Freesurfer June 2010

freesurfer@nmr.mgh.harvard.edu

97 participants
138 discussions

Order of Image Processing in the Longitudinal Stream and Multi-site scanning
by Meg Dennison 03 Jun '10

03 Jun '10

Hi, My question relates to the order of processing images from different time points in the longitudinal stream. The base-line images I have were collected in 2006, but many of these images are of poorer quality than those collected in 2008 at follow up. Given this description from Han et al., 2006: "The longitudinal scheme differs from the original procedure in three major steps: preprocessing, intensity normalization and surface deformation. *Assuming that a series of scans of the same subject are obtained at different time points, the data from time point one is first processed using the original procedure. For the processing of later time points, the three major steps mentioned above are modified.* First, a linear registration is computed between the image volume of a later time point and that of the first time point. Note that the volume itself is not transformed, but only the registration matrix is stored and will be used in later steps. Second, at the intensity normalization step, instead of re-computing the WM control points, the control points (automatically computed) from time point one are mapped to the current volume using the previously computed linear registration, which are then used to estimate the bias field. Third, at the surface deformation step, instead of starting the deformation from the topology-corrected WM tessellation, the gray/white and pial surfaces reconstructed from time point one are first transformed using the linear registration and then used to initialize the deformation for the gray/white and pial surfaces respectively for the current time point. Such an initialization scheme reduces the problem of deformable model methods being sensitive to initialization and local optimality (Dale et al., 1999; Xu et al., 1999; Han et al., 2005a). It also eliminates variation in initial surface tessellation and topology correction since these two steps are no longer needed in the processing of later time points." Would it make sense to use the better quality images, which in this case are those collected at time point 2, as the "baseline" when processing in the longitudinal stream to get a more accurate result for time point 1? Additionally, is there any consensus about the degree to which the longitudinal processing stream assists in overcoming variance due to multi-site scanning? Thanks in advance for any help on these issues, Kind Regards, Meg Dennison ------------------------------- PhD Candidate / Masters Clinical Psychology Psychological Sciences Melbourne University -------------------------------

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label2label with two subjects directories
by Garth Coombs 02 Jun '10

02 Jun '10

Hi Doug & Freesurfer experts, Is there a way to run mri_label2label to copy a label from one subject to another in a different SUBJECTS_DIR, or do the subjects have to be in the same directory for label2label to work (e.g. vs_subject1 in SUBJECTS_DIR_A to subject1_anat in SUBJECTS_DIR_B)? I am having trouble with specifying the source and target registration/white matter files. The subjects in both directories are the same, the only difference being which version of freesurfer the recons were run with and a slight difference in the naming convention. I tried just copying the file, but when I tried to visualize the label, it looked incorrect. Below are the outputs I got when running mri_label2label. When I do not use the --srcsurfreg & --trgsurfreg flags, I get very similar errors, but with shorter path names that it cannot find. Thanks for your help! -Garth When I try: setenv SUBJECTS_DIR /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/ cd /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/ mri_label2label --srclabel /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label --srcsubject vs_aric --trglabel /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label --trgsubject aric_anat --regmethod surface --hemi lh --srcsurfreg /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg --trgsurfreg space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg I get this error: srclabel = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label srcsubject = vs_aric trgsubject = aric_anat trglabel = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg trgsurfreg = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 SUBJECTS_DIR is /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects FREESURFER_HOME is /usr/local/freesurfer/stable4 Loading source label. /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label Found 158 points in source label. Starting surface-based mapping Reading source registration /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg MRISread(/autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg): could not open file No such file or directory ERROR: could not read /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg When I try changing the subjects directory: setenv SUBJECTS_DIR /space/brownie/3/users/gcoombs/SUBJECTS_DIR/ cd $SUBJECTS_DIR mri_label2label --srclabel /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label --srcsubject vs_aric --trglabel /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label --trgsubject aric_anat --regmethod surface --hemi lh --srcsurfreg /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg --trgsurfreg space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg I get this error: srclabel = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label srcsubject = vs_aric trgsubject = aric_anat trglabel = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/label/ffa_lh_indiv.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg trgsurfreg = /space/brownie/3/users/gcoombs/SUBJECTS_DIR/aric_anat/surf/lh.sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 SUBJECTS_DIR is /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR FREESURFER_HOME is /usr/local/freesurfer/stable4 Loading source label. /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label /space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/label/ffa_lh_indiv.label Found 158 points in source label. Starting surface-based mapping Reading source registration /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg MRISread(/autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg): could not open file No such file or directory ERROR: could not read /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/vs_aric/surf/lh./space/dinah/1/users/balaji/SUBJECTS_DIR/subjects/vs_aric/surf/lh.sphere.reg

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Re: [Freesurfer] autorecon2 error
by Nick Schmansky 02 Jun '10

02 Jun '10

mri_ca_label can be downloaded from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… copy it your $FREESURFER_HOME/bin n. On Mon, 2010-05-31 at 03:25 -0400, Martin Reuter wrote: > Yes, looks like the one I fixed. Nick can point you to a download for the > fixed files. > > Best, Martin > > > ----- Original Message ----- > From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > To: "Gabriel Go.Es." <gabriellbk(a)hotmail.com> > Cc: "free surfer" <freesurfer(a)nmr.mgh.harvard.edu>; "Reuter, Martin -- > Martin Reuter" <mreuter(a)nmr.mgh.harvard.edu>; "Martin Reuter" > <reuter(a)mit.edu> > Sent: Sunday, May 30, 2010 4:50 PM > Subject: Re: [Freesurfer] autorecon2 error > > > Hi Gabriel, > > I think Martin fixed this bug, didn't you Martin? > > Bruce > > On Sun, 30 May 2010, Gabriel Go.Es. wrote: > > > > > > > Dear FreeSurfers > > I run an autorecon1 using the flag -no-wsgcaatlas > > for skullstripping, I'm using > > freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0, you may find attached > > the recon-all_status log > > for any information you may need > > Then I was trying to run the autorecon2: recon-all -subjid -autorecon2 > > when it gives the following error message: > > > > > > ------------------------------------------------------ > > > > Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT > > 2006 x86_64 x86_64 x86_64 GNU/Linux > > > > $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ > > > > /root/trabajo/freesurfer/bin/recon-all > > > > PWD /root/trabajo/freesurfer/subjects/MP2RAGE_2/mri > > > > CMD mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z > > /root/trabajo/freesurfer/average/RB_all_2008-03-26.gca > > aseg.auto_noCCseg.mgz > > > > > > mri_ca_label GCA sequential renormalization: label 28 not consistently > > computed. > > > > not using caudate to estimate GM means > > setting label Left_Cerebellum_Cortex based on Right_Cerebellum_Cortex = > > 1.05 x + 0 > > estimating mean gm scale to be 1.16 x + 0.0 > > estimating mean wm scale to be 1.00 x + 0.0 > > estimating mean csf scale to be 0.43 x + 0.0 > > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt > > Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT > > 2006 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Fri May 28 14:57:45 CEST 2010 > > > > ------------------------------------------------------------------- > > > > > > > > any suggestions and help will be so appreciated > > > > Best > > > > Gabriel > > > > ¿Sabes que La Gente de Hoy tiene GUARDAESPALDAS contra el Spam? > > Con las alertas de Hotmail no perderás detalle de tu correo. ¡Contrátalo > > ya! > > _________________________________________________________________ > > ¿Quieres conocer trucos de Windows 7? ¡Los que ya lo usan te los cuentan! > > http://www.sietesunpueblodeexpertos.com/index_windows7.html > > > 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. > >

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compatibility question
by Jason Connolly 01 Jun '10

01 Jun '10

Dear Free Surfers, I'm having a problem I've seen posts about in the archive, but have not been able to see the solution to it. If I start tksurfer bert rh pial (as the example says), the display only shows a small fraction of the brain and nothing more. I've tried some of the suggestions such as zooming, the 'Auto redraw' option, but to no use. I have tried on two of our Linux machines, with CentOS 5, either logged in locally or remotely with NoMachines. I've got external video cards and the GLX gears works fine at ~100 FPS (remotely) and ~1000FPS (locally). The machines have 8 processors, are 64 bit, 500 GB+ hard drives and 4GB of RAM, and external NVIDIA compatible video cards. A colleague who is running Fedora 11 has no problems. Is this an OS type problem and any way to fix it? Thanks in advance for your help Best wishes, -Jason

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Using peak activation voxels to determine structural areas of interest
by Nathan Dankner 01 Jun '10

01 Jun '10

Hello all. I am considering using peak activation voxels (with coordinates either in talairach or MNI space) gleaned from fmri studies in our lab to determine a priori areas of interest for examining group differences in cortical thickness. Is this something that is possible in freesurfer? In particular, I would ideally like to be able to tell freesurfer how large of an area to examine around a particular peak voxel for each subject as opposed to tracing an ROI each time. I am not particularly well versed in the technical aspects of things such as blurring kernels, but I am assuming that the amount of blurring done by freesurfer will affect the ideal circumference of any sphere around this peak voxel. Any suggestions as to how to go about this? Please let me know if any more information is necessary. Thanks, Nathan

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Exporting volumes from freesurfer subject folder
by Weisinger, Brian (NIH/OD) [E] 01 Jun '10

01 Jun '10

Is there any fast way to take out a specific volume from a group of subjects so as to where I could pull out the caudate and hippocampus volumes for each person to analyze statistically between groups? Thank you, Brian Weisinger

2 1

make_average_subject with large cohorts
by Marie Schaer 01 Jun '10

01 Jun '10

Hello everybody, I have a problem running make_average_subject for a large number of subjects (>400) on a Mac Intel. I tried with different Freesurfer versions (all the log outputs are attached). Using the freesurfer version 4.3 and 4.4 the make_average_subject script always stop at the 297th subject with the error "Cannot allocate memory". I already tried to uncomment the line "limit descriptors unlimited" or to set it to various values, as proposed in the mailing list, but without success (it always stop at the 297th subject). Then I tried with the Freesurfer version 4.5 (therefore I had to recompute the lh.inflated.H and lh.inflated.K which are not automatically produced in previous versions), but with the 4.5 version I got a strange "license error" message in the middle of the script (and my licence is certainly fine as I can run any other script without problems). Does anyone have an idea? Many thanks in advance for your precious help, Marie

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using custom .tif files and .gcs files
by Danny Kim 01 Jun '10

01 Jun '10

Hi all, I was wondering if there are flags you can specify to use your own .tif and .gcs files in -autorecon3 processing pipeline. Currently, I am calling up individual processes to double check the results, but in the long run it would be useful to just automate this. Thanks Danny,

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Freesurfer June 2010