Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Recon-all -long
by Jürgen Hänggi 25 Nov '09

25 Nov '09

Dear FS experts Am I right that the input for step 3 in recon-all -long are the already cross-sectionally processed images from step 1 and not the raw images that I used to create these cross-sectionally images? Thanks for clarification Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division 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[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 1

talairach failure
by Ritobrato Datta 24 Nov '09

24 Nov '09

Hello All, I ran recon-all on a subject and got the following error -------------------------------------------- talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Nov 19 16:17:54 EST 2009 /jet/subjects/MC/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) recon-all exited with ERRORS at Thu Nov 19 16:17:55 EST 2009 =======================END LOG FILE======================= The brain is quite rotated from upright alignment, which is likely the problem. Any suggestions on how to do it or whether I should ? Thanks Ri

1 0

convert/reconstructing with mrdc
by Jesse Bledsoe 24 Nov '09

24 Nov '09

Hello, So far I have had no problems running recon-all with .mnc files but could use some guidance converting/reconstructing brains processed with AFNI (MRDC). There are 120 MRDC files in the T1 directory. I believe I need to run mri_convert on these MRDC files but am unsure of what the correct command would be? Thanks in advance, Jesse

2 1

qdec.table.dat
by Matt Warner 24 Nov '09

24 Nov '09

Hi, I am trying to run qdec for group analysis of subcortical and cortical volumes. I have all of my data in an excel sheet (subject ID, age, gender, volumes of various structures) and am trying to convert this into a file that will be able to be opened in qdec. I use a Mac, and I have exported the sheet into text-edit and then resaved it as "qdec.table.dat". This .dat file opens perfectly in text-edit. However, when I go to load the table into qdec it gives me an error: "error loading the data table" Is the dat file I created not compatible with qdec? If so, is there another way in which I can transfer my data into a dat file? Thank you very much in advance for your help, Matt

2 2

memory error 2
by Gonzalo Rojas Costa 24 Nov '09

24 Nov '09

Hi: I got the following fatal error: CORRECTING DEFECT 61 (vertices=98413, convex hull=24013) Excessive topologic defect encountered: could not allocate 896316630 edges for retessellation Cannot allocate memory Linux image 2.6.28-16-generic #55-Ubuntu SMP Tue Oct 20 19:48:24 UTC 2009 i686 GNU/Linux How can I correct it ?... I have a PC with 2.5 GB RAM, and iit is the first processing that fails with an error related to memory... Why ?... Is it really a memory problem ?... There is a tip and trick that allows me to correct it ?... Sincerely, Gonzalo Rojas Costa

2 2

memory error
by Gonzalo Rojas Costa 24 Nov '09

24 Nov '09

1 0

sup temporal plane 3-D view (Neuroimage 2006)
by Oya, Hiroyuki 24 Nov '09

24 Nov '09

Dear Freesurfer, I am impressed with 3d-view of the supra temporal lobe in your Neuroimage(2006) paper (fig2). I am also trying to create such 3d view of supra temporal plane. If you could tell me the procedure to create it, that would be greatly appreciated. Thanks. Hiroyuki Oya

2 1

segfault from freeview.bin
by Mark J. Pearrow 23 Nov '09

23 Nov '09

Hi all, We are consistently getting segfaults with core dumped from freeview.bin when trying to open MGZ files that are larger than some (undetermined) threshold. We are running the 4.5.0 CentOS 4 x86_64 binary package on Ubuntu 9.04 Workstation. Upon opening freeview and attempting to load one of the larger files, the application crashes and dumps core, and leaves the following in the error.log: CTABreadASCII(/u2/meeshy/Desktop/Amy Activation Screenshots/SAD_022/lh_Novelobjects_social/EFvNF.png): badly formed file mghRead: encountered error executing: 'zcat /u2/meeshy/Desktop/I29/flash20_100um_avg_rotatedKH11112009_mfg_new.mgz',frame -1, errno 12 mghRead: encountered error executing: 'zcat /u2/meeshy/Desktop/I29/flash20_100um_avg_rotatedKH11112009_mfg_new.mgz',frame -1, errno 12 (running that same zcat command from the command line works fine) Loading the resulting core into gdb: meeshy@ba7:~$ gdb `which freeview.bin` ./core [mumble mumble reading symbols] ... Core was generated by `freeview.bin'. Program terminated with signal 11, Segmentation fault. [New process 2415] #0 0x00007f1c91defcd0 in ?? () from /usr/lib/libGL.so.1 (gdb) list 1 /usr/pubsw/packages/vtk/5.2.0/src/Utilities/DICOMParser/DICOMFile.cxx: No such file or directory. in /usr/pubsw/packages/vtk/5.2.0/src/Utilities/DICOMParser/DICOMFile.cxx (gdb) bt #0 0x00007f1c91defcd0 in ?? () from /usr/lib/libGL.so.1 #1 0x00007f1c91de430f in _fini () from /usr/lib/libGL.so.1 #2 0x00007f1c9257f354 in ?? () from /lib64/ld-linux-x86-64.so.2 #3 0x00007f1c89f2d6ed in exit () from /lib/libc.so.6 #4 0x00007f1c89f155ad in __libc_start_main () from /lib/libc.so.6 #5 0x00000000005b89ea in _start () These are around 250MB in size. Smaller files load just fine. mjp

2 1

bias field compute & apply
by Chris Hyatt 23 Nov '09

23 Nov '09

Hi, In a recent Freesurfer mailing list question, someone asked how they could correct temporal lobe intensity normalization problems for a large number of subjects without having to add control points for every subject (very time consuming). The recommendation from Bruce Fischl was: " One thing you can try if the patterns of loss are stereotyped is to take 10 or 20 subjects or so and correct them by adding control points, then use mri_compute_bias to compute the common component of the bias field. You can then apply that to the other subjects in your study with mri_apply_bias. Nick can probably suggest a good way to slot this into the recon-all process" From, the command line, the usage of mri_compute_bias is: mri_compute_bias [options] <subject 1> <subject 2> ... <output volume> But what are the [options], if any? Next, the bias field output volume <bias_vol>, in MGH format I presume, is then applied to each subject as follows mri_apply_bias [options] <input_vol> <bias_vol> <output_volume> Again, are there any options here? Also, what should be the input_vol (e.g., brainmask.mgz, T1.mgz) and output volume name? Lastly, has Nick suggested a good way to 'slot this into the recon-all process', as yet? I'm having many of the same temporal lobe intensity normalization problems as other folks and want to avoid adding controls points to hundreds of T1 images. Thanks for your help. Chris

2 1

running my own data
by Mark.Gay＠unlv.edu 23 Nov '09

23 Nov '09

1 0

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