Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

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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Skull Stripping Problem
by iag iag 04 Mar '05

04 Mar '05

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thickness measures
by Kirk, Gregory 03 Mar '05

03 Mar '05

HI all, wrt useing freesurfer for obtaining cortical thickness there are the lh.thickness etc. and the theoretical paper in the citations, but I have not found things that would show me how to derive things like, average thickness for an individual, average thickness of a region or thickness at a point for an individual. I need it seems a way to interpret the two thickness files, i.e. mapping the numbers therin to a point on the geometry. thankx Greg

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Re: tkmedit's label files
by George Papadimitriou 03 Mar '05

03 Mar '05

Hi guys, I need to convert a label file into analyze, and see if I can import it to the Syngo as an ROI. How can I do this? I recall reading in an FS-FAST manual about a label2roi program. I don't see it in the standard nmr environment. I'd really appreciate your input. George P. On Wed, 2 Mar 2005, Ruopeng Wang wrote: > > Hi George, > > I have no idea what tkmedit's label file is. I never used tkmedit for > real. But I remember some time ago, someone, maybe Judith, converted one > to Analyze format, with help from one of tkmedit's developers (maybe > Doug). > > Ruopeng > > On Wed, 2 Mar 2005, George Papadimitriou wrote: > >> Hi Ruopeng, >> >> Are you familiar with tkmedit's label files? They are used to select an >> ROI. I would like to convert them into ANALYZE and import them into the >> Syngo. Have you done this before? What are your suggestions? >> >> Thanks, >> George P. >> >

2 4

(no subject)
by Harshad Shanbhag 03 Mar '05

03 Mar '05

Hi all, My earlier error was due to perl not properly configured. Thank you all for the help. However, on running recon-all -stage1 -subjid TEST, I am now getting the error message mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status Please help me out. Thank you, Harshad.

2 1

Error: Nu Correct
by Harshad Shanbhag 01 Mar '05

01 Mar '05

Hi all, I am trying to use FreeSurfer to overlay FSL data. On running the command $ recon-all -stage1 -subjid TEST I get the following error, Nu Intensity Correction Tue Mar 1 14:54:08 EST 2005 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=1.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc nu_correct: Command not found. ERROR: nu_correct I do have MNI Tools installed, in the freesurfer folder. Please let me know what I should do. Thank you. Harshad.

2 1

run-recon-monkey
by Reza Rajimehr 28 Feb '05

28 Feb '05

Hi, I have a question regarding convertion of raw multi-echo data to bfloat format. I used the following command in seychelles: pbsubmit -c "run-recon-monkey /space/stego/5/users/wim/edgar050218 1 6 7 8 > edgar050218_1.out" -p -m reza@nmr.... The converstion has been done succesfully for one functional run but then it has been stoped and there is the following error message: ??? Error using ==> reshape To RESHAPE the number of elements must not change. Error in ==> /homes/4/greve/anders/mdh_io/read_mdh_adc_VA21.m On line 114 ==> adc_data = reshape(adc_data, 2, mdh.SamplesInScan); Error in ==> /homes/4/greve/anders/mdh_io/read_mdh_adc.m On line 5 ==> [adc_data, mdh] = read_mdh_adc_VA21(fid); Error in ==> /homes/4/greve/anders/mdh_io/read_mdh_and_mrprot.m On line 151 ==> [adc_data, mdh] = read_mdh_adc(fid,VersionNum); Error in ==> /homes/4/greve/anders/recon_Monkey_fMRI.m On line 199 ==> [kdat1,krev1,ktim1,pcdat1,pcrev1,pctim1,h1] = .. . I do not know what this error message refers to. I would be thankful if anyone has a suggestion. Best Wishes, Reza -- ******************************** Reza Rajimehr, M.D. NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

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Tksurfer Error
by Harshad Shanbhag 24 Feb '05

24 Feb '05

Hello, I am facing a problem in running tkmedit or tksurfer. So I looked up the posts and found a thread which explained using tkmedit.static instead of tkmedit. I did that and I could run tkmedit. However, I can't find the tksurfer.static file in that same directory. Please let me know how I could run tksurfer. I get this error message when i run tksurfer from the command line. tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory. Thank You. Sincerely, Harshad.

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Freesurfer