Freesurfer March 2005

freesurfer@nmr.mgh.harvard.edu

28 participants
35 discussions

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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spherical surface problem
by raffaele raffaele 09 Mar '05

09 Mar '05

Hi all, after process volume, create surface and manually edit topological defects procedure, I did fix surface topology process. When fix surface topology process finished I try to view spherical surface but an all grey sphere appears. What can I do? Thanks Raffaele Esposito Pisa Italy _________________________________________________________________ Blocca le pop-up pubblicitarie con MSN Toolbar! http://toolbar.msn.it/

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Convert procedure
by Luca Roccatagliata 08 Mar '05

08 Mar '05

Hi, I have problems with the convert/average procedure. I acquired 124 sagittal slices with a SPGR sequence. Is the conversion from sagittal plane to coronal plane included in this step? I tried to load .dcm and. img files. First of all, are they both compatible with mri_convert? I tried with 1 volume file in analyze format, but Freesurfer didn't recognize the header and I had to set it manually. I noted that, even giving the command save, a new file .hdr was not created at this point: the .hdr file created when converting from dcm to analyze was only present in the folder. Then it asked also for .dcm files. This is the error it gave me, after starting the volume interpolation: reading /binfs/freesurfer_alpha/subjects/provaANAsag/mri/orig/001/1.2.840.113619.2.135.3596.375144.5930.1108451068i00001.hdr... mri_read(): couldn't determine type of file /binfs/freesurfer_alpha/subjects/provaANAsag/mri/orig/001/1.2.840.113619.2.135.3596.375144.5930.1108451068i00001.hdr /binfs/freesurfer_alpha/bin/Linux/mri_average: MRIread(/binfs/freesurfer_alpha/subjects/provaANAsag/mri/orig/001/1.2.840.113619.2.135.3596.375144.5930.1108451068i00001.hdr) failed Thanks in advance, Laura Bonzano Luca Roccatagliata

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averaging curvature
by Rutvik Desai 07 Mar '05

07 Mar '05

I averaged the curvature of 20 hemispheres using mris_average_curvature, in the hopes of producing something like the average7 brain with major sulci and gryi displayed. This can be used to display group functional data. However, the resulting curvature looks nothing like average7. Seems that there is a lot of anatomical variability (after spherical registration) so the major structures are hard to see clearly in the average. How was the average7 surface created, and is there anything I am doing incorrectly? I have also tried this with 10 and 30 brains, and the results are similar. I have also averaged sulcal depth instead of curvature, and those maps are also not clean like average7. % mris_average_curvature lh.curv lh smoothwm s1 s2 s3 s4...s20 lh.avg20.curv thanks, Rutvik

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Freesurfer March 2005