Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

mkbrainmask failed
by Jia Liu 14 Mar '05

14 Mar '05

Dear group- When I tried mkbrainmask-sess with my data, I encountered an error (see below), and the program aborted. Could any one tell me how to fix this problem? I am using the newest version available from FreeSurfer download site. Thanks, jia zion:/nfs/home/jliu/data/test/mystudy> mkbrainmask-sess -sf sessid_re001_2 -df sesspar ---------------------------------------------------------------------------- -------------------- /nfs/home/jliu/data/test/20040527rd Sun Mar 13 16:49:50 CST 2005 -------------------------------------------------- /nfs/home/jliu/data/test/20040527rd/bold mkbrainmask -i 005/f -o masks/brain -thresh 0.1 -umask 2 -------------------------------------------------- Scratch Dir is /tmp/mkbrainmask_22219 # ---------- Converting bvolume to .img ------------------ # mri_convert 005/f_000.bshort /tmp/mkbrainmask_22219/f.img Reading 005/f_000.bshort ... Reading 005/f_001.bshort ... Reading 005/f_002.bshort ... Reading 005/f_003.bshort ... Reading 005/f_004.bshort ... Reading 005/f_005.bshort ... Reading 005/f_006.bshort ... Reading 005/f_007.bshort ... Reading 005/f_008.bshort ... Reading 005/f_009.bshort ... Reading 005/f_010.bshort ... Reading 005/f_011.bshort ... Reading 005/f_012.bshort ... Reading 005/f_013.bshort ... Reading 005/f_014.bshort ... Reading 005/f_015.bshort ... Reading 005/f_016.bshort ... Reading 005/f_017.bshort ... Reading 005/f_018.bshort ... Reading 005/f_019.bshort ... Reading 005/f_020.bshort ... reading from 005/f_000.bshort... INFO: bvolumeRead: min = 0, max = 1480 TR=1.50, TE=32.00, TI=32.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -0.990268, 0.139173) k_ras = (-0, 0.139173, 0.990268) writing to /tmp/mkbrainmask_22219/f.img... Analyze Output Matrix -3.125 0.000 -0.000 104.375; 0.000 -3.095 0.668 146.084; 0.000 0.435 4.753 -44.536; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 3 # ---------- Using FSL's BET to Extract Brain------------------ # This program has not been compiled for this data type /nfs/home/jliu/data/test/20040527rd/bold bet /tmp/mkbrainmask_22219/f /tmp/mkbrainmask_22219/brain -m -f 0.1 ERROR: bet failed ERROR: mkbrainmask failed Exit 1

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Transformations
by Lars Tjelta Westlye 14 Mar '05

14 Mar '05

Hi, I'm having some problems using the talairach command on scewed T1 volumes (the subject has been scewedly scanned). The talairach coordinates (mni Talairach) does not seem to transform the volume properly, resulting in scewed segmentations when I manually insert the mni Talairach coordinates into the mri_filled command. (that is, mni Talairach coordinates for lh, rh, c.callossum and pons). Are there any alternative transformation commands which may solve this issue? Best wishes, Lars Tjelta Westlye

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FreeSurfer/FSL course
by Bruce Fischl 12 Mar '05

12 Mar '05

--------------------------------------------------------------------- Announcing: FSL & FreeSurfer Course 18-22 July 2005 - Boston, USA Organised by FMRIB Centre, University of Oxford and Martinos Center for Biomedical Imaging, MGH/MIT/HMS http://www.fmrib.ox.ac.uk/fslcourse/2005 --------------------------------------------------------------------- We are pleased to announce the 2005 FSL & FreeSurfer course in Waltham, Boston, USA. 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 at most two attendees per computer. By the end of the course, attendees should be able to fully analyse their own FMRI and MRI data sets. The course is aimed at both new and existing users of these packages and will cover both basic and advanced features. The methods covered include * Functional MRI analysis: - GLM-based analysis of FMRI data including Bayesian multi-subject statistics (FSL - FEAT) - Model-free (ICA) analysis of FMRI data (FSL - MELODIC) * Cortical-flattening of images and its applications (FreeSurfer): - Cortical flattening for improved FMRI analysis, including inter-subject averaging - Group studies of cortical morphometry; thickness, folding, surface area, volume * Structural MRI analysis: - Image registration and unwarping (FSL - FLIRT/FUGUE) - Brain extraction and tissue-type segmentation (FSL - BET/FAST) - Structural spatial statistical analysis e.g. atrophy (FSL - SIENA/SIENAX) * Analysis of diffusion-weighted imaging data, including tractography and related applications (FSL - FDT) * Paradigm optimisation (Optseq) --------------------------------------------------------------------- For more information and to regsiter, visit: http://www.fmrib.ox.ac.uk/fslcourse/2005/ ---------------------------------------------------------------------

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converting Siemens data
by Renat Yakupov 11 Mar '05

11 Mar '05

Hello, everyone. I am trying to convert Siemens structural images into COR images. If I do it from the GUI, it wont read the headers and even if I enter all the info manually, it would still say: "Convert (040004_S01) filed - working on: orig/mpr.easy/-unset-". What does it mean? Also, what do I enter in "Image Name Format" field if the image file names are something like 040004_S01_.2.98.2005.03.11.09.57.26.875000.10693070.IMA and both numbers 98 and 10693070 are changing in different filenames? However, if I try to do it with mri_convert routine, it would give me an error: "siemensRead(): file cols (18771) not divisible by image cols (926031904)". Now what is that supposed to mean? Does anybody every had problems like these before? As for images I use, I simply transferred them from the scanner as is without any additional work on them. Thank you beforehand. Regards, Renat.

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inflated and pial node mismatch
by Ronald E Bryan (rbryan＠Princeton.EDU) 11 Mar '05

11 Mar '05

I wasn't able to run the afni programs 3dVol2Surf or MapIcosahedron on the Freesurfer surfaces since the number of nodes in the smoothwm vs pial surfaces differed: ** invalid surfaces, different # nodes (166167,166157) How can we best resolve this difference in the node numbers? thanks, -Ronnie

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mris_convert help
by Rudolph Pienaar 11 Mar '05

11 Mar '05

Hi all - I'd like to convert a FreeSurfer surface to ASCII format - essentially so that I can import it into say an external 3D viewer program. I understood that 'mris_convert' converts a surface to ASCII. For a given subject with say an inflated right hemisphere surface, I've tried called it using > mris_convert rh.inflated rh.inflated.txt but the resultant file is also a binary (i.e. *not* text). I have also tried > mris_convert -c rh.curv rh.inflated rh.inflated.txt this produces a much smaller resultant file, which is still binary. Any help? Cheers --R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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(no subject)
by tao＠ucsd.edu 10 Mar '05

10 Mar '05

Hi Bruce: Thanks! I tried on a previous .tri file, and got the same answer. But when I tried a surface file from "save surface" in TkSurfer, it looks weird, and the total vertex number is not 163842, which is the standart in ic7.tri. Furthermore, it seems that we can only generate half brain surface everytime. That might be the reason that caused the strange result. > Would you please give me some advice? regarding how to generate a whole brain surface file with the same amount vertex of ic7? > >> >> Thanks a lot! >> >> Tao >> >> >> Bruce Fischl wrote: >> >>> actually, you can just use the surfaces ico[34567].tr (7 is the highest res). That is, use the topology from them, but copy the vertex positions from the average surface. I think Matti (ccd) has done this. >>> >>> cheers, >>> Bruce >>> >>> On Wed, 9 Mar 2005, Tao Song wrote: >>> >>>> >>>> Hi Bruce: >>>> >>>> Thanks for your quick reply. Actually, I can get a .tri file by save surface as ... , then use mris_convert, and can read it. It is a very very high resolution tessellation of the brain, which looks similar as the result in TkSurfer, except color. And the coordinate system is already RAS. Is this the ICO surfaces (I checked wideman-one webpage, seems that both ICO and TRI are triangular surfaces)? Then if we want to choose first n points, (I suppose that you talk about n vertices), I have to get rid off the faces that include vertices other than the selected n vertices. I wonder if my understanding is correct? I tried it on surface generate by ""save surface as", there are large holes in the mesh. I also tried it on mris_converted rh.pial and lh.pial, I wonder do I need to combine those two together, to obtain a whole brain? >>>> >>>> Thanks Again! >>>> >>>> >>>> >>>> >>>> Bruce Fischl wrote: >>>> >>>>> the decimation code only finds equally spaced points, I don't think it generates a tesselation. One way to downsample is to map onto on of the ico surfaces, then pick the first n points, where n is one of the downsampled icosahedra. Otherwise, I think there are other people who have written surface downsampling packages. >>>>> >>>>> cheers, >>>>> Bruce >>>>> >>>>> On Wed, 9 Mar 2005 tao(a)ucsd.edu wrote: >>>>> >>>>>> Hi: >>>>>> >>>>>> I am trying to generate a down sampled tessellation file from inflated >>>>>> pial in TkSurfer. I used write decimation in tool->surface menu, and can >>>>>> find vertices. How can I fill the boundary of those points, and save the >>>>>> vertices and faces, so that I can get a new .tri file? >>>>>> >>>>>> Thanks a lot! >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Expert Preferences
by Marie Schaer 10 Mar '05

10 Mar '05

Hi everybody, I am using Freesurfer to measure the cortical thickness, and I was wondering if there was any way to specify the WMFilter Expert Preferences when running recon-all -stage1 from the commandline? Thanks in advance, Marie Schaer

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Re: [freesurfer] spherical surface problem
by raffaele raffaele 10 Mar '05

10 Mar '05

Hi Brien, I tried loading the ?h.curv or ?h.sulc file, but the all grey sphere always appears. I downloaded recostructed tutorial data from download freesurfer area and I have the same problem. Thanks Raffaele Esposito _________________________________________________________________ Blocca le pop-up pubblicitarie con MSN Toolbar! http://toolbar.msn.it/

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(no subject)
by tao＠ucsd.edu 09 Mar '05

09 Mar '05

Hi: I am trying to generate a down sampled tessellation file from inflated pial in TkSurfer. I used write decimation in tool->surface menu, and can find vertices. How can I fill the boundary of those points, and save the vertices and faces, so that I can get a new .tri file? Thanks a lot!

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