Freesurfer January 2008

freesurfer@nmr.mgh.harvard.edu

54 participants
69 discussions

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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Checking for spikes
by Brittany Cassidy 06 Aug '08

06 Aug '08

Hello all, I was looking for a general way to check for spiking from Freesurfer or the FSFast stream. Any ideas are appreciated. Thanks! -Brittany

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documentation of the Freesurfer output and directory structure?
by Turner, Jessica 02 Jul '08

02 Jul '08

Hi experts-I have to document for some non-Freesurfer users what is in all the Freesurfer 3.05 subdirectories from an analysis. We have come up with a lot of it from the Wiki pages and tutorials, but there are some things that still aren't clear (what exactly is the bem directory for? What exactly is the mri_nu_correct.mni.log file? Etc.). Is it laid out clearly somewhere? I've seen the pages about which files are created by what process, etc. and it seems like it should say somewhere what these directories and files really are, I'm just missing it. Thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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spmregister-sess vs. autoreg-sess
by Tsung-Ren Huang 17 Mar '08

17 Mar '08

Dear Freesurfers, There seems to be two ways for functional/structural registration. One is spmregister-sess, and the other is autoreg-sess. What are the differences between these two scripts? Which one do you prefer to use and why? Thanks! Tren

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Matlab and Freesurfer
by Robert Baldwin 09 Mar '08

09 Mar '08

Hello- I am new to Freesurfer and Matlab. I have Matlab 7.4.0 installed on an Intel Mac. I just installed Freesurfer. Now when I start Matlab I get the following warnings: Warning: Name is nonexistent or not a directory: /matlab. In path at 110 In startup at 4 In matlabrc at 255 Warning: Name is non existent or not a directory: /toolbox. In path at 110 In startup at 11 In Matlabrc at 255 I have tried adding the freesurfer folder to these files to the path for matlab, but the error still occurs. Any suggestions on how to get this error to quit? Thanks! -Robert

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Problem make_average_subject
by Juergen Haenggi 19 Feb '08

19 Feb '08

Dear FS experts I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error: [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% I set the descriptor limit to 4096, but the make_average_subject command will not start anymore. Any idea what is wrong here? Thanks in advance 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) -----------------------------------------------------------

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alloc: invalid block
by George He 31 Jan '08

31 Jan '08

Hi, I am following the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OverlayFeatStatisticalM… At this command, tksurfer bert lh inflated -overlay ./fbert1.feat/stats/zstat1.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot tksurfer runs OK but when I click on any button between "show curvature" and "draw outlined labels", it crashes and gives this error: % alloc: invalid block: 0xbb6c80: 0 0 0 Here is the section copied from bugr output: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/packages/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 RedHat release: Fedora release 8 (Werewolf) Kernel info: Linux 2.6.23.9-85.fc8 x86_64 --------------------------------------------------------------------- any suggestions how to correct this? Thanks, George

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displaying the result of group analysis in thickness or p-value
by Woo-Suk, Tae 30 Jan '08

30 Jan '08

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear FreeSurfer experts.I have finished the FreeSurfer analysis using (version 3.04) in the patients with depression.But, the result using qdec was displayed only in T-value.I'd like to know how can I display the result of group analysis in thickness (mm) and statistical p value.Best regards.Woo-Suk, Tae Ph.DChucheon, Korea

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recon-all error @ mris_volmask...
by Cameron Ellis 30 Jan '08

30 Jan '08

Hi, I am receiving this error for every subject I send through recon-all. I am checking for edits that need to be made but it seems very odd that 30 subjects or so would all error out at the same step. Any suggestions? Cameron Subject 'Ponce_033d2': make all recon-all -s /autofs/space/grouch_004/users/ponce/Ponce_033d2 -hemi lh -cortribbon INFO: SUBJECTS_DIR is /autofs/space/grouch_004/users/ponce Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/stable4 -rw-rw-r-- 1 cameo zenuwgp 1257898 Jan 29 17:38 /autofs/space/grouch_004/users/ponce/Ponce_033d2/scripts/recon-all.log Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Cortical ribbon mask Wed Jan 30 11:41:19 EST 2008 /autofs/space/grouch_004/users/ponce/Ponce_033d2/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance Ponce_033d2 Segmentation fault Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Jan 30 11:41:42 EST 2008

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Aseg.stats file
by Jared Conley 30 Jan '08

30 Jan '08

FreeSurfer Community, Is there an easy, quick way to regenerate the aseg.stats file? This particular file was deleted accidentally for a few subjects and we wondered if we could quickly recreate this file without having to run recon-all again. All the other files in the subject directory are present. Thanks in advance, Jared

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Freesurfer January 2008