Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

viewing group analysis results
by Chacko Cherian 06 Apr '07

06 Apr '07

Hello users, I am doing the group analysis stats results...using FDR correction 0.01 and checking the pial surface with curvature and overlay. I see this line come up whenever i change the FDR..is this some kind of error which I need to be concerned about? surfer: Error sending tcl command OverlayLayerChanged: bad window path name ".fsgdf-0" Thanks in advance. Regards Chacko. ____________________________________________________________________________________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097

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Re: Freesurfer and R
by Alessandro Gagliardi 05 Apr '07

05 Apr '07

I ended up trying a bit of a hack, and it seems to have worked, but I don't know if I can trust it. I used the AnalyzeFMRI package in R to output my data in an Analyze file. I had to change the voxel size and origin in the header manually. And then I copied a .mat file from another 3D Analyze file produced by FreeSurfer with the same dimensions as my output and named it the same as my new Analyze file. I don't really know how the .mat file works, so as I said, I don't know if I can trust it. The .mat file is from a the same data that I'm analyze in R, so it should have the same orientation. Perhaps one of the FreeSurfer gurus can tell me if this is a really stupid thing to do or not. Regards, -Alessandro On 4/4/07, freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Date: Wed, 04 Apr 2007 09:10:45 +0200 > From: Glenn Lawyer <d.g.lawyer(a)medisin.uio.no> > Subject: [Freesurfer] Freesurfer and R > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <46134F75.2070803(a)medisin.uio.no> > Content-Type: text/plain; charset="iso-8859-1" > > 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) > } > } >

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Recommended Linux flavour
by Alex Wade 05 Apr '07

05 Apr '07

We are about to install a few Linux workstations, primarily to run Freesurfer and MNISuite. Can I check on what the best Linux flavour is? Do you still recommend CentOS 4? thanks Alex -- A.R. Wade Ph.D. Associate Scientist The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115 tel. 415 345 2083 fax. 309 416 6533

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erroneous 'no space left on device' error
by Kathryn Devaney 04 Apr '07

04 Apr '07

Hi all, I am trying to run an analysis in /space/stego/2/ (on machine 'whatever') and I can run mkanalysis, but when I try to run selxavg, I get the following error, in both std and dev environments: whatever:subj27/mystudy% selxavg-sess -sf sessid -df sesspar -analysis m4_fmc -noomnibus INFO: WhitenFlag = 0 -------------------------------------------------------------- selxavg-sess logfile is /autofs/space/stego_002/users/kdevaney/m4/subj27/mystudy/log/selxavg-sess-bold-m4_fmc-070404224944.log -------------------------------------------------------------- ------------------------------------------- /autofs/space/stego_002/users/kdevaney/m4/subj27 Wed Apr 4 22:49:45 EDT 2007 INFO (subj27): RunList = 003 004 005 007 008 009 010 011 012 013 014 015 cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cat: /tmp/countncond.11619: No such file or directory however: whatever:subj27/mystudy% df . -h Filesystem Size Used Avail Use% Mounted on bronto:/local_mount/space/stego/2 63G 5.7G 57G 10% /autofs/space/stego_002 There is clearly plenty of space left. Any help is appreciated, thanks! Katie

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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

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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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Freesurfer