Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

optseq2 and tnullmin/max
by Chapman, Hanah 09 May '12

09 May '12

Dear list, I have an optseq2 question, and would very much appreciate your time. I'm having difficulty calculating the required number of timepoints. I'd like to use --tnullmin and --tnullmax so as to have a null event in between each trial, with a duration of 4-8 sec. I have 16 conditions, 6 repeats/run, 2s trials, 2s TR. I computed that a run would need 16*6 = 96 timepoints for the trials. Then there would be 96 null events (to have one between each trial), so with an average 6s duration for nulls, a run needs 96*6/2 = 288 timepoints for the nulls, so 96+288 = 384 tp total. However, when I run optseq2 with these parameters, I still get nulls that are longer than 8s, and there is evidently extra time left over, since the last null event is 70 sec long. I'm using the following code: --ntp 384 --tr 2 --psdwin 0 20 --tnullmin 4 --tnullmax 8 --nkeep 6 --o outfile --nsearch 1000 \ --ev DD 2 6 \ --ev DF 2 6 \ --ev DP 2 6 \ --ev DN 2 6 \ --ev FF 2 6 \ --ev FD 2 6 \ --ev FN 2 6 \ --ev FP 2 6 \ --ev PP 2 6 \ --ev PD 2 6 \ --ev PN 2 6 \ --ev PF 2 6 \ --ev NN 2 6 \ --ev ND 2 6 \ --ev NF 2 6 \ --ev NP 2 6 I understand that the 4-8s range may be too tight, and relaxing it is not a big deal. However, I tried 4-10s, and still has the problems with nulls > 10s and extra time at the end. Thank you for your time, Hanah Chapman Postdoctoral Fellow The Ohio State University

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longitudinal study in counterbalance design
by lordowen 09 May '12

09 May '12

Hi all: We performed a thickness change study which related to the menstrual cycle. We scanned subjects during different menstrual phases in a counterbalance manner. Thus when we conduct a longitudinal analysis, we need to set time point according to the actual scanning order (i.e., 1st scan as Tp1 and so on) or according to the phase (i.e., menstruation phase as Tp1 and other phase as TpN)? Thanks for your suggestion. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Post Doctoral Research Fellow Integrated Brain Research Unit Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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file format of patch file (?h.full.patch.3d )
by Cris Lanting 09 May '12

09 May '12

Dear all, I'm trying to access and read a binary patch file (like ?h.full.patch.3d) rather than a converted ascii file. I've found a description of the lay-out of such a file at http://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats that in turn links to http://wideman-one.com/gw/brain/fs/surfacefileformats.htm: Patch File -Binary *Location (byte)* *Item* *Types* *Comment* 0 PointCount Int4 Count of points to follow (Updated 2003-07-06) ? + ?n vtx x y z Int4, Int2, Int2, Int2 vtx is special: (mris->vertices[k].border)?-(k+1):k+1; See below for explanation (Updated 2003-07-06) However, things may have changes over time and I was wondering whether the lay-out is still the same. It would really help if someone could indicate the (correct) order, type and size of the bytes in the binary patch file. I.e., it seems to start with a count of the number of vertices that constitute the patch (int4), followed by a vertex-index (int4), and the coordinates (x,y,z; each int2) for each of the vertices. What I don't know is how many bytes (and their type) are used to code each of those elements. Note that the description of the w-files (the output of mri_vol2surf) seems to be ok: W ("Weight") Format *Location (byte)* *Item* *Type* *Comment* 0 Latency Int2 2 Count Int3 Count of vertex-value pairs to follow 5 + 7n VertexNum Int3 5 + 7n + 3 VertexVal Float4 mris_convert uses %f I can read those in easily (although I have no idea what latency means...): Thanks! Cris Cris Lanting, PhD MRC Institute of Hearing Research Science Road, University Park Nottingham NG7 2RD Phone: +44 - (0)115 9223431 cris(a)ihr.mrc.ac.uk <ana(a)ihr.mrc.ac.uk>

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Entorhinal Cortex
by Alan Francis 09 May '12

09 May '12

Hi Imagers: Is there a command that will allow you to extract the volumes of the EC from the Entorhinal Ex vivo label ? I need to extract this in 77 brain scans. thanks ~ Alan BIDMC/ Boston

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Running recon-all fails during autorecon-2 -careg step
by Sarosh, Cyrus 09 May '12

09 May '12

I have run recon-all on multiple subjects and have had it fail at the same step every time with the same error. I am using VirtualBox with the provided Disk Image and Windows 7. 0560: dt=0.001750, rms=0.358 (0.039%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z GCAMwrite:: the popen error code is: 12 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Tue May 8 16:45:14 EDT 2012 /home/virtualuser/freesurfer/subjects/test/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test exited with ERRORS at Tue May 8 16:45:15 EDT 2012 Has anyone had this issue and resolved this problem? Thanks for your help. - Cyrus ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Entorhinal Ex vivo label
by Alan Francis 09 May '12

09 May '12

Hi Ruopeng: Is there a command that will allow you to extract the volumes of the EC from the Entorhinal Ex vivo label ? I need to extract this in 77 brain scans. thanks ~ Alan BIDMC/ Boston

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Reading thickness data
by Kevin Chen 09 May '12

09 May '12

Hi all, I'm new to FreeSurfer and I was wondering if there are any methods or software to read the ?h.thickness files and perhaps as a result get a list or table of all the vertices and their corresponding thickness? Also, is there a way to convert the vertex-based thickness files into voxel-based thickness data? Thanks in advance and best regards, Kevin

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Recon-all WARNING: tag image orientation not found
by Mary Ellen Koran 09 May '12

09 May '12

Hi, I'm getting the error WARNING: tag image orientation not found during the mri_convert step of recon-all. The log file is attached here. I am using version freesurfer_v.5.1.0 on Linux RHEL6. I am submitting a job to qsub (command lines in script FSscript3 attached). Any help would be greatly appreciated! Thanks!

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Error with recon-all
by Ed Gronenschild 09 May '12

09 May '12

Hi, I'm using the version of recon-all that Nick provided at April 17 to be able to run nu_correct prior to the Talairach stage. (I'm on a Mac, OSX 10.6, version v5.1.0). The command given was recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ -clean-tal -s subject. recon-all stopped and issued the following error: cp: ../surf/lh.orig_corrected: No such file or directory. Note that I included the option -no-wsgcaatlas to get a better skullstripping because in the default mode the skulltripping was bad. With this option it looks good. I got the above error regularly for other subjects as well and by including the -no-wsgcaatlas option recon-all finished without error, except for the present case. Cheers, Ed

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LongitudinalTutorial and long-tutorial dataset.
by Natacha Beck, Ms 08 May '12

08 May '12

Hi, I tried to run longitudinal analysis, I started by reading the LongitudinalTutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) In order to follow the tutorial, I downloaded the longitudinal tutorial dataset (long-tutorial.tar.gz) here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data. I uncompressed it in $FREESURFER_HOME/subjects. But I saw some symbolics links, for example: Mon May 07 user1 /Applications/freesurfer/subjects/long-tutorial =>find . -name "00*.mgz" -type l -ls 16661742 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/001.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/001.mgz 16661743 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/002.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/002.mgz ... 16678379 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/001.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/001.mgz 16678380 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/002.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/002.mgz My problem is that the target files do not exist. Is it a problem in the dataset ? or have I missed a step ? Thanks. Natacha Beck

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Freesurfer May 2012