Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Freesurfer error: Load Time Course causes abort
by raij＠nmr.mgh.harvard.edu 14 Sep '07

14 Sep '07

Hi guys, On machine inv (more or less the same error on machine ai) nmr-dev-env (same error on nmr-std-env) cd /space/cuzco/2/users/raij/avml_fmri_mctogether/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT fsaverage tksurfer fsaverage lh inflated -overlay avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr -timecourse avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr Output: surfer: current subjects dir: /space/cognito/5/users/raij/subjects_mri/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/cuzco_002/users/raij/avml_fmri_mctogether surfer: Reading header info from /space/cognito/5/users/raij/subjects_mri//fsaverage/mri/T1.mgz reading group avg surface area 822 cm^2 from file surfer: vertices=163842, faces=327680 INFO: bvolumeRead: min = 0, max = 0 *** glibc detected *** corrupted double-linked list: 0x00000000060b7db0 *** Abort Oddly enough, on machine ai, if I leave out the -timecourse part of the command line, the FreeSurfer window opens with the correct overlay and I can scroll through conditions and time points. Further, if I then manually load the timecourse from File/Load Time Course... menu, this works giving the time course display just as it should Even more oddly, on machine inv (which is spanking new and has lots of RAM etc) even the above basic command line with only loading the overlay gives the above glibc error. I have 8 subjects * 66 labels = timecourses of 528 labels to extract, which makes this clearly a script job - the only practical solution would be to find a way to make the command line work. Suggestions? For example, could it be that this has something to do with nvidia drivers? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Possible to pass 2 identical analyses but with different names to intergroupavg-sess?
by Dan Dillon 13 Sep '07

13 Sep '07

Dear FreeSurfers, I have two groups (patients vs. controls) whose data I'd like to compare using intergroupavg-sess. Here's the problem: I ran identical analyses on the two groups, but they were named differently (e.g., "control_analysis" vs "patient_analysis"). Is there a way to run intergroupavg-sess without having to either re-name or re-run one of these analyses? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:dillon@wjh.harvard.edu> dillon(a)wjh.harvard.edu

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New Neuroscience Forum
by Toby Fernsler 12 Sep '07

12 Sep '07

Hello World, Announcing a new neuroimaging-specific forum as well as a data analysis and programming consulting business, at http://neuroimagingnetwork.com/ ABOUT THE FORUM The forum is intended to be an informal central site for neuroimaging researchers and professionals to discuss and troubleshoot the various software and hardware they use, as well as announce and discuss workshops, meetings, jobs, sell used lab equipment, etc. It is a modern, versatile forum running on vbulletin and hosted on a high- bandwidth VPS by HostICan, who have a 99.9% average uptime rating. Forum Organizational Highlights: * Forums for troubleshooting and discussing each software and hardware product, such as FreeSurfer and Net Station. Don't see your software? Let me know and I'll add it. * Forums for upcoming meetings, job postings, grant opportunities, lab equipment resale, etc. Forum Technical Features: * Customizable login allows for creation of an avatar (icon to represent yourself), fields to describe yourself, attach a picture, provide contact information and enter your CV/Resume. * Advanced search capabilities allow you to search by forum, thread, author, etc. * Social features allow you to see who is logged in (and login anonymously), message them, and make buddy and ignore lists. * Subscribe to forums and threads and receive email notification of new posts. * Threads can be moved, moderated, edited, closed etc. * It's pretty. Please check it out at: http://neuroimagingnetwork.com/forums/ I will of course be participating in discussions and answering questions, and as a former developer of EEGLAB, a mathematician and Matlab expert I will provide better-than-average responses on those topics. If you happen to want more detailed assistance I have... ABOUT FERNSLERSERVICESLLC This is my consulting/contracting business for assistance/analysis with EEGLAB as well as other data-mining, mathematical, programming, and neuroscience-related tasks. Troubleshooting and debugging. Order up a program and I'll write it. Send me your data and I'll tell you what's interesting about it in nice graphics and down-to-earth language. You may find details about rates and services here: http://neuroimagingnetwork.com/fernslerservicesllc/index.html Thank you for your attention. Hope to meet you on the forum! Toby Fernsler

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recon-all flags -normalization2 and -maskbfs
by Greg Harris 12 Sep '07

12 Sep '07

Dear FreeSurfers, I am trying to be a user of 'recon-all -make all'. The method stops when it attempts the step 'recon-all -s $(subj) -hemi lh -finalsurfs'. The problem at that point is that the file mri/brain.finalsurfs.mgz does not exist. The command to create this file, the only possible command if we go through rec on-all, is 'recon-all -s $(subj) -maskbfs'. Doing this command by hand after the error permits a repeated 'recon-all -make all' command to continue happily. One plausible place to fix this is in bin/recon-all.makefile, at or about line 83-84: $(BRAIN): $(BRAINMASK) $(NORM) recon-all -s $(subj) -normalization2 recon-all -s $(subj) -maskbfs i.e. add the step for making the brain masked brain.finalsurfs.mgz file after the -normalization2 step. Would this be correct, and should I do this or something like it? Sincerely, Greg

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error.. help?
by Britni Crocker 12 Sep '07

12 Sep '07

after autorecon2, I sometimes get this error: preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: nan +- nan [100000.0 --> -100000.0] GM: nan +- nan [100000.0 --> -100000.0] mri_segment: class statistics not finite - check input volume! Linux theta.cis.jhu.edu 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:30:58 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Sep 5 15:49:00 EDT 2007 how do i fix this? britni _________________________________________________________________ Kick back and relax with hot games and cool activities at the Messenger Café. http://www.cafemessenger.com?ocid=TXT_TAGHM_SeptHMtagline1

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FW: [Freesurfer] ?h.volume files
by Juergen Haenggi 12 Sep '07

12 Sep '07

Dear Bruce, dear Freesurfer users Thanks a lot for the advice. But when using mri_concate in order to average the volumes, there is the following error: "Error: dimension mismatch" between the lh.volume files of the subjects. We used following syntax: [thickness, f] = read_curv('lh.thickness') ; [area, f] = read_curv('lh.area') ; volume = thickness .* area; write_curv('lh.volume', volume, nfaces); mri_concat --i Subjects_*_Kopie/surf/lh.volume --o average_lh_volume --mean ERROR: dimension mismatch between Subjects_Control01_Kopie/surf/lh.volume and Subjects_Control02_Kopie/surf/lh.volume Thanks in advance Best regards Juergen On 11.9.2007 23:24 Uhr, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > read_curv will return that also: > > [thickness_vector, nfaces] = read_curv('lh.thickness') ; > > I'm a bit worried that you have a dimension mismatch. That shouldn't > happen. > > Bruce > > > On Tue, 11 Sep 2007, Juergen Haenggi, > Psychological Institute wrote: > >> Dear Freesurfer users >> >> I computed ?.volume files by using several commands sent by Bruce. Instead of >> using the save_mgh.m command, which not really worked because there was a >> dimension mismatch later when using mri_concat, we used write_curv.m. I need >> the number of faces in the surface to write ?h.volume files. Where can I get >> these numbers? Is it the file called f created in the Matlab current >> directory after running read_curv multiplying area times thickness, and >> write_curv? >> >> Thanks in advance >> Best regards >> Juergen Haenggi >> >> ------------------------------------------------- >> 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) ----------------------------------------------------------- ------ End of Forwarded Message

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Spherical ROIs areas in the fsaverage
by jorge luis 12 Sep '07

12 Sep '07

Hello all I have made changes in the thickness values in some regions of a left hemisfere of a subject surface after mapped it onto the fsaverage sphere. The changes were made to have areas close to these in the left colum of the following table: My area Freesurfer number of vertices 20 mm2 27.88 mm2 (37) 30 mm2 35.09 mm2 (47) 40 mm2 39.17 mm2 (52) 50 mm2 56.89 mm2 (76) 60 mm2 44.05 mm2 (59) I computed the region areas in the fsaverage surface by adding the areas of the triangular faces inside these regions using the spherical coordinates of the vertices and the Heron formula for the triangle area. The freesurfer sphere mapping is based in minimal metric distortion, so, why the freesurfer computed areas for these regions are different(the second column in the table)? In both cases the same surface vertices were found to be inside of the regions (the third column in the table) I would like to have more insight on how freesurfer compute the area of a given ROI in the fsaverage spherical surface. In advance thank you ____________________________________________________________________________________ Sé un Mejor Amante del Cine ¿Quieres saber cómo? ¡Deja que otras personas te ayuden! http://advision.webevents.yahoo.com/reto/entretenimiento.html

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Segmentation Probability Values
by James N. Porter 11 Sep '07

11 Sep '07

Hello FreeSurfers- At any point in the recon-all processing stream does a voxel by voxel map of segmentation probability values get generated? If not, are that at all obtainable through post-processing methods? -- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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?h.volume files
by Juergen Haenggi, Psychological Institute 11 Sep '07

11 Sep '07

Dear Freesurfer users I computed ?.volume files by using several commands sent by Bruce. Instead of using the save_mgh.m command, which not really worked because there was a dimension mismatch later when using mri_concat, we used write_curv.m. I need the number of faces in the surface to write ?h.volume files. Where can I get these numbers? Is it the file called f created in the Matlab current directory after running read_curv multiplying area times thickness, and write_curv? Thanks in advance Best regards Juergen Haenggi ------------------------------------------------- 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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Fwd: Re: [Freesurfer] Average Volume
by Rafael Huber 11 Sep '07

11 Sep '07

---------- Forwarded message ---------- From: Rafael Huber <rafael(a)huberworld.ch> Date: 11.09.2007 09:19 Subject: Re: Re: [Freesurfer] Average Volume To: Doug Greve <greve(a)nmr.mgh.harvard.edu> Hy Doug, Thank you for your help. I tried to do it with your advice, but when i runned "mri_concat --i SUBJECTS*/surf/lh.volume.mgz --o lh.volume --mean" i always got an error message called "ERROR: dimension mismatch between SUBJECT1/surf/lh.volume.mgz and SUBJECT2/surf/lh.volume.mgz". I created all the volume.mgz files in the same way in matlab. Do you have an idea? Thanks in advance. Best Regards Rafael 2007/9/4, Doug Greve <greve(a)nmr.mgh.harvard.edu>: > > Try following the instructions for doing a thickness study, ie, run > mris_preproc specifying lh.volume.mgz as the measure, then run either > mri_glmfit with --osgm or run mri_concat with --mean. > > doug > > > > > On Mon, 3 Sep 2007, Rafael Huber wrote: > > > Our goal is to get a file of average volume. As i understand the make > > average command it takes the whole information of e.g. ?h.thickness > > out of every /surf folder of every subject and creates an average > > ?h.thickness file and saves it to /average/surf. i try to do the same > > with the ?h.volume.mgz files, which we created with the matlab command > > you proposed us. we made it as far that we have two ?h.volume.mgz > > files in each subjects surf folder and we would like to continue the > > group analyses process. > > > > > > Hi Rafael, > > > > sorry, I don't understand. What do you mean " Problems appeared later > > on, because we didn't find a difference in the average folder compared > > to using the command without lh.volume.mgz files in the surf folder." > > What problems? What kind of differences are you looking for and how? > > > > Bruce > > > > > > On Mon, 3 Sep 2007, Rafael Huber wrote: > > > > Dear freesurfer users > > > > Do you have an idea how to create an average ?h.volume file? > > > > Our goal is to create a file with average volumes for our subjects, to > > follow the group analysis. We know that the idea of using a volume > > measure isn't implemented in the freesurfer software. We runned the > > make_average_subject command in hope to find something like an > > ?h.volume file in the average folder as there are files for the other > > measures like thickness, area, curvature. > > Before we runned the make_average command we followed the advice of > > Bruce Fischl to create .mgh files in matlab with the following > > command: > > > > [thickness, f] = read_curv('lh.thickness') ; > > [area, f] = read_curv('lh.area') ; > > volume = thickness .* area; > > save_mgh(volume, 'lh.volume.mgz', eye(4)); > > > > This functioned very well and we got our lh.volume.mgz files in the > > surf folder. Problems appeared later on, because we didn't find a > > difference in the average folder compared to using the command without > > lh.volume.mgz files in the surf folder. We're now not sure if we > > should continue like normal, or what exactly to do. Has somebody an > > idea. > > > > Best regards > > > > Rafael Huber > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > 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 > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Rafael Huber Student Division of Neuropsychology Institute of Psychology University of Zurich

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