Freesurfer August 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
75 discussions

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

qdoc BadMatch error
by Andrew Reid 17 Sep '07

17 Sep '07

Hi, Just installed version 4.0.0 and tried to execute qdec. When I do so I get the following error. Any ideas what it means and how to remedy it? Reading /home/typically/freesurfer/lib/tcl/tkUtils.tcl Using /home/typically/freesurfer/lib/tcl/fsgdfPlot.tcl X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 66 (X_PolySegment) Serial number of failed request: 4721 Current serial number in output stream: 4724 I am using Ubuntu Fiesty. Thanks in advance, Andrew Reid Department of Neurophysiology and Neuroinformatics UMC St. Radboud Nijmegen, The Netherlands

3 2

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

4 5

New Freesurfer v4.0.0
by Nick Schmansky 04 Sep '07

04 Sep '07

A new version of Freesurfer is now available for download from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download The list of new features, bug fixes, and known issues is found on the ReleaseNotes page: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Users are reminded that in general, subjects should be processed by a single version of Freesurfer (ie. in a group study, subjects should not have been processed by different versions of Freesurfer). Older versions of Freesurfer are available upon request. The Freesurfer Team.

6 16

?h.volume vertex-wise
by Juergen Haenggi 30 Aug '07

30 Aug '07

Dear Freesurfer users We would like to analyze cortical volumes vertex-wise. We recognized that ?h.volume are not produced by the recon-all command. I have read the questions posted some days ago by Rafael Huber concerning the same problem. One proposed solution was to multiply ?h.area times ?h.thickness at each vertices. To do this read_curv.m and the write_curv.m functions in MATLAB were suggested. We tried it but failed maybe due to our insufficient knowledge in MATLAB programming. The first step (read_curv.m) works and produced a vector of curvature (small negative values) instead a vector of thickness (positive values between 1.5 and 3.5 mm) as we expected. What happens here? The command write_curv.m does not work at all. Is there any short documentation about multiplying images in MATLAB? We appreciate any suggestions about that issue. 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) -----------------------------------------------------------

2 1

xform avesurf-> subject
by Kirk, Gregory 29 Aug '07

29 Aug '07

Hi All, I want to click on a point on my average surface for my group and ' save point' load a T1 or orig subject in the group with tkmedit and 'goto saved point' i.e. map by the inverse of the transform that embeded the subject surface into the average surface and see the point on the structural that mapped to it. Seems I remember this can be done, I have to load a transform I think. looked through the docs and mail archive but perhaps I was not thinking of the best key to search the archive. thankx Greg.

2 1

resampling thickness
by Goldman, Aaron (NIH/NIMH) [C] 29 Aug '07

29 Aug '07

Hi, for a group of subjects, I was interested in getting ascii files for each subjects' thickness, resampled to an average subject. I know how to do the resampling using something like: mris_preproc --fsgd fsgd.txt --target average --hemi lh --meas thickness --out file.mgh but was wondering what I'd need to do to get individual files that can be read by a text editor, rather than the one big mgh file. Is there some kind of flag or subsequent command I can add to do that? Thanks, -Aaron-

2 1

ReconAllDevTable Q.
by Jamie Hanson 28 Aug '07

28 Aug '07

Which version of Freesurfer is the ReconAllDevTable on the wiki for? Is it for v.3.0x or v.4.0? ... has anything changed in that regard for v.4.0? jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 Phone: (608) 262-5148 ***Please note my new email: jamielarshanson(a)gmail.com***

2 1

Standard deviation map
by Inês Souta 28 Aug '07

28 Aug '07

Hello, After computing the average thickness of an average subject (prior to Qdec), how can I estimate and get a map of standard deviations of the thickness measures across the subjects I've averaged. Thanks, Ines

2 1

TICV references of Freesurfer
by Woo Suk, Tae 28 Aug '07

28 Aug '07

Dear Freesurfer developers. I'd like to know the detail process of total intracrainal volume (TICV) measurement by Freesurfer. Would you recommend the directly or indirectly related articles on TICV measurement? Woo Suk, Tae Seoul, Korea

2 1

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Freesurfer August 2007