Freesurfer

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30132 discussions

Re: [Freesurfer] Question about the orientation of input image in FreeSurfer. Thanks a lot!
by Douglas N Greve 07 Nov '11

07 Nov '11

> On Nov 4, 2011, at 10:46 PM, yaping wang <ypwang.npu(a)gmail.com > <mailto:ypwang.npu@gmail.com>> wrote: > >> Hi, Dear Dr Fischl, >> Sorry to interrupt you. >> I have a simple question to ask you. It's about the orientation of >> the input image for FreeSurfer. The version I used now is version 4.5.0. >> >> First I referred to the "README" in ${FreeSurfer_Dir}/subjects, but I >> didn't found the directory named "ernie". >> So I referred the following images for the input image orientation: >> ${FreeSurfer_Dir}/subjects/bert/mri/orig/001.mgz (002.mgz and 003.mgz) >> and >> ${FreeSurfer_Dir}/subjects/bert/mri/rawavg.mgz >> ${FreeSurfer_Dir}/subjects/bert/mri/orig.mgz >> >> I show them in "FreeSurfer_sample.JPG", the first row is the 001.mgz >> (the orientations of 002.mgz and 003.mgz are same with 001.mgz, so I >> just show 001.mgz), the second row is the the rawavg.mgz and the >> orig.mgz. >> From http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable, I >> think 001.mgz (002.mgz and 003.mgz) is the input image, and the >> rawavg.mgz and orig.mgz are the following two output images. >> >> I test out data with "RAS" orientation as input image, it also gets >> the following two output image, and the orig.mgz has the same >> orientation as the sample image of Freesurfer. I show them in >> "ourTestData.JPG". Same with the previous figure, the first row is >> our input image, and the second row is the following two output >> images. But the origin is so different. So I have the following >> questions: >> >> 1. What's the correct orientation FreeSurfer request? >> Is it correct for the orientation of the input image of our test >> data? >> I have found that it can applied to "RAS" and "LAS" direction for >> "mri_watershed". So the input image can be any orientation, is it >> correct? FreeSurfer does not require any particular orientation. The orientation information needs to be correct. Inside of FreeSurfer, it will automatically be converted to LIA. >> >> 2. Will the "mri_robust_template" or "mri_add_xform_to_header" change >> the orientation of the input image to the orientation FreeSurfer request? No. >> >> 3. What's the meaning of the origin shown in MRIcro? It comes from >> the template or ...? >> If the "orig.mgz" of our test data has reoriented to the >> orientation of FreeeSurfer, why the origin is different the >> "orig.mgz" of FreeSurfer sample data? >> And why it's changing for our test data (from the input data--> >> rawavg.mgz---> orig.mgz, it's always changing)? I don't know what MRIcro is doing. The origin usually means the xyz of the first voxel. FS changes the orientation to LIA (and voxel size to 1mm) because this is assumed in all subsequent processing. doug >> >> Thank you so much! >> >> Best. >> Yaping >> <FreeSurfer_sample.JPG> >> <ourTestData.JPG> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] different lengths of runs
by Douglas N Greve 07 Nov '11

07 Nov '11

Hi Maryam, which version are you using? It should be fine to have different length runs (it was a problem in older versions). If you really need to make them the same length, using mri_convert with the --ndrop option to remove the last few time points. doug Maryam Vaziri Pashkam wrote: > Hi Doug, > > In one of my experiments I have 8 runs. 3 of these runs have 190 TRs > and 5 of them have 192 TRs. The difference is only that there is a 4 > sec fixation period in the end of the 5 longer runs which I dont > really need. Otherwise the 8 runs could potentially be combined. Is > there anyway that I could combine the runs in my experiment? The > Selxavg3 does not let me analyze the 8 runs together as they have > different lengths. Is there anyway to get rid of the last two TRs in > the 5 longer runs and combine the runs in the analysis? I had an idea > to import my .nii files to Matlab, cut off the last two TRs and then > save them as .nii files again. Would that work? Is there a better way > to do this? > > Thanks, > Maryam -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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dimensions of input and annot for mri_segstats
by Linda Douw 07 Nov '11

07 Nov '11

Hi all, I have nifti files containing the surface-projected time series data of a subject (obtained using procsurffast), both lh and rh. These time series are projected onto fsaverage5, and are 3414 x 1 x 3 time points, where 3414*3 = 10242 are the number of vertices for each hemisphere. Now, I would like to extract the mean time series for 138 ROIs, which are defined in an annotation called sparc I made: mris_divide_parcellation fsaverage5 lh aparc.annot sparc.txt lh.sparc I would assume that these files are now of the same dimensions. However, when I run: mri_segstats --i /subject/surf/subject_projectedto_fsaverage5.nii.gz --avgwf /subject1/ts_lh.txt --annot fsaverage5 lh sparc it crashes because the dimensions are not the same (the segmentation is 10242 x 1 x 1). They do both overlay nicely on fsaverage5 inflated using tksurfer. What may cause this mismatch? And is there a solution? Thanks, Linda

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Re: [Freesurfer] mri_cvs_register can not find
by lzollei＠nmr.mgh.harvard.edu 06 Nov '11

06 Nov '11

Hi Martin, Could you give more details? Which version of mri-cvs-register are you using? Was there a log file that you could share also? Thanks, Lilla ------Original Message------ From: Martin Kavec To: Freesurfer mailing list To: Lilla Zollei Subject: mri_cvs_register can not find Sent: Nov 4, 2011 03:44 Hi all, I am trying to run mri_cvs_register but for some reasons it always terminates with: ERROR: Can not find or read $SUBJECTS_DIR/MY_SUBJECTS/cvs/combined_tocvs_avg35__elreg_aseg.m3z My command is as follows: mri_cvs_register --mov MY_SUBJECT Indeed the file is not there, but another one with the exactly the same name, but different suffix .tm3d is there. Anybody encountered similar problem? Any idea what can be wrong? Thanks in advance, Martin Sent via BlackBerry by AT&T

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Visulaization of FreeSurfer-defined ROI
by Jade 04 Nov '11

04 Nov '11

Hello Freesurfer experts, I am a beginner in using Freesurfer. I want to make a figure illustrates a specific area of ROIs (e.g., lh. hippocampus). How can I visulaize the Freesurfer definded ROIs? Thanks in advance!

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func2roi-sess question
by Khena Swallow 04 Nov '11

04 Nov '11

Hi, I've been using func2roi-sess for region of interest analyses and was hoping that someone here could answer what might be a pretty basic question. Does anyone know when in the analysis stream the data from voxels in an ROI are averaged? I can think of two possibilities. The first is that the BOLD data are first averaged and then the response of the ROI to different types of events is estimated. The other possibility is that the model estimates are first calculated for each voxel, and these are averaged to produce a single estimate for the ROI. I've read through the func2roi-sess help page and still have some doubt about what the answer is. Any help on clarifying which of these approaches func2roi-sess uses would be greatly appreciated! Thanks! Khena -- Khena M. Swallow, Ph.D. Research Associate Department of Psychology University of Minnesota

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Error During Talairach Transform
by Joshua Lee 04 Nov '11

04 Nov '11

#@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 /home/virtualuser/freesurfer/subjects/test005/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm I am receiving the error (pasted below) on about half of my scans, despite all cans using same protocol. I detect no obvious issue with the quality of the images. I have original dicoms, and am using mri_convert to save into a single .mgz (or .nii, doesn't neem to make a difference), and the unpredictability of the error makes diagnosis problematic. TKMedit2 reveals absolutely wacky registrations. I am processing on Freesurfer 5.1, and have replicated issue on two different installations. I am designing a new longitudinal study inheriting the same imaging protocol and I do not want to get in a situation demanding manual editing of the talairach. Can anyone help me out? Thanks, Joshua ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0030, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 EDT 2011 For more details, see the log file /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805

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Re: [Freesurfer] .license error
by Bruce Fischl 04 Nov '11

04 Nov '11

Hi Nooshin you should post this type of question to the list so others can answer. Are you sure that the file /Users/nzadeh/freesurfer/.license exists? thanks Bruce On Tue, 1 Nov 2011, Zadeh, Nooshin N. wrote: > > Hi and Good afternoon > > I have downloaded the FS and in next steps to set it up, I got the license and made a file and copied that license and saved on the "/Users/nzadeh/freesurfer" named "license". but when I start reconning one subject I received the following error message. When I changed the name of license file to ".license" it says that file would be hidden. After that, with reconning the subject again, I received same error message. With running other FS commands, I get the same error message. Can you please guide me how can I install FS properly and where is my mistake? I appreciate your time. > > > ERROR: FreeSurfer license file /Users/nzadeh/freesurfer/.license not found. > 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. > > Thanks > Nooshin > > >

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Longitudinal pipeline question
by Irene Altarelli 04 Nov '11

04 Nov '11

Dear Fs experts, I am running a longitudinal dataset through the longitudinal pipeline, and noticed that for one subject, although we kept everything the same (sequence, coil etc) the two timepoints' brainmasks look different: timepoint one (in the attached snapshot, gs_tp1) looks as if it has been smoothed, compared to timepoint two (gs_tp2). I have checked some other images from this subject, and the same seems to occur for orig.mgz, but not for rawavg.mgz. Any idea on what could be causing the difference would be greatly appreciated. Thanks in advance, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23

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[Fwd: [FSL] Announcement: The 2012 FSL & FreeSurfer Course]
by Nick Schmansky 04 Nov '11

04 Nov '11

---------------------------- Original Message ---------------------------- Subject: [FSL] Announcement: The 2012 FSL & FreeSurfer Course From: "Mark Jenkinson" <mark(a)FMRIB.OX.AC.UK> Date: Thu, November 3, 2011 12:54 pm To: FSL(a)JISCMAIL.AC.UK -------------------------------------------------------------------------- We are pleased to announce the 2012 FSL & FreeSurfer Course, to be held in Auckland, New Zealand (May 14-18). It will run immediately after the ISMRM conference, which will be in Melbourne, Australia. The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with one computer provided for every two attendees. After completing the course, attendees should be able to analyse their own FMRI and MRI data sets. The course lasts 5 days, from May 14-18, 2012. Numbers of attendees are strictly limited and are available on a first-come-first-served basis. For full information and to register for the course, please go to: http://www.fmrib.ox.ac.uk/fslcourse/current.html Regards, course organisers. Dr Mark Jenkinson University Research Lecturer Head of Structural Image Analysis FMRIB Centre, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222769 (fax 222717) mark(a)fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~mark

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