Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Normalization
by Ana Arruda 06 Oct '12

06 Oct '12

Hello, I'm working on hippocampus segmentations obtained by Freesurfer to compare with manual and FSL segmentations. Do I have to normalize to make these comparisons more accurate? If so, what volume do I have to use? I've read about eTIV but I would like to confirm if there is any value for normalization purpose in the aseg.stats file. What does ICV include? Does it include the CSF between the brain and the skull? Best regards, Ana Arruda

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cortical parcellation question
by Daniel Ferreira 06 Oct '12

06 Oct '12

Dear experts, I have a couple of questions regarding the cortical parcellation atlas that is used in Freesurfer: 1) I would like to know if it is possible to obtain the Desikan-Killiany atlas in 3D analyze/nifti format. With each region of the brain assigned a discrete integer number (for example the all of the voxels of the left inferior temporal lobe have an intensity = 1, or the whole of the left hippocampus = 2). 2) Are the Harvard-Oxford cortical and subcortical atlases that can be downloaded with FSL the same as the cortical parcellation atlas that is used in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the left inferior temporal cortex in the Freesurfer cortical parcellation = the left inferior temporal cortex in the Harvard-Oxford atlas downloaded with FSL) Many thanks Daniel Ferreira

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I want to know a simple thing in tksurfer
by Seulgi Eun 06 Oct '12

06 Oct '12

I'm using 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0' and I have a problem. I used a command 'tksurfer fsaverage lh inflated -ov surfdata' on teminal. Then, I used 'configure overlay display' in veiw>configure>overlay to set proper threshold. I could set approximate threshold values easily by mouse. But I wanted to set the values by keyboard inputs(exact numbers). I think there is a way to type numbers(in my case, it is unable to type any words on the edit boxes). How can I do?

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transfer label from high-resolution mesh to low resolution mesh
by Longchuan Li 05 Oct '12

05 Oct '12

Hi, all I am trying to transfer some labels on a high-resolution white surface mesh (~100K) to a corresponding low-resolution white mesh(~10K) that is generated using FS function "mris_decimate". Could someone tell me what is the most efficient way to realize that? Many thanks in advance! Longchuan

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Import/export out of curry
by Inati, Souheil (NIH/NIMH) [E] 05 Oct '12

05 Oct '12

Has anyone used freesurfer segmentations/labels in Curry? -- Souheil Inati, PhD Staff Scientist Functional MRI Facility NIMH/NIH/DHHS souheil.inati(a)nih.gov

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Re: [Freesurfer] tracula question
by Anastasia Yendiki 05 Oct '12

05 Oct '12

Hola Fernando - Please send questions about tracula to the freesurfer list and not me personally, so that all users may benefit. This issue will be resolved in the next version. For now, if you're on a unix system that doesn't have the jot command, you'll just have to specify the runlist in your configuration file, even if you want to process all subjects on your list. So if you have 5 subjects for example: set runlist = (1 2 3 4 5) Hope this helps, a.y On Fri, 5 Oct 2012, Fernando Ventrice wrote: > Dear Anastasia Yendiki, > I have been trying to use TRACULA and I think I'm doing something wrong. Because it keeps on giving me this error (I tried within tcsh and bash): > > fventrice@xubuntu1204x64fleni:~$ trac-all -prep -c ${TUTORIAL_DATA}/diffusion_tutorial/scripts/dmrirc_single_subject > jot: Command not found. > INFO: SUBJECTS_DIR is /media/LEVIATAN01/LaboINEBA/testing_TRACULA/diffusion_recons > INFO: Diffusion root is /media/LEVIATAN01/LaboINEBA/testing_TRACULA/diffusion_tutorial > Actual FREESURFER_HOME /home/fventrice/CONTAINER_FLENI/Programs/freesurfer > > I use freesurfer and fsl perfectly well. I have also tried with the new version of trac-all. But keeps on giving the same error. > Best regards and thanks! > Fernando Ventrice > > El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. > http://www.fleni.org.ar > > >

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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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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.

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