Freesurfer

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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. >> >

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(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.

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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.

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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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Error running recon from command line
by Harshad Shanbhag 23 Feb '05

23 Feb '05

Hello, I installed FreeSurfer according to instructions on the website. To overlay FSL data, I used the following instructions from the FMRIB website. avwswapdim TEST x -z y TEST_reorient slices TEST_reorient bet TEST_reorient TEST_brain -f 0.4 mri_convert /home/bbernal/freesurfer/subjects/TEST/mri/orig/001/TEST_brain.img . recon-all -stage1 -subjid TEST However, the program gives me errors at this stage. I saved the error messages to the file that I have attached. Could you please have a look at it and help me with this. Thank you. Sincerely, Harshad.

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Cortical thickness correlated with age
by Claus Tempelmann 23 Feb '05

23 Feb '05

Hi everybody, for quite a while we have been comparing the cortical thickness between groups of patients and I hope we did everything as we should. Now, we have been trying to look for the correlation between cortical thickness and age and somewhere we seem to make a mistake. I know that it's difficult for you to find this mistake as there are many possible sources. Nevertheless, I hope that somebody has an idea ;-) Let me describe what we did: 1. We have a group of subjects, for all of the subjects we went through the steps of segementation, inflating, sphering, morphing ... 2. We edited a simple mtx-file named PatBas-Alter1.mtx (this is not the complete group, we just started with a few subjects to check the method). This file has only two columns, column 1 is the name of the subject in the SUBJECTS_DIR, column 2 is the age of the subject: Patient_2_Baseline 33 Patient_4_Baseline 42 Patient_5_Baseline 27 Patient_6_Baseline 40 Patient_7_Baseline 35 Patient_9_Baseline 48 Patient_10_Baseline 31 Patient_12_Baseline 29 Patient_13_Baseline 33 Patient_14_Baseline 37 Patient_15_Baseline 36 Patient_16_Baseline 41 Patient_17_Baseline 41 Patient_18_Baseline 26 Patient_21_Baseline 30 Patient_22_Baseline 37 3. We run mris_glm with a script or directly from the command line: (we are using version 1.18, 2003/06/30 20:40:38 greve) mris_glm --design $mtxfile.mtx --surfmeas thickness --hemi lh --trgsubj average7 --nsmooth 50 --gcv 0 0 1 --sigt sigt_$outputname-lh.w paint 4. We render sigt_$outputname-lh.w on the inflated surface of average 7. The result is surprising. Everywhere in the brain the cortical thickness shows a high positive correlation (t-values between 9 and 12) with age. Obviuosly, that's nonsense but I haven't seen any error message. 5. To check what may have happened we edited the mtx-file according to the motto the last will be the first, high age is assigned to young subjects and viceversa. 6. The resulting t-maps look very similar. They are not identical but again the cortical thickness shows a high correlation with (now faked) age, again we get t-values between 9 and 12. Any ideas what might have happened? I'm sure that we made something very stupid but what can that be?? Our mtx-file has only two columns. Can that be a problem?? Thanks in advance for all suggestions Claus ----------------------------------------------------------------------- Claus Tempelmann email: Claus.Tempelmann(a)medizin.uni-magdeburg.de Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany

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Workstation Spec
by maryfitz＠indigo.ie 22 Feb '05

22 Feb '05

I am about to purchase a workstation which will be used to run Freesurfer. Can you tell me the recommended specification for suitable hardware and OS. Many thanks Mary Fitzsimons Epilepsy Programme Beaumont Hospital Dublin -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ .

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