Freesurfer August 2004

freesurfer@nmr.mgh.harvard.edu

20 participants
30 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

cortical thickness stats.
by L.Scheef＠uni-bonn.de 30 Aug '04

30 Aug '04

Dear list members! I would like to analye cortical thickness data and wonder which is the best way to proceed... So far I have processed the data using recon all (including manual top fixing). This includes the registration using the average7 subj. on the sphere. 1) Is it a valid approach to use the coreg. on the average7 or should I take a similar approach as used by VBM building a study specific template and do the coreg step on this template once again. 2) For doing the cortical thickness group analysis (using mris_glm) it seems to be the best to use a specific group average. Is there any "ready to use script" which I could use to build the average_study data and all the stuff needed by mris_glm? 3) Which files should be calculated to use them later for the stat. analysis and overlay? Many thanks for your help! Best wishes, Philppe and Lukas Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef(a)uni-bonn.de

2 5

bert's data
by Daniel Schwartz 27 Aug '04

27 Aug '04

I'm just starting to learn FreeSurfer, and am trying to go through bert's data step by step. When I click "Read Header" in the Setup Structural Scan Parameters, after selecting "COR-.info", it returns "-unset-" in the file type field. When I try this with another data set (mine) it does the same thing. Are the formats the problem? Is this something that I've done wrong? Thankyou for ANY help you can give me... -Daniel Daniel Schwartz, CIC Functional Brain Imaging Lab Oregon Health & Sciences University 3181 SW Sam Jackson Pk. Rd. Portland, OR 97239 (503) 494-6494

2 1

skull striping issue
by camilo 27 Aug '04

27 Aug '04

Hi everyone, I am having problems with the skull striping. I see that there is some skull left on the brain images, and also on the wmfilled images. I tryed, to lower the prefloding height in the RMSkull menu on the expert preferences. It did not work. Then I select the option "Don't use watershed analyze", but agian it did not work. Is there anythig else I can do? Thanks, Camilo

1 0

midbrain question
by camilo 25 Aug '04

25 Aug '04

Hi everyone, I was just wondering if any of you knew if the midbrain is supposed to show up on the white matter filled images. Thanks, Camilo

2 1

mris_fix_topology error
by Jonathan Wisco 25 Aug '04

25 Aug '04

Hi, how do I fix the following error (taken from log file): Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterationscould not allocate 16022 edges for retessellation Cannot allocate memory INFO: Src volume /tmp/mritotal_30123/orig_8_dxyz.mnc INFO: Target volume /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/average_305_8_dxyz.mnc DimSizes: 3, 86, 110, 68, 1 DataType: 1 MINC Linear Transform 2.0000 0.0000 0.0000 -86.0950 0.0000 2.0000 0.0000 -126.5100 0.0000 0.0000 2.0000 -58.2500 0.0000 0.0000 0.0000 1.0000 Done reading minc reading T1 volume from T1... reading wm segmentation from wm... 55686 ambiguous faces found in tessellation 3 of 63 overlapping edges discarded retessellating defect 1 with 16022 vertices (convex hull=76251). ERROR: mris_fix_topology exited with non-zero status ------------------------------------------ Filesystem 1k-blocks Used Available Use% Mounted on gam:/local_mount/space/gam/2 240362656 83370280 144782576 37% /autofs/space/gam_002 ------------------------------------------ recon-all exited with errors at Wed Aug 25 15:38:31 EDT 2004 Thanks, Jon -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital-NMR Center Building 149, 13th St., Mailcode 149-2301 Charlestown, MA 02129-2060 jjwisco(a)nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422

2 1

Freesurfer and brainstem
by camilo 25 Aug '04

25 Aug '04

Hi everyone, I have been runnig into some problems with the freesurfer. The problem is that the brainstem still appears on the white matter filled images. I have tryed to do what they tell you to do on the manual (go to expert preferences and in the WMFill menu, set the coordinates for the pons and callosum points). Even I do that, I still get the brainstem on the reconstructions. Does any one have any idea on how to solve this inconvenient? Thanks, Camilo

2 1

Motion registration
by camilo 25 Aug '04

25 Aug '04

Hi everyone, I am using the register.csh script to motion correction. SOme how the motion correted images are not saved in the directory that I specified, and I get this "error" message: /autofs/space/rao_001/users/patrickp/auditory_eegfmri/aepfmri05/3danat mri_convert -raw 256 256 256 uchar /tmp/reg.res+orig.BRIK 002MC mri_convert: unknown flag "-raw" type mri_convert -u for usage Does anyone have any idea why this is happening? Thanks, Camilo

2 1

mri_label2label cannot find label file
by Darren Weber 24 Aug '04

24 Aug '04

Hi, the mri_label2label program is reporting that it cannot find the label file. That is: ***************************************************** srclabel = vertices.label srcsubject = ucsf_mh trgsubject = ucsf_aw trglabel = vertices.label regmethod = surface srchemi = rh trghemi = rh trgsurface = pial srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 SUBJECTS_DIR is /netopt/freesurfer/subjects FREESURFER_HOME is /netopt/freesurfer Loading source label. mri_label2label: could not open label file vertices.label No such file or directory ERROR reading vertices.label ***************************************************** I have located the label file in the 'ucsf_mh/label/' directory. The label file is called 'rh-vertices.label' and the command line is: mri_label2label --srclabel vertices.label --srcsubject ucsf_mh \ --trglabel vertices.label --trgsubject ucsf_aw \ --regmethod surface --hemi rh --trgsurface pial I've tried variations on this, including mri_label2label --srclabel rh-vertices.label ... --hemi rh and the full path to the label file. I also checked the format of the label file, to ensure it is the same as similar .label files in the ucsf_mh/label directory (I even used one of those files, which were generated by freesurfer routines). Also, I check the SUBJECT_DIR environment variable, no problem there. Any ideas? Best, Darren -- Darren L. Weber Postdoctoral Fellow Dynamic Neuroimaging Laboratory, Center for Molecular and Functional Imaging, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94143-0946, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber Address for express mail/deliveries: 185 Berry Street, Suite 350, San Francisco, CA 94107 "People travel to wonder at the height of the mountains, at the huge waves of the seas, at the long courses of the rivers, at the vast compass of the ocean, at the circular motion of the stars; and they pass by themselves without wondering." --St. Augustine (b. 354, d. 430) "A good traveler has no fixed plan and is not intent on arriving." --Lao Tzu

1 0

mri_probedicom
by Chekema Nayasha Prince 24 Aug '04

24 Aug '04

Is there a way to get mri_probedicom to let you scroll through dicom images instead of viewing each image slice by slice? If not, is there something else available with freesurfer that will allow you to look at the dicom images? -Keyma

2 1

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Freesurfer August 2004