Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

Re: [Freesurfer] [TRACULA] short thin tracks
by Anastasia Yendiki 05 Oct '12

05 Oct '12

Hi Akvile - I'm attaching a screenshot of the FA map and primary eigenvectors from your data set through the corpus callosum and cingulum areas. You'll see that the eigenvectors are not oriented correctly, which probably means that there's something wrong with the gradient directions in you bvecs file. Looking at the eigenvectors from the tensor fit is important when troubleshooting - the FA alone doesn't tell the full story since it's invariant to rotation of the vectors. Hope this helps, a.y On Wed, 3 Oct 2012, A. Lukose wrote: > Dear Anastasia, > > Thank you very much for your reply. I have uploaded the requested > directories (in a zip file tracts.zip) of one subject (I have run several, > but all of them look the same). Thank you very much in advance! > > Kind regards, > Akvile Lukose > > > > On 27/09/2012 18:34, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > >> >> Hi Akvile - Sorry for the late response, I was out of town for a bit. >> >> At first glance it looks like all the tracts are stuck where they're >> initialized. This might happen occasionally for a tract if initializing >> it >> is tricky (i.e., if the subject is not well aligned to the atlas, if the >> brain mask has a hole, etc), which is why the reinit option exists. But >> I've never seen it happen to all tracts, so something's fishy here. >> >> If you upload all the tracula-related directories for this subject (dmri, >> dlabel, dpath, scripts), I'll take a look. >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange >> >> a.y >> >> On Thu, 13 Sep 2012, Akvile Lukose wrote: >> >>> >>> Hello Freesurfers, >>> >>> I ran into a problem running TRACULA that I couldn't solve myself, and >>> I would really >>> appreciate if you could have a look. >>> >>> I am running a FS 5.1 on mac os x 10.7.4 (intel 64bit) machine with >>> 16GB RAM. >>> >>> I extracted the bvals and bvecs with the dcm2nii converter and adjusted >>> the format to >>> what FS expects (scans acquired on a non-Siemens scanner). >>> >>> I attach the dmrirc file as well. >>> >>> First, I had a memory problem (cannot alloc memory) during the prep >>> stage. The new >>> compiled update from here >>> (http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula )helped >>> and prep stage finished without any errors. >>> >>> I was not able to run bedpostx from dmrirc configuration file. I could >>> work around it >>> by running bedpostx directly on dmri directory (as described >>> here >>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html) >>> . Then >>> I had a problem with symlinks, I created them manually and after that >>> it worked >>> fine, I had all the output files as listed here >>> (http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html) >>> >>> -path worked also without any errors, but I keep getting very short >>> thin tracks (all >>> tracks) (snapshot attached). There is nothing wrong with the >>> aparc+aseg.mgz. I tried >>> rerunning every stage after I added option "set reinit=1" (as described >>> here >>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21990.html) >>> , but >>> unfortunately it didn't help. >>> >>> Do you have any ideas how to fix it? Thank you very much in advance! >>> >>> Kind regards, >>> >>> Akvile Lukose >>> >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> ----- >> Geen virus gevonden in dit bericht. >> Gecontroleerd door AVG - www.avg.com >> Versie: 2012.0.2221 / Virusdatabase: 2441/5295 - datum van uitgifte: >> 09/27/12 > > > >

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Rejoindre mon réseau sur LinkedIn
by Luisa Leo via LinkedIn 04 Oct '12

04 Oct '12

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freesurfer problems
by Nucleos P 04 Oct '12

04 Oct '12

I am currently using a Linux Workstation with Redhat. I recently installed Freesurfer on this computer. It works fine on the other computers... These are the errors I am getting: (The important points are in Bold) proc_fs test_mgi MGI2 #############start: /usr/local/freesurfer/bin/proc_fs Thu Oct 4 16:31:57 EDT 2012 ################# #############start: recon-all Thu Oct 4 16:31:57 EDT 2012 ################ Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/MGI2 Actual FREESURFER_HOME /usr/local/freesurfer Linux goodman 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/MGI2/test_mgi * mri_convert /usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562 /usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562 /usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig/001.mgz * -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562... #-------------------------------------------- #@# MotionCor Thu Oct 4 16:32:16 EDT 2012 *ERROR: no run data found in /usr/local/freesurfer/subjects/MGI2/test_mgi/mri. Make sure to have a volume called 001.mgz in /usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig. If you have a second run of data call it 002.mgz, etc.* See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux goodman 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s test_mgi exited with ERRORS at Thu Oct 4 16:32:16 EDT 2012 For more details, see the log file /usr/local/freesurfer/subjects/MGI2/test_mgi/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting #############end: Thu Oct 4 16:32:16 EDT 2012 ################# [prasad@goodman scan_todo]$ *The mri_convert is supposed to create the mri/orig/001.mgz file and works on the other workstations... Here is the script in detail: * #!/bin/tcsh ####################################################### # Program: proc_fs # # Author: Dhruman Goradia # # Date: 09/19/2010 # # Description: Runs freesurfer preprocessing # ####################################################### set program = $0 echo "#############start: $program `date` #################" if ( $#argv != 2 ) then echo "${program}: Wrong no of arguments" echo "Usage: ${program} dicomdir fs_subdir" exit endif set dirdcm = "/usr/local/freesurfer/subjects/scan_todo" set fs_subid = $1 set study_id = $2 set file1 = `ls ${dirdcm}/${fs_subid}/raw | head -n 1` setenv SUBJECTS_DIR "/usr/local/freesurfer/subjects/${study_id}" echo "#############start: recon-all `date` ################" if ( -f ${SUBJECTS_DIR}/${fs_subid}/mri/orig/001.mgz) then recon-all -s $fs_subid -all else *#mkdir -p ${SUBJECTS_DIR}/${fs_subid}/mri/orig #mri_convert ${dirdcm}/${fs_subid}/raw/${file1} ${SUBJECTS_DIR}/${fs_subid}/mri/orig/001.mgz recon-all -i ${dirdcm}/${fs_subid}/raw/${file1} -s $fs_subid -all* endif echo "#############end: `date` #################" exit * Here is the LICENSE file: FreeSurfer Software License Agreement ("Agreement") Version 1.0 (February 2011) This Agreement covers contributions to and downloads from the FreeSurfer project ("FreeSurfer") maintained by The General Hospital Corporation, Boston MA, USA ("MGH"). 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2 1

mris_pmake options
by octavian lie 04 Oct '12

04 Oct '12

Dear all, I need to measure the distance between 2 points on the same hemisphere for subject A, in the common surface space as I have to compare it with the distance between other 2 points for subjects B, C... I used mris_pmake --subject A --hemi rh --surface0 sphere.reg --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:1,endVertex:2 Questions: 1. Is the calculated path the geodesic, in this case spherical, measure that can be directly compared with that from another subject, or not? 2. How could I compare the distance on the pial surface of subject 1 (vertex 1-vertex 2) to subject 2 (vertex 1 to2). Is changing --surface0 argument to pial enough? (In the Recon-all Dev table, sphere.reg is an imput to generating label/?h.aparc.annot, which in turn is used to generate ?h.pial surfaces, does that mean that pial surfaces from 2 subjects are already registered?) 3. I do not understand the choice of defaults for --surface0 (inflated) , --surface1 (smoothwm), curve 0 and 1. This is not surprising, since I do not have the math expression for the cost function available; just wondering, what is the reason to have inlated as the default for surface 0? Do I need to change any of the auxilliary terms used above with sphere.reg to accomplish what I want to accomplish? 4. Last, is there a way to mark the vertices for these geodesic path on the main surface used in order to use then for label creation? Your insight is very important, thank you, Octavian.

2 1

how to get freeview run on ubunto
by yawu Liu 04 Oct '12

04 Oct '12

Hi Freesurfers, I have installed Freesurfer 5.1 in my Ubunto. I run analysis with testing and our won data without problem. But when I run: d4201z-CELSIUS-M470-2:/usr/local/src/freesurfer/subjects/long-tutorial> freeview -v OAS2_0001/mri/norm.mgz, then Error message appears:freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. Any help is appreciated! Best Regards, Yawu

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fixing the talairach.xfm
by Eric Cunningham 04 Oct '12

04 Oct '12

Hi, I have a few very basic clarification questions regarding the recon-all processing pipeline. I am currently following the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Near the end of the page, it instructs me to rerun the whole process using my new talairach, using the command: recon-all -all -subjid [subjid] Questions: (1) Since the talairach file is created during recon-all, wouldn't rerunning the whole process overwrite my freshly edited file with whatever it came up with the first time? (2) Assuming the answer to question 1 is 'no', can i rerun the process in steps (-autorecon1, then -autorecons 2 and 3) without overwriting my freshly edited file? (3) Are there any files that are unusual in their likelihood of being overwritten? (e.g. running recon-all -all will overwrite aseg.stats but not talairach.xfm) Thank you for your help, -Eric

2 1

More than two time-points in longitudinal base = Memory allocation error?
by Liz Bowman 03 Oct '12

03 Oct '12

Hello, I have several patients scans taken over multiple time points (up to nine time points in some patients). I thought I might be able to use these to create a base template for longitudinal processing, however the process fails and exits with errors if I try to create a base with more than two time points from a patient. This is a sample of the error log of the most recent attempt, with three timepoints: Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.876663 Iteration(f): 2 -- diff. to prev. transform: 0.0148738 Iteration(f): 3 -- diff. to prev. transform: 0.00156813 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.263086 Iteration(f): 2mri_robust_template(1035) malloc: *** mmap(size=262144) failed (error code=12)*** error: can't allocate region*** set a breakpoint in malloc_error_break to debugMRIalloc(256, 256, 256): could not allocate 262144 bytes for 68th slice Cannot allocate memoryDarwin 550D-UOM88670.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 recon-all -s KSx3 exited with ERRORS at Mon Jul 23 10:15:13 EST 2012 For more details, see the log file /Applications/freesurfer/subjects/KSx3/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I would be grateful for any advice. Regards, EA Bowman

3 4

is skull strip needed
by Gregory Kirk 03 Oct '12

03 Oct '12

if there is extra skull left after skull stripping but the pial surface is fine ( i.e. the left skull did not get included in the pial surface ) is it nessesary to adjust watershed parameters or manually remove it and reprocess the data set ? I am thinking it is not needed if it is not causing an error in the surface. thanks greg

2 1

A question about downsmapling mulitple surfaces (white, pial, sphere) for registration
by Longchuan Li 03 Oct '12

03 Oct '12

Hi, FreeSurfer experts Currently, I am planning to run tractography using wm surfaces as seed masks and pial surfaces as stop masks implemented in FSL. In order to make fibers go through one hemisphere to another, I need to remove the medial wall from both seed surfaces and the pial surfaces. However, as the original surfaces' resolution is too high, I will need to downsample the surfaces first, in order to manage the computational time to a reasonable time limit. My strategy is like this: (1) downasample the sphere, pial and white from original 700K to 10K using "mris_decimate" with a factor of 0.1 (2) register the subject's downsampled sphere to the template surface sphere (3) transfer the label file with medial wall excluded from the template space to the subject's sphere space based on the warping file. (4) convert the label file to seed mask (based on white surface) and stop mask (based on pial surface). using a FSL tool My questions are: (1) Can surface-based registration be properly done when I used the downsampled version of the sphere to register to the template's sphere? (2) As my pial, sphere and white surfaces are downsampled separately by repeatedly using the "mris_decimate", will they still have that point-to-point correspondence as the original ones? I would appreciate if anyone could help on this and point out any potential problems and/or better strategies Longchuan

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Re: [Freesurfer] Lesioned brain (surface) registration to fs average
by octavian lie 03 Oct '12

03 Oct '12

Actually, the white matter is affected too within the resection bed. Just to make sure, using mri_label2label with surface option to pass a label from subject 1 to subject 2 is equivalent to registering that label to fsaverage via sphere.reg for that subject, then transferring the label from fs average to subject 2 via sphere.reg for subject 2. I assume I can use it to transfer the label to fsaverage as well; is it better or same/equivalent to use mri_surf2surf vs mri_label2label to transfer a label from one subject to another Thank you very much, Octavian.

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Freesurfer October 2012