Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

%GM, %WM, %CSF wrt ICV - including cerebellum
by Juranek, Jenifer 28 Feb '07

28 Feb '07

I'd like to compute %GM, %WM, %CSF wrt ICV (eTIV)...including cerebellum gray/white. Are the values returned by mris_wm_volume and mris_volume for cortical surfaces only (excluding cerebellum)? So, in this case... 1) are the values in aseg.stats appropriate for both cerebral and cerebellar fractions? 2) should a combination of cortical GM & WM from mris_volume be added to the cerebellar gm & wm values reported in aseg.stats to get TOTAL_GM and TOTAL_WM? 3) is it true that CSF= ICV - GM(cerebral and cerebellar) - WM(cerebral and cerebellar) Any advice is greatly appreciated... Many Thanks, Jenifer Juranek

2 1

error testing freesurfer installation
by Mishkin DERAKHSHAN 28 Feb '07

28 Feb '07

Hi, I just installed the rh9 version of fressurfer. I am running Ubuntu 6.10. I had the libtiff.so.3 error, which I seemed to have fixed by just making a sym link to libtiff.so.4 ( I hope that is okay). Now I get this error about the aseg.mgz.gz not existing. It looks like it isn't looking in the mri/ dir as it should be. mishkin@thinkpad:/usr/local/freesurfer$ tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt libGL warning: 3D driver claims to not support visual 0x5b Talairach transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /usr/local/freesurfer/subjects/bert/mri/transforms/talairach.xfm zcat: /usr/local/freesurfer/subjects/bert//aseg.mgz.gz: No such file or directory mghRead(/usr/local/freesurfer/subjects/bert//aseg.mgz, -1): read error Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl These are the only things i've added to my .bashrc : export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh which produces this output: -------- freesurfer-Linux-rh9-stable-pub-v3.0.5 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni GSL_DIR /usr/local/freesurfer/lib/gsl FSL_DIR /usr/local/freesurfer/fsl Did I forget to set a variable somewhere? thanks, mishkin

2 1

Output of mri_volcluster
by Dan Dillon 28 Feb '07

28 Feb '07

Dear FreeSurfers, I'm trying to replicate some functional analyses that were originally done in SPM2, and am using mri_volcluster. Here's my command: mri_volcluster --in Old8/bold/taumax30_2_21/tal-ffx/RSF_v_NIF/sig --in_type bfloat --reg Old8/bold/taumax30_2_21/tal-ffx/register.dat --thmin 3 --minsizevox 8. I've noticed that the size (in voxels) and number of clusters changes if I play with the -sign flag. I am confused by this. Here's the output not using the -sign flag: Cluster Size(n) Size(mm^3) TalX TalY TalZ Max 1 28 1792.0 -19.80 -96.70 8.53 5.28907 2 8 512.0 39.60 26.79 -8.07 4.15380 3 9 576.0 99.00 16.69 -54.67 4.09661 4 10 640.0 87.12 63.11 18.95 -3.82155 5 13 832.0 67.32 -42.44 5.81 3.79067 6 11 704.0 -39.60 -16.43 59.78 -3.62503 7 11 704.0 -87.12 -75.98 -43.30 -3.59305 8 73 4672.0 43.56 -22.33 19.54 -3.43893 9 18 1152.0 43.56 -44.81 -41.49 -3.16065 10 8 512.0 -51.48 -32.30 53.20 -3.09981 11 15 960.0 -63.36 -20.49 56.30 -3.00613 12 48 3072.0 -71.28 -7.20 11.41 -3.00547 And here's the output with sign set to positive: Cluster Size(n) Size(mm^3) TalX TalY TalZ Max 1 35 2240.0 -19.80 -96.70 8.53 5.28907 2 21 1344.0 39.60 26.79 -8.07 4.15380 3 13 832.0 99.00 16.69 -54.67 4.09661 4 10 640.0 -71.28 33.20 -35.31 3.91335 5 21 1344.0 67.32 -42.44 5.81 3.79067 6 9 576.0 35.64 -88.58 15.49 3.63267 Why does the size of the first cluster change? Also, where is cluster 4 from the second output in the first output? Is there some re-calculation going on here? Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: dillon(a)wjh.harvard.edu

2 1

aparc -> voxels program?
by Graham Wideman 28 Feb '07

28 Feb '07

Folks: I'm hoping that there's an aparc --> voxels program. That program might be mri_aparc2aseg, but I wanted to check first if that's the best way to go and whether there are particular options to know about and so on. Basically I want a program that inputs a parcellation, and outputs a label mri where each voxel that's fully or partially between the white and pial surface gets labelled with the parcellation label from the vertex (white or pial) that it's closest to. (A variation that would also work for our purpose would label voxels even beyond that, possibly all voxels). This seems like it's probably already been done, hence my asking. I'm thinking that *might* be what mri_aparc2aseg does... but I'm not clear what the wiki description is trying to say: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_5faparc2aseg?action=highlight… First, it appears from Example 1 that mri_aparc2aseg does something interesting when run with basically no specific command line arguments, so presumably using default input files. But then what is the purpose of --ribbon? Then the description talks about the automatic segmentation volume as though it's an input separate from the ?h.ribbon, yet there are no parameters related to that. And finally the --noribbon flag is mentioned as turning something off, but it's not clear what it's turning off. Bottom line: I'd appreciate some clarification as to which program does what I want, and if it's mri_aparc2aseg, then what options are appropriate to do the simple version of the task where it ignores existing aseg and ribbon. Thanks, Graham

2 3

Re: Files uploaded for you on Martinos Center FileDrop site
by Anil Roy 28 Feb '07

28 Feb '07

Yes, if I just run the raw files, then the brain crashes so I don't get any output. But the background values are high in the orig.mgz file also and the xfm is not accurate. afni however is able to process all these raw files without a problem including the talairach and skull strip. Is there some flag or something that I have to use or is there no way to fix this. Thanks, Anil. On 2/28/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > hmmm, the high background is there in the 001.mgz also, so it's not an > afni thing. Do you see this in all your images? > > On Tue, 20 Feb 2007 > aroy85(a)gmail.com wrote: > > > > > The following files have been uploaded to the Martinos Center FileDrop > site > > by Anil Roy for you to download: > > > > (1) 001.mgz > > > > > > > > These files will expire in 30 days. > > > > To view or download these files, go in your web browser to: > > > > > https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5075/89/4def6e0… > > > > DO NOT SHARE this web address with anyone else. It is your personal > access key to the files. > > > > Overall Comment about files from Anil Roy: > > > > Bruce, Here is the 001.mgz > > > > > > >

2 1

Re: [Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site
by Anil Roy 27 Feb '07

27 Feb '07

Hi Bruce, I've been trying to improve the talairach xfm and try different things with afni, but so far nothing has worked out. The brain still crashes at the skull strip. I fed in the afni skull strip to resume the pipeline from autorecon2 but the segmentation was really bad, with the white matter surface not accurate. Did you have any suggestions for the background values. Any ideas. Thanks, Anil. On 2/21/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > Hi Anil, > > I got the email, but I'm out of town and won't get to it until next week > Bruce > On > Wed, 21 Feb 2007, Anil Roy wrote: > > > I think my last email didn't get through. Bruce, I've uploaded the > 001.mgz. > > It should arrive in your mailbox. I can upload it again if there was any > > problem. > > > > Thanks, > > > > Anil. > > > > On 2/20/07, Anil Roy <aroy85(a)gmail.com> wrote: > >> > >> Its uploaded > >> > >> On 2/20/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> > > >> > I need the 001.mgz > >> > On Tue, 20 Feb 2007, Anil Roy wrote: > >> > > >> > > Bruce, I had uploaded the orig.mgz for Nick. I think you should > find > >> > the > >> > > link below. I can also upload the 001.mgz for you. > >> > > There are no dicoms because the scan is from a GE scanner (120 > slices, > >> > > >> > > details are below)and all the files are named as I.??? > >> > > I could also upload these files for you. > >> > > > >> > > Anil. > >> > > > >> > > On 2/20/07, Bruce Fischl < fischl(a)nmr.mgh.harvard.edu > wrote: > >> > >> > >> > >> I think it's something afni is doing, but I'm not sure. Did you > give > >> > us > >> > >> the data before conversion (either the dicoms or the 001.mgz) > >> > >> > >> > >> On Tue, 20 Feb 2007, > >> > >> Anil Roy wrote: > >> > >> > >> > >> > Hey Freesurfers, > >> > >> > > >> > >> > I fed freesurfer the brainmask.mgz generated by AFNI. autorecon2 > >> > and > >> > >> > autorecon3 ran fine with no errors but the resulting surfaces > are > >> > not > >> > >> very > >> > >> > accurate. > >> > >> > > >> > >> > Bruce, you mentioned that my background values were too high. Is > >> > there a > >> > >> way > >> > >> > to reduce them so that freesurfer can do the watershed without > any > >> > >> glitches. > >> > >> > > >> > >> > Thanks, > >> > >> > > >> > >> > Anil. > >> > >> > > >> > >> > On 2/15/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> > >> >> > >> > >> >> I think it's because your background values are so high. > >> > >> >> On Thu, 15 Feb > >> > >> >> 2007, Anil Roy wrote: > >> > >> >> > >> > >> >> > Thanks a lot Nick. > >> > >> >> > > >> > >> >> > I'll try to convert the AFNI skull strip into brainmask and > nu > >> > and > >> > >> see > >> > >> >> if I > >> > >> >> > can resume the pipeline. > >> > >> >> > > >> > >> >> > I put in the new values for the xfm and ran recon-all again > with > >> > the > >> > >> >> > notalairach flag. > >> > >> >> > > >> > >> >> > recon-all -s Nl-TAl-001 -notalairach -all > >> > >> >> > > >> > >> >> > However, it still quits at the watershed step. I ran another > >> > brain > >> > >> where > >> > >> >> the > >> > >> >> > raw images were dcm and it ran fine so the problem is > definitely > >> > >> >> something > >> > >> >> > specific to this brain. > >> > >> >> > > >> > >> >> > Nick, I know that autorecon1 ran fine for you so I really > have > >> > no > >> > >> clue > >> > >> >> why > >> > >> >> > my machine quits at the watershed step even with the > transform > >> > you > >> > >> gave > >> > >> >> me. > >> > >> >> > > >> > >> >> > Any clues, suggestions? > >> > >> >> > > >> > >> >> > Thanks a lot, > >> > >> >> > > >> > >> >> > Anil. > >> > >> >> > > >> > >> >> > On 2/14/07, Nick Schmansky < nicks(a)nmr.mgh.harvard.edu> > wrote: > >> > >> >> >> > >> > >> >> >> Anil, > >> > >> >> >> > >> > >> >> >> Here is the transform (the contents of the talairach.xfmfile) > >> > that > >> > >> I > >> > >> >> >> generated: > >> > >> >> >> > >> > >> >> >> Transform_Type = Linear; > >> > >> >> >> Linear_Transform = > >> > >> >> >> 9.265516e-01 5.678305e-04 2.317888e-03 3.736965e-01 > >> > >> >> >> -8.173273e-04 8.513330e-01 8.824052e-02 -1.653205e+01 > >> > >> >> >> - 2.688466e-03 -1.064786e-01 9.460568e-01 1.780552e+01 ; > >> > >> >> >> > >> > >> >> >> Remember to use the -notalairach flag with recon-all when > you > >> > create > >> > >> > >> > >> >> the > >> > >> >> >> new talairach.xfm file, so that it doesnt get overwritten. > >> > >> >> >> > >> > >> >> >> 4GB is plenty to run Freesurfer, so it is strange that > >> > mri_watershed > >> > >> is > >> > >> >> >> encountering out-of-memory errors. > >> > >> >> >> > >> > >> >> >> Nick > >> > >> >> >> > >> > >> >> >> > >> > >> >> >> On Wed, 2007-02-14 at 17:20 -0600, Anil Roy wrote: > >> > >> >> >> > Also, I ran it on a Red Hat system and I'm still getting > the > >> > error > >> > >> so > >> > >> >> >> > I don't think it is a machine specific problem. Any > >> > suggestions. > >> > >> >> >> > > >> > >> >> >> > Thanks. > >> > >> >> >> > Anil. > >> > >> >> >> > > >> > >> >> >> > On 2/14/07, Anil Roy < aroy85(a)gmail.com> wrote: > >> > >> >> >> > Here are the details of the acquisitions: > >> > >> >> >> > > >> > >> >> >> > Images acquired on a 3T Signa scanner with a > standard > >> > GE > >> > >> head > >> > >> >> >> > coil. 3D T1-weighted spiral volume scan (120 > slices, > >> > >> >> 1.4875-mm > >> > >> >> >> > thick, TR = 20 msec, TE = 6 msec, 40 degrees flip > >> > angle, > >> > >> 256 > >> > >> >> * > >> > >> >> >> > 192 matrix) > >> > >> >> >> > > >> > >> >> >> > The machine has 4 gigs of RAM. Also, AFNI is able > to > >> > >> >> talairach > >> > >> >> >> > and skull strip. Is there a way I can input the > files > >> > from > >> > >> > >> > >> >> >> > AFNI to Freesurfer to resume the recon-all > pipeline. > >> > >> >> >> > > >> > >> >> >> > Nick, is there a way for me to see your reg so > that I > >> > can > >> > >> be > >> > >> >> >> > sure that its not my created xfm that is causing > >> > this > >> > >> >> >> > problem. > >> > >> >> >> > > >> > >> >> >> > Thanks, > >> > >> >> >> > > >> > >> >> >> > Anil. > >> > >> >> >> > > >> > >> >> >> > > >> > >> >> >> > On 2/14/07, Bruce Fischl < > fischl(a)nmr.mgh.harvard.edu> > >> > > >> > >> wrote: > >> > >> >> >> > why is the background so high? Also, what > >> > field > >> > >> >> >> > strength was this at? There > >> > >> >> >> > looks to be dielectric-like center > >> > brightening. > >> > >> The > >> > >> >> >> > contrast isn't terrible > >> > >> >> >> > though. > >> > >> >> >> > > >> > >> >> >> > On Wed, 14 Feb 2007, Nick > >> > >> >> >> > Schmansky wrote: > >> > >> >> >> > > >> > >> >> >> > > Bruce, > >> > >> >> >> > > > >> > >> >> >> > > the orig.mgz can be downloaded via the > >> > filedrop, > >> > >> >> see > >> > >> >> >> > link in email > >> > >> >> >> > > below. > >> > >> >> >> > > > >> > >> >> >> > > or i have copied it to: > >> > >> >> >> > > > >> > >> >> >> > > >> > >> >> >> > /autofs/space/minerva_001/users/nicks/subjects/anil/mri > >> > >> >> >> > > > >> > >> >> >> > > N. > >> > >> >> >> > > > >> > >> >> >> > > > >> > >> >> >> > > On Wed, 2007-02-14 at 17:02 -0500, Bruce > >> > Fischl > >> > >> >> >> > wrote: > >> > >> >> >> > >> put the .mgz somewhere and I'll take a > >> > look. > >> > >> And > >> > >> >> >> > make sure it's the > >> > >> >> >> > >> orig.mgz, which is un-normalized > >> > >> >> >> > >> > >> > >> >> >> > >> > >> > >> >> >> > >> On Wed, 14 Feb 2007, Nick Schmansky > wrote: > >> > > >> > >> >> >> > >> > >> > >> >> >> > >>> Anil, > >> > >> >> >> > >>> > >> > >> >> >> > >>> The image has almost no > contrast. I've > >> > >> attached > >> > >> >> a > >> > >> >> >> > TIFF of one slice. > >> > >> >> >> > >>> How was this acquired? Bruce, any > idea > >> > why it > >> > >> > >> > >> >> >> > would be so white? > >> > >> >> >> > >>> > >> > >> >> >> > >>> Nick > >> > >> >> >> > >>> > >> > >> >> >> > >>> > >> > >> >> >> > >>> On Wed, 2007-02-14 at 16:10 -0500, > >> > >> >> >> > aroy85(a)gmail.com wrote: > >> > >> >> >> > >>>> The following files have been > uploaded > >> > to the > >> > >> >> >> > Martinos Center FileDrop site > >> > >> >> >> > >>>> by Anil Roy for you to download: > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> (1) orig.mgz > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> These files will expire in 30 days. > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> To view or download these files, go > in > >> > your > >> > >> web > >> > >> >> >> > browser to: > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> > >> > >> >> >> > > >> > >> >> >> > >> > >> >> > >> > >> > >> > https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc… > >> > > >> > >> > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> DO NOT SHARE this web address with > >> > anyone > >> > >> >> >> > else. It is your personal access key to > the > >> > >> files. > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> Overall Comment about files from Anil > >> > Roy: > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> Hi, > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> Attached is the orig.mgz file for the > >> > subject > >> > >> > >> > >> >> >> > that quits at the watershed step. > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> Thanks, > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> Anil. > >> > >> >> >> > >>>> > >> > >> >> >> > >>>> > >> > >> >> >> > >>> > >> > >> >> >> > >> > >> > >> >> >> > >> > >> > >> >> >> > > > >> > >> >> >> > > > >> > >> >> >> > > > >> > >> >> >> > > >> > >> >> >> > > >> > >> >> >> > > >> > >> >> >> > _______________________________________________ > >> > >> >> >> > Freesurfer mailing list > >> > >> >> >> > Freesurfer(a)nmr.mgh.harvard.edu > >> > >> >> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> >> >> > >> > >> >> >> > >> > >> >> > > >> > >> >> > >> > >> > > >> > >> > >> > > > >> > > >> > >> > > >

2 2

tissue segmentation output file
by nayoung＠cis.jhu.edu 27 Feb '07

27 Feb '07

Hello, I am wondering if I can get a mask(labelled volume) for each tissue types - not a structure. I can see that Freesurfer is generating a surfaces between gray/white and gray/CSF. Can I get a volume which correspond to WM/GM/CSF? Thank you. Nayoung

2 1

file conversion
by Lindsay Casmaer 27 Feb '07

27 Feb '07

I am trying to run the first recon-all command on Seimens dicom files to convert to mgz. I moved the files for each acquisition to a separate directory ex: 001 002 003, 3 subdirectories each containing the files for each scan acquisition. I then run the command recon-all -i 447-5-440.ima -i 447-6-568.ima -i 447-4-312.ima -s 030217_vc11174 -where 447-5-440.ima, 447-6-568.ima, and 447-4-312.ima are the first files that appear in each acquisition directory. The error I get is "cannot find 447-5-440.ima". Any help would be greatly appreciated. Do I need to run this command from the directory where the files are located? Do I need to set my SUBJECTS_DIR each time to the individual session? Thank you. Lindsay Casmaer Washington University in St. Louis lcasmaer(a)artsci.wustl.edu

3 2

segmentation
by Sasha Wolosin 26 Feb '07

26 Feb '07

In freesurfer, is there any way to run a gray/white matter segmentation within the cortex? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

3 6

Question about trials w/subject errors
by Dan Dillon 26 Feb '07

26 Feb '07

Dear FreeSurfers, We are running a paradigm that occasionally elicits erroneous responses from subjects. In our mkanalysis step, we have 13 conditions-10 are legit, and codes 11, 12, 13 correspond to various kinds of errors. Thus, we only use the first 10 codes in mkcontrast, etc. However, occasionally we have a subject who makes no errors. How should we account for this? Is it okay to just change the # of conditions in the mkanalysis .info file (from 13 to 10) and then run selxavg on these folks? Can we then average their data in with people who have all 13 conditions? Thanks! Dan Dillon

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