Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

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

Error in template initialization.
by Hui Zheng 23 Nov '09

23 Nov '09

Hi all, We have a problem in longitudinal processing. The mri_robust_template somehow chopped off a part of the brain (attached image). Any idea how to correct this? With this "partial" template, the longitudinal processing of phase 1 and 2 data were also wrong. This is the second subject I was checking. I hope it is not a common problem. I can provide the subject's data if necessary. Thanks, Zheng Hui

3 4

create volumes from surfaces
by Martin Ystad 23 Nov '09

23 Nov '09

Hi, I'm working on a fractal dimension analysis of the pial- and white-matter surface. The matlab script that calculates the fractal dimension needs binary nifti-files as input. Since FreeSurfer creates the surfaces I need, here's what I want to do: I'd like to convert the pial and white-matter surfaces (separately) to .nii-volumes (e.g. 256x256) where the voxels intersected by the respective surfaces are white, and everything else is black. Furthermore, I'd like to do this for individual subregions of each surface; for example only the precentral gyrus or the whole frontal lobe, so that only the voxels intersected by the surface belonging to the specific label I choose appear white, and everything else is black. How do I get this output from FreeSurfer? Thanks, Martin Ystad PhD-candidate, University of Bergen, Norway

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Freesurfer November 2009