Freesurfer February 2005

freesurfer@nmr.mgh.harvard.edu

19 participants
22 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

4 3

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 ********************************

1 0

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.

2 1

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.

2 1

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

1 0

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/ .

2 1

Cluster version of FreeSurfer
by Satrajit Ghosh 21 Feb '05

21 Feb '05

Is there a cluster/parallel version of freesurfer available? Thanks, Satra -- Satrajit S. Ghosh Postdoctoral Associate Speech Communication Group Research Laboratory of Electronics, MIT

2 1

new tkmedit and tksurfer
by Wan Park 17 Feb '05

17 Feb '05

I am supposed to have libtiff, glut, tclkt, tix and blt installed, but I still receive this message: for volume: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished for surface: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished Curiously, I did not have this problems before the new binaries. Do you think that may be a line or it is more about env? thanks! wan

2 1

surface atlas
by Nguyen, Thang Q 16 Feb '05

16 Feb '05

Hello all, I have a question: What atlas freesurfer uses when it parcellates the final surface? If I were using a different atlas for my functional volumes, can I warp the data to the proper atlas? Thank you, Thang Nguyen

2 1

Re: [Freesurfer] new binaries for tkmedit and tksurfer
by Wan Park 16 Feb '05

16 Feb '05

hi kevin, i reinstalled fink and installed the blt package. then i copied the new binaries. now i cannot open the tkedit nor the tksurfer. these are the messages i receive: when i press volume: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished when i press surface: Command Finished env tksurferinterface=csurf patchname= /usr/local/freesurfer_package/freesurfer/bin/Darwin/tksurfer -22970 rh white -tcl /tmp/TmpTclSurf.20719 dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tksurfer can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished any suggestion? thanks a lot, wan On Feb 14, 2005, at 2:15 PM, Kevin Teich wrote: > > Do you have BLT installed via Fink or FinkCommander? > > > On Sun, 13 Feb 2005, Wan Park wrote: > >> hi teich, >> >> i went to this place: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ >> tkmedit_tksurfer-20050211-Darwin.tar.gz >> >> and I Unziped it in a temp directory, then move bin/tkmedit and >> bin/tksurfer into your freesurfer/bin/Darwin directory, and the >> lib/tcl/* files into freesurfer/lib/tcl. >> >> now when i put: >> >> $tksurfer >> >> i receive this new message: >> >> dyld: tksurfer can't open library: /sw/lib/libBLT.2.dylib (No such >> file or directory, errno = 2) >> Trace/BPT trap >> [ogden:freesurfer_package/freesurfer/subjects] wpark% >> >> how can i solve this problem? >> >> thanks >> >> wan > > -- > Kevin Teich >

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Freesurfer February 2005