Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Matching slice location in dicoms to the .mgz format
by Trina Kok 04 Apr '07

04 Apr '07

Hi all, I have a question on matching slice location between dicoms and the freesurfer output. I have a set of 120 dicom files and I ran it through the autorecon process in freesurfer. From the viewer with tkmedit, there are 180 files (slice 218 to 39 in trans view) that corresponded to scanning, i.e. with some image scanned. I think the rest of the 256 slices are interpolations, but how does the 180 slices map to the 120 dicom files? I'm asking because I am trying to map a dicom file with a specific slice location to the .mgz images. Thank you. Regards, Trina

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Freesurfer and R
by Glenn Lawyer 04 Apr '07

04 Apr '07

Hi, I'm also using R to look at some FreeSurfer data, mostly to play with significance values. To do this, I convert them to ascii (mris_convert) and load them into R with the read.table function. When I am done, I write a new ascii file, mris_convert it back to a *.w or *.sig, and load it into tksurfer. The function to write the file is trivial, but here it is for completeness: ## more FreeSurfer specific stuff. ## the modified significance values in a text file called "fdr.txt" ## posindex is a global variable tracking which pvalues were ## positive in the original sig file ## (recall that FS stores sig values as log10(sig), with the ## sign indicating direction of effect) ## vindex is a global variable tracking the vertex number ## associated with a given sig value write.fs.output <- function(){ fdr <- dget('fdr.txt') fdr <- log10(fdr) fdr[posindex] <- fdr[posindex] * -1 cat("0.000\n", length(fdr), "\n", file="AA-TT_cmfdr.ascii") for (i in 1:length(fdr)){ cat(vindex[i], fdr[i], "\n", sep="\t", file="AA-TT_fdr.ascii", append=TRUE) } } -- -------------------------------------- I'm only in it for the glory . + Glenn Lawyer + + +352 661 967 244 + + Instituttgruppe for psykiatri + + Seksjon Vinderen + + PB 85 Vinderen + + 0319 Oslo + + http://folk.uio.no/davidgl + +++++++++++++++++++++++++++++++++++:)

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segmentation fault during autorecon 2
by Mithra 03 Apr '07

03 Apr '07

Hello FS Group, I get "segmentation fault" error during autorecon2 step. I checked the talairach transformation. It seemed to be fine. The skull strip did not seem to be correct. I manually edited the brainmask.mgz and saved the data. But still I get the error. I am not sure what the problem is. Any help would be great! I have the output form mri_info for the original surface. . Thanks. Mithra. Output for mri_info: mri_info $SUBJECTS_DIR/asm1_004/mri/orig.mgz Volume information for /usr/pubsw/freesurfer/subjects/asm1_004/mri/orig.mgz type: MGH dimensions: 301 x 301 x 301 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 301.000 xstart: -150.5, xend: 150.5 ystart: -150.5, yend: 150.5 zstart: -150.5, zend: 150.5 TR: 4.97 msec, TE: 1.21 msec, TI: 500.00 msec, flip angle: 11.00 deg rees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 40.3653 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -26.5037 talairach xfm : /usr/pubsw/freesurfer/subjects/asm1_004/mri/transforms/talairach .xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 150.5000 0.0000 0.0000 1.0000 -110.1347 0.0000 -1.0000 0.0000 123.9963 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 150.5000 -0.0000 -0.0000 -1.0000 123.9963 0.0000 1.0000 0.0000 110.1347 0.0000 0.0000 0.0000 1.0000

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FreeSurfer & R
by Alessandro Gagliardi 03 Apr '07

03 Apr '07

Hello Emily and other FreeSurfer useRs, I'm having trouble getting data out of R and back into FreeSurfer and I was wondering how you did it. The tksurfer doesn't seem to like the .img files that the AnalyzeFMRI package produces (perhaps because it doesn't have a .mat file to go with it). I've tried to convert ascii files into Analyze and MGH files using mris_convert, but tksurfer doesn't like those either. Any help would be greatly appreciated. Thanks! -- Alessandro Gagliardi Integrative Neuroscience Program Rutgers University Mind Brain Analysis alessandro(a)gagliardi.name

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Freesurfer and FSL integration
by Frederick Powell 03 Apr '07

03 Apr '07

I would like to run FSL and Freesurfer on my Linux compter. I have noticed that within Freesurfer I have a FSL directory. I have also visited the FSL website and noticed an entire downloadable version of FSL. I would like to be able to use my structural MPRAGE images that I have analyzed in Freesurfer and combine them with DTI images for ROI tractography and FA calculations. Do I need to download the version of FSL from the website? Secondly how should it be sourced so that FSL and Freesurfer are able to run together ( will I encounter any binary issues)? If you could respond with details. I am a novice to installing programs using a Linix machine. I am specifically talking about how to source the program and get it up and running. Thanks -- Frederick G. Powell

2 1

recon-all failing from script
by Martin Kavec 03 Apr '07

03 Apr '07

Hi, I am trying to further script (Bash) the autorecon1 and subcortseg. The script just sets the path to the received dicom data, gets some info from the dicom header and starts the autorecon1 followed by subcortseg. The things work well when executed from the command line, but if I execute the script from another script, I get the following error during autorecon1: mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.23434/src.mnc transforms/talairach.auto.xfm Use of uninitialized value in join or string at /opt/freesurfer/mni/bin/mritotal line 462. mritotal: Couldn't find configuration file mritotal.cfg anywhere in :/opt/freesurfer/mni/bin/../etc/mni_autoreg ERROR: mritotal failed, see transforms/talairach.log Thanks for help in advance. Martin

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skull strip for monkeys
by Paul Aparicio 02 Apr '07

02 Apr '07

Hello All, I am having a very difficult time getting skullstrip to work on my monkey anatomical data set. Are there any suggestions on how to get it to work properly? Thanks in advance Paul

2 1

freesurfer & nohup
by Istvan Akos Morocz 02 Apr '07

02 Apr '07

does anybody know if FreeSurfer can be run in combination with the unix command 'nohup' like: nohup recon-all -autorecon-all -subjid fs & so that one is able to logout after beginning of the process without halting all computation ? thanks, bye, pisti ----- pisti(a)bwh.harvard.edu

2 2

autorecon1 failures
by Derin Cobia 02 Apr '07

02 Apr '07

Two questions for two different subjects during autorecon1: 1. The initial skull strip on this subject left too much extra-cerebral material. Subsequent attempts at using the wsatlas or manual adjustment of the wsthresh have resulted in this error: *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 1960516 Find the largest 110-component...mriSegmentReallocateVoxels: could not alloc 1048381 voxels for sno 8343 Cannot allocate memory done And identify it as the main brain basin...Segmentation fault Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Apr 2 15:02:05 CDT 2007 #-------------------------------------------------------------- Are there too many voxels? I've looked, but couldn't find any information on how to fix this one. 2. This subject continues to fail with errors during intensity normalization. Here is the output: #-------------------------------------------- #@# Intensity Normalization Mon Apr 2 15:46:47 EDT 2007 /disk/conte_raid1/freesurfer/conte_mprage/021219_5734/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.830 -0.117 -0.004 -3.656; 0.116 0.833 -0.323 -26.577; 0.004 0.028 0.075 84.152; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Apr 2 15:46:49 EDT 2007 #--------------------------------------------- I've checked the talairach.xfm and it is bad. It seems I remember someone on the list saying that a -nold flag could fix this, but I couldn't find any info on the wiki about it. Any suggestions? Can I still salvage this subject? Thanks for all of your help! -Derin

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control points
by lgutierrezg＠comz.org 02 Apr '07

02 Apr '07

How often do you use control points to fix white matter? Because I do not have clear when I have to use it, despite I have read the example in the website. Thanks Best Regards Leticia Gutierrez

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Freesurfer