Vp18 >> SNPs_Vp19 SNPs_Vp20 SNPs_Vp21 SNPs_Vp22 SNPs_Vp23 SNPs_Vp24 SNPs_Vp25 >> SNPs_Vp26 SNPs_Vp27 SNPs_Vp28 SNPs_Vp29 SNPs_Vp30 SNPs_Vp31 SNPs_Vp32 >> SNPs_Vp33 SNPs_Vp34 SNPs_Vp35 SNPs_Vp36 SNPs_Vp37 SNPs_Vp38 SNPs_Vp39 >> SNPs_Vp40 SNPs_Vp41 SNPs_Vp42 SNPs_Vp43 SNPs_Vp44 SNPs_Vp45 SNPs_Vp46 >> SNPs_Vp47 SNPs_Vp48 SNPs_Vp49 SNPs_Vp50 SNPs_Vp51 SNPs_Vp52 SNPs_Vp53 >> SNPs_Vp54 SNPs_Vp55 SNPs_Vp56 SNPs_Vp57 SNPs_Vp58 SNPs_Vp59 SNPs_Vp60 >> SNPs_Vp61 SNPs_Vp62 SNPs_Vp63 SNPs_Vp64 SNPs_Vp65 SNPs_Vp66 SNPs_Vp67 >> SNPs_Vp68 SNPs_Vp69 SNPs_Vp70 SNPs_Vp71 SNPs_Vp72 SNPs_Vp73 SNPs_Vp74 >> SNPs_Vp75 SNPs_Vp76 SNPs_Vp77 SNPs_Vp78 SNPs_Vp79 SNPs_Vp80 SNPs_Vp81 >> SNPs_Vp82 SNPs_Vp83 SNPs_Vp84 SNPs_Vp85 SNPs_Vp86 SNPs_Vp87 SNPs_Vp88 >> SNPs_Vp89 SNPs_Vp90 SNPs_Vp91 SNPs_Vp92 >> 'csh: Unknown option: `- >> Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. >> [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] >> juergenh% >> >> >> Best regards >> Juergen >> >> >> On 3.1.2008 21:03 Uhr, "Doug Greve" <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu> wrote: >> >> >> >>> >>> >>> This is a problem when it attempts to create an "average" aseg. As a >>> stop-gap measure, I've created a new version that will not stop the >>> execution if this stage fails. You can get it from here: >>> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_v >>> ol >>> ume >>> >>> doug >>> >>> Juergen Haenggi, Psychological Institute wrote: >>> >>> >>> >>>> >>>> Dear FS experts >>>> >>>> I tried to average the brains of 92 subjects. We used a MacPro Quad >>>> with 5 GB RAM and about 10 GB virtual memory. When running >>>> make_average_subject the following error occurred: >>>> >>>> Checking 91 >>>> /Applications/freesurfer/subjects/average/tmp/make_average_vol-tmp/seg-SNPs >>>> _V >>>> p92.mgh >>>> >>>> nframestot = 92 >>>> Allocing output >>>> mri_concat(13587) malloc: *** vm_allocate(size=262144) failed (error >>>> code=3) >>>> mri_concat(13587) malloc: *** error: can't allocate region >>>> mri_concat(13587) malloc: *** set a breakpoint in szone_error to debug >>>> MRIalloc(256, 256, 256): could not allocate 262144 bytes for 14117th >>>> slice >>>> >>>> Cannot allocate memory >>>> [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] >>>> juergenh% >>>> >>>> Does it really mean there is too less memory or is it a similar >>>> problem occurred in other software, i.e. memory acquisition >>>> restriction by the Java Runtime Environment? >>>> Is there any possibility, beside buying more RAM, to run >>>> make_average_subject with the available 5 GB RAM? >>>> >>>> Thanks in advance and Happy New Year >>>> Best regards >>>> Juergen >>>> >>>> >>>> ------------------------------------------------- >>>> Juergen Haenggi >>>> Ph.D. (Dr. des.) >>>> Division of 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(a)psychologie.uzh.ch (email) >>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>> http://www.juergenhaenggi.ch (private website) >>>> ------------------------------------------------- >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> >>> >> >> >> >> ----------------------------------------------------------- >> Juergen Haenggi >> Ph.D. (Dr. des.) >> Division of 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(a)psychologie.uzh.ch (email) >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> http://www.juergenhaenggi.ch (private website) >> ----------------------------------------------------------- >> >> >> >> ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Input parameters
by SANCHEZ BENAVIDES, GONZALO 10 Jan '08

10 Jan '08

Hello, I'm new with FreeSurfer and I need some help. We want to run cortical thickness analysis in batch on a big computer system and the technician asked me for the "input parameters" to run automatically several studies. Where can I find information about this, please? Thank you. -------- Abans d'imprimir aquest missatge, si us plau, comprova que és realment necessari. El medi ambient és cosa de tots. Antes de imprimir este mensaje, por favor, comprueba que es realmente necesario. El medio ambiente es cosa de todos. Before printing this e-mail, please make certain it is absolutely necessary. The environment is everybody's business. -------- La informació continguda en aquest missatge i en qualsevol fitxer adjunt és confidencial, privada i d'ús exclusiu per al destinatari. Si no és la persona a la qual anava dirigida aquesta informació, si us plau, notifiqui immediatament l'enviament erroni al remitent i esborri el missatge. Qualsevol còpia, divulgació, distribució o utilització no autoritzada d'aquest correu electrònic i dels seus adjunts està prohibida en virtut de la legislació vigent. La información contenida en este mensaje y en cualquier fichero adjunto es confidencial, privada y de uso exclusivo para el destinatario. Si usted no es la persona a la cual iba dirigida esta información, por favor, notifique inmediatamente el envío erróneo al remitente y borre el mensaje. Cualquier copia, divulgación, distribución o utilización no autorizada de este correo electrónico y de sus adjuntos está prohibida en virtud de la legislación vigente. The information included in this e-mail and any attached files is confidential and private. If you are not the intended recipient, please notify the sender and delete this message immediately. Dissemination, forwarding or copying of this e-mail and its associated attachments is strictly prohibited in accordance with current legislation. --------

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segmentation of brain of age 8-13
by BumSeok Jeong 09 Jan '08

09 Jan '08

Dear freesurfer experts, I got uncorrected segmentation results, especially occipital cortex, from brain of age 8-13. I found similar problem in adult brain in freesurfer mailing list and the resolving answer like below. "use the control points with the mri_ca_normalize flag as part of the aseg. I've not used the command much, but you should be able to add the flag '-f tmp/control.dat' to the normal mri_ca_normalize command to run this step" Do I have to do any procedure for brain of age 8-13 in addition to suggestion like above? Thanks, bsjeong

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Gray Matter Mask - twist on previous post
by Emily Trittschuh 09 Jan '08

09 Jan '08

Dear Group, Back in April, Anil Roy posted a question about methods to generate a gray matter mask that can be fed into AFNI . . . I'm wondering if the opposite can be done? Can a functional mask made in AFNI be fed easily into Freesurfer? Currently this mask is saved as a NIFTI dataset. Thank you. Emily Emily Trittschuh, PhD Neuropsychology Post-doctoral Fellow Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11-579 Chicago, IL 60611 phone 312/503-1155 fax 312/908-8789

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qdec & study-specific average
by d.g.lawyer＠medisin.uio.no 08 Jan '08

08 Jan '08

Hi, We are using our own average subject in a study, and want to use qdec. We ran recon-all -qcache -target our_study_average on all subjects in the study to make the qdec smoothed files. When I press the analyze button on the design tab, Qdec by default tries to load <subjid>/surf/lh.thick.fwhm10.fsaverage.mgh which of course does not exists. It should be looking for <subjid>/surf/lh.thick.fwhm10.our_study_average.mgh which does exist. How can I tell qdec to look for the right qcached data? +glenn

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cortical thickness normalization
by Paul Greenberg 07 Jan '08

07 Jan '08

Dear Freesurfers, When comparing cortical gray matter volumes between groups it is appropriate to normalize subject's mean cortical volume in each cortical parcellation by their eTIV. Is there a corresponding value appropriate for normalizing cortical thickness? Would mean cortical thickness for a single hemisphere be an appropriate normalization factor? We are interested in comparing cortical thickness between a control group and a group of people with a degenerative brain disease. Thanks very much, Paul -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg(a)ucsd.edu

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(no subject)
by rohrer＠dementia.ion.ucl.ac.uk 07 Jan '08

07 Jan '08

We are having trouble posteriorly with delineating the pial and white matter surfaces in scans with lots of atrophy. I include 2 pictures which highlight the problem. We would greatly appreciate your opinion on dealing with this. best wishes Jon

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optseq2: "glibc detected" error?
by Sheeva Azma 04 Jan '08

04 Jan '08

Hello, I am trying to run optseq2 but i am getting an error message. Here is the command I use: optseq2 --ntp 160 --ev AL 4 16 --ev AR 4 16 --ev PL 4 16 --ev PR 4 16 --o AS --nkeep 12 --log ASfMRI --nsearch 10000 --psdwin 2 20 --tnullmin 2 --tnullmax 8 --tr 2 --sum ASfMRI-sum here is the error message: INFO: Setting srand48() seed to 614559 optseq2 $Id: optseq2.c,v 2.12 2006/12/29 02:09:11 nicks Exp $ NoSearch = 0 nSearch = 10000 nKeep = 12 PctUpdate = 10.000000 nCB1Opt = 0 seed = 614559 Ntp = 160 TR = 2 TPreScan = 0 PSD Window = 2 20 2 nEvTypes = 4 EvNo Label Duration nRepsNom 1 AL 4.000 16 2 AR 4.000 16 3 PL 4.000 16 4 PR 4.000 16 PctVarEvReps = 0 VarEvRepsPerCond = 0 PolyOrder = -1 tNullMax = 8 tNullMin = 2 outstem = AS AR1 = 0 No refractory penalty Cost = eff OutStem = AS Summary File = ASfMRI-sum nTaskAvgs = 36 INFO: LogFile is ASfMRI outstem = AS *** glibc detected *** free(): invalid next size (normal): 0x00000000005af3e0 *** Abort I have tried this on multiple machines and I have been getting the same type of error. Thanks in advance for any help - Sheeva FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.2-20080104 RedHat release: CentOS release 4.6 (Final) Kernel info: Linux 2.6.9-67.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: veles SUBJECTS_DIR: /space/perun/3/users/cylix/Subjects PWD: /space/veles/1/users/sheeva/AS-fMRI-stim

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Freesurfer January 2008