Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

Statistical tests on Tracula's path spline
by Yuwen Hung 02 Oct '15

02 Oct '15

Hi, Thanks for the great FreeSurfer Course this past week. After running through Tracula and extracted the path stats (by voxel) across all subjects, can I apply mri_glmfit to test the group differences using the generated txt file that has all subject's diffusion meassure (e.g., FA) along particular spline voxels (the pathstats.byvoxel.txt, for example)? Thanks! ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: 01 October 2015 12:00 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 140, Issue 3 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. WM segmentation error longitudinal stream (Adam, Ruth) 2. Test incoming emails - (pablo najt) 3. Re: dt_recon (Alshikho, Mohamad J.) 4. mri_convert doubles file size when changing TR header information (Shaun Patel) 5. Re: PVE correction tool within the V 6 beta (m.bahri(a)ulg.ac.be) 6. Re: Error Messages for Accessing Bin (Bruce Fischl) 7. Re: Calculate the cortical thickness in patients with brain tumor (Bruce Fischl) 8. Re: Calculating local gyrification using CIVET's surface file ('.obj') (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Thu, 1 Oct 2015 14:35:30 +0200 From: "Adam, Ruth" <Ruth.Adam(a)med.uni-muenchen.de> Subject: [Freesurfer] WM segmentation error longitudinal stream To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <AF867463-A1D8-432B-A4F3-83396DB900B1(a)med.uni-muenchen.de> Content-Type: text/plain; charset="us-ascii" Hi all, We have run longitudinal analysis on two time points. The resulting longitudinal WM surface for both time points excludes large parts of the cortex. The cross sectional surfaces and the wm.mgz are correct. The base wm.mgz also seems to be fine, however, the base white and pial surfaces do not follow the wm volume properly. We have rerun the longitudinal anlaysis (recon-all -long) according to the cheat sheet: 1. marking the base wm.mgz border with 255 voxel value (instead of 110) 2. adding control points to the base wm.mgz but it did not change the original result. Any idea how this can be fixed? Thank you very much in advance! Best, ruthi ------------------------------ Message: 2 Date: Thu, 1 Oct 2015 13:27:37 +0000 From: pablo najt <pablonajt(a)hotmail.com> Subject: [Freesurfer] Test incoming emails - To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BLU181-W20EA2FE3E891F70E4CF592AE4C0(a)phx.gbl> Content-Type: text/plain; charset="iso-8859-1" I am sending this message as a test since my income emails from FS stopped working on the 29 of September.Regards

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Cannot change min threshold in Configure Overlay Display TKSurfer
by Oana Georgiana Rus 02 Oct '15

02 Oct '15

Dear developers/users? When I load a *mgh.sig* file in *TkSurfer* and I go on *Configure Overlay Display* and want to change the *min Threshold on 1.3* or wathever number I can't edit or do that? did somebody encounter the same problem? How can you solve it? Thank You. -- Oana Georgiana Rus PhD Student Neuroimaging Center TUM-NIC Klinikum rechts der Isar Technische Universität München Einsteinstr.1 81675 München Raum 5.8 Tel. 089 4140 7971

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Hippocampus visualisation
by Erik O'Hanlon 02 Oct '15

02 Oct '15

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Post-doctoral Positions in Affective Neuroscience at McLean Hospital/Harvard Medical School
by Poornima Kumar 01 Oct '15

01 Oct '15

Two post-doctoral positions are available within the Laboratory for Affective and Translational Neuroscience at McLean Hospital/Harvard Medical School, directed by Diego A. Pizzagalli, Ph.D. The laboratory is part of the Center for Depression, Anxiety and Stress Research (CDASR), a vibrant research center that embraces a multi-disciplinary approach to improve our understanding of the psychological, environmental, and neurobiological factors associated with depression, anxiety and related disorders across the lifespan ( http://cdasr.mclean.harvard.edu/) Currently ongoing studies in Dr. Pizzagalli’s laboratory focus on reward processing, stress responsivity, and executive functioning in a range of populations including individuals with major depression, mood spectrum disorders, as well as at-risk samples (e.g., offspring of parents with MDD; individuals with past MDD). These studies employ a variety of approaches, including high-density EEG, fMRI, PET, MRS, molecular genetics, and assays of hormonal/inflammatory markers, and often a treatment component (e.g., CBT). Opportunities will be available to pursue independent research and interdisciplinary collaborations across Harvard Medical School. Depending on research focus, candidates will have access to three research-dedicated human MRI scanners (3 T, 4 T) and one animal MRI scanner (9.4 T), as well as 128-channel EEG systems. A strong background in EEG/ERP or fMRI techniques is required, and clinical training is a plus. To apply, send a CV and a cover letter describing your research interests, and arrange for three letters of recommendation to be sent to David Crowley ( djcrowley(a)mclean.harvard.edu) Review of applications will begin immediately (expected start date: Summer 2016). McLean Hospital, which is an affiliate of Harvard Medical School, is an Equal Opportunity Employer. As an equal opportunity employer, McLean seeks qualified candidates for all posted employment opportunities without regard to race, color, age, religion, gender, national origin, disability or veteran status. McLean particularly welcomes applications from minorities, women, and persons with disabilities.

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Re: [Freesurfer] Registering set of extracted hippocampus
by Chester Dolph 01 Oct '15

01 Oct '15

Hello, Rewording to clarify in case the wording was confusing. What I would like to do is to use each registered ROI for intensity based analysis. I am confused how to use Freesurfer to register and align about three axis. I understand there is variability with positioning the head within the scanner of MRI. I am guessing one solution might be to align each ROI centroid to the same location. This seems to be a trivial concept, but I was hoping there was a simple way of doing this using Freesurfer tools. I appreciate your time and help. Thanks, Chester > On Sep 11, 2015, at 5:31 PM, CHESTER DOLPH <cdolp001(a)odu.edu> wrote: > > Dear experts, > > I look like to register a set of extracted hippocampus to a common atlas. Here is my workflow: > > I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocampus do not seem aligned in terms of the axial axis. > > I have been looking at the registration tools at: > > https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration> > > Would someone please make a recommendation of a freesurfer tool well suited to registering a set of extracted left or right hippocampus to a common atlas? Also is there a flag to indicate the region, for instance from the look up table: $FREESURFER_HOME/FreeSurferColorLUT.txt > > Thanks, > Chester

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Re: [Freesurfer] Error Messages for Accessing Bin
by Bruce Fischl 01 Oct '15

01 Oct '15

can you try chmod a+x on one of them and see if it can then be executed? e.g.: chmod a+x /home/tle7/freesurfer/bin/mri_convert /home/tle7/freesurfer/bin/mri_convert and see if you get an error. If not, you probably downloaded the wrong hardware version cheers Bruce On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote: > > Hello, > When I run the command "sFSstart" on version 5.0.0, I am receiving the > messages below. Would you please explain to me what the problem is? It > seems like there is trouble accessing the bin. > Thank you > > -------- freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /home/tle7/freesurfer > FSFAST_HOME /home/tle7/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /home/tle7/freesurfer/subjects > MNI_DIR /home/tle7/freesurfer/mni > tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2 > studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter > H 0 > checking sid number 00152-DT2 > 1 > 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm > Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 > Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 > INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects > Actual FREESURFER_HOME /home/tle7/freesurfer > Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP > Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary > file not executable. > /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file > not executable. > /home/tle7/freesurfer/bin/mri_robust_register: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_robust_template: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_and: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_or: Exec format error. Binary file not > executable. > /home/tle7/freesurfer/bin/mri_fuse_segmentations: Exec format error. > Binary file not executable. > /home/tle7/freesurfer/bin/mri_segstats: Exec format error. Binary file > not executable. > -cw256 option is now persistent (remove with -clean-cw256) > /home/tle7/freesurfer/subjects/00152-DT2_v5 > > mri_convert/home/tle7/freesurfer/subjects/practicemotherdaughter/rawdata/00152-DT2/MR. > 1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm > /home/tle7/freesurfer/subjects/00152-DT2_v5/mri/orig/001.mgz > > /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file > not executable. > Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP > Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 00152-DT2_v5 exited with ERRORS at Mon Sep 28 10:43:57 > PDT 2015 > > tle7@sni-vcs-gotlib:~$ > > > >

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Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
by Anastasia Yendiki 01 Oct '15

01 Oct '15

It's trying to find a file called SUBJECTS_DIR/Enzo_recon1/dti.nii. This is a relative path, i.e., it's trying to find it under the directory where you are currently cd'd. This seems like a problem with defining paths properly for unix, rather than a tracula problem per se. On Wed, 30 Sep 2015, andrea cristina Lima wrote: > I got the error below. Could you help me? I've already check the dti file and it seems Ok. Tks > > macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c > /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt > > INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer > > INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1 > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local -log > SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd > > #------------------------------------- > > /Applications/freesurfer/bin/trac-preproc > > #------------------------------------- > > #@# Image corrections Wed Sep 30 11:27:28 BRT 2015 > > mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz > > mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz > > niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from SUBJECTS_DIR/Enzo_recon1/dti.nii... > > Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; > root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015 > > > -- > Andrea Cristina de Lima PardiniCV: http://lattes.cnpq.br/0921194840474573 > >

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Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')
by Bruce Fischl 01 Oct '15

01 Oct '15

Hi Kie Woo can you run mris_euler_number on those surfaces to see if they are topologically correct? cheers Bruce On Thu, 1 Oct 2015, Nam, Kie Woo wrote: > > Dear experts, > > > > I’m trying to calculate local gyrifcation index using CIVET’s surface file > (‘.obj’). > > > > > > > > > > First, I’ve successfully done ‘CIVET --> FreeSurfer’ conversion and created > a ‘.pial’ file - below are the commands that worked for ‘CIVET --> > FreeSurfer’ and ‘FreeSurfer --> CIVET’ conversions. > > CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big > Endian)): “ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj > -o_fs lh.pial; mris_convert lh.pial.asc lh.pial” > > FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): “ConvertSurface > -i_fs lh.pial -o_mni lh.pial” > > > > > > > > > > Then, I ran “recon-all -s Subject -localGI”, but it keeps crashing with the > following message. > > ************************************************************************ > > lGI for vertex number 5501 of the outer mesh is 4.1122 > > lGI for vertex number 5601 of the outer mesh is 0.86156 > > lGI for vertex number 5701 of the outer mesh is 3.8343 > > ... remeasuring lGI value for vertex iV = 5801. It may take a few minutes. > > WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high > (lGI=62.3205)... > > ...lGI computation will be stopped. This may be caused by topological > defects, check mris_euler_number on the pial surface. > > ************************************************************************ > > > > The link below suggests rerunning “recon-all -autorecon2-wm -randomness”, > but it’s not an option for me because I have no other FreeSurfer compatible > files except “.pial”. > > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html > > > > > > > > So, could there be any solution for this? > > > > > > > > Best wishes, > > > > Kie Woo > > >

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Hippocampal subfields
by von Polier, Georg Ferdinand Anto 02 Dec '14

02 Dec '14

Dear FreeSurfers, I am just finishing a paper using output from Hippocampal subfields and recognized that the current version has been deprecated. I am interested in volumes of the whole hippocampus. Are these volumes still valid and can you estimate when a new version will be available? Can you provide maybe a brief comment on the decision to deprecate the current version? Best regards, Georg

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error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n
by zhang mingxia 02 Dec '14

02 Dec '14

Dear freesurfer experts, I got this error when I analysis the retinotopic data by this code: selxavg3-sess -a rtopy.self.lh -sf sessid The version of freesurfer is v5.1.0. What does this error mean? What should I do? Thank you for your support! Mingxia

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