Freesurfer February 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
87 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

2 4

CentOS 5.1 and freesurfer and tksurfer
by tulu＠ms36.hinet.net 06 Mar '08

06 Mar '08

Dear FS experts, I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I start tkmedit, it looks fine. In tksurfer, it just appear a sliver of surface without error message. In console, it stock on reading vertex. Is there anyway to correct it ? Thanks replay Kl chen

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finding WM hypointensities
by Thomas Doering 04 Mar '08

04 Mar '08

Hello, i wonder if there is a possibility to identify the recognized WM hypointensities with tkmedit - something like labeling the WM hypointensities. Thanks for help, Thomas

3 2

RE: annotation binary files into ascii format
by Teddy Youn 01 Mar '08

01 Mar '08

Hi everyone, Thanks again for your help from my previous query. I had a question about how to convert the binary format of the annotation file to ascii format, similar to using mris_convert to surface files from binary to ascii. Is there an equivalent program that does the same thing for annotation files? Thanks very much, -Teddy Youn Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

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question about moving from freesurfer to afni and keeping registration
by Jena B. Hales 29 Feb '08

29 Feb '08

2 1

Qdec "map label to subjects" error
by nels5614＠umn.edu 29 Feb '08

29 Feb '08

Hello, I have a question in regards to the "map label to subjects" feature in Qdec. Basically, I draw and save a label, and then try to map the label to all of the subjects in my SUBJECTS_DIR, but while running mri_label2label, I get this error: > ERROR: there is a vertex in the label that cannot be matched to the > surface. This usually occurs when the label and surface are from > different subjects or hemispheres or the surface has been changed since > the label was created. Label point 7: vno = 166358, max = 163842 command > failed: mri_label2label --srclabel > /home/bfs-raid1/ryanm/FREESURFER/142_FAE2_blade/v4/freesurfer-from-blade/qdec/lh.parahippocampal_cp --srcsubject fsaverage --trgsubject 18208 --trglabel /home/bfs-raid1/ryanm/FREESURFER/142_FAE2_blade/v4/freesurfer-from-blade/qdec/lh.parahippocampal_cp --regmethod surface --hemi lh I have three groups I am trying to compare, 2 proband groups, and 1 control group. So, I constructed separate .dat files and label files for each- one comparing controls vs. group1, and the other comparing controls vs. group2. I seem to be able to run analyses fine on the data, I am just having problems with the "map label to subjects" feature. The order in my .dat files does differ from the order of datasets in my SUBJECTS_DIR, I don't know if this has anything to do with my error. Any advice/suggestions would be greatly appreciated. Thanks! Miranda Nelson

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Freesurfer February 2008