Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

FreeSurfer use in dogs
by Marjorie Milne 08 Jul '11

08 Jul '11

Hello Freesurfers, I would like to use FreeSurfer to analyse brain morphology in dogs but do not know if the techniques can be applied in this species. Does anyone have experience using FreeSurfer in dogs, and any tips to get the techniques to work? Regards, Marjorie Milne

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question about qdec
by ZhiLiangLong 07 Jul '11

07 Jul '11

Hi all: I have three groups of subjects (major depression disorder,slight depression disorder and contrast),i want to use qdec to obtain the statistical significant areas containing difference of cortical thickness measurment among them. But there are some errors appearing when i run the group analysis: ERROR: QdecGlmDesign::GenerateContrasts: factor 2 must have 2 levels I think the error is related to the diagnosis.levels file which has 3 levels because i can run it successfully after removing any one of them.But i don't know why. Can you give me some help or suggestions? I have saved error information into the error.log file(see attachments)

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more on fieldsign problems-
by Michelle Umali 07 Jul '11

07 Jul '11

Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors: 1) ran recon-all -all 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d rh.occip.patch.flat 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 paradigm rtopy.par -nskip 4 fwhm 0 5) selxavg3-sess -a rtopy.self.rh -s sj09 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09 When I looked at the fieldsign map using: 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign all I got were blue and red speckles. The polar and eccentricity maps seemed ok. Any help would be great. Michelle

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preprocessing qc
by Chindhuri Selvadurai 07 Jul '11

07 Jul '11

Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

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Re: [Freesurfer] Error with Tksurfer
by Bruce Fischl 07 Jul '11

07 Jul '11

Hi Antonella, did bert inflated look ok on the other computer? Usually this problem goes away if you update the video card driver. cheers Bruce On Thu, 7 Jul 2011, Antonella Kis wrote: > Good afternoon Bruce, > > I am still trying to fix my error related to the surface image display when using tksurfer bert lh inflated. As you saw the image looks weird and what I in the mean time I > tried something: I save the weird surface displayed by that computer using SAVE SURFACE AS and I transfers this file nsmed by me lh.bertsurf to another computer. When I > looked on the image using > tksurfer bert lh bertsurf, the surface that came up was exactly like the bert lh inflated should be, having the same number of vertices and faces. Can you or somebody else > give me some advice on what to do so I can get the same display on the other computer? Seems that everything is well calculated just the surface display/image is looking > weird on that computer. What can be the problem? I attached the saved surface from the computer where it looked weird so the called "weird surface". > > Also can I save a surface and loaded in freesurfer but not as a tiff image? What's the best way to save my volumes and/or surfaces? > > Thank you very much for your help. > Antonella > > > > >

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talaraich ERROR
by Carolina Valencia 07 Jul '11

07 Jul '11

Hi FSexperts, I have a case of a child with *Hydrocephalus and cortical dysplasia, the patient has a subcutaneous ventriculo-peritoneal shunt that produces an artifice in all MRI sequences, I try to recon-all but it exit with ERROR* #-------------------------------------------- #@# Talairach Failure Detection Thu Jul 7 11:03:21 COT 2011 /home/cvalencia/freesurfer/subjects/volumetria/hptu_vol04/hptu_vol04/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux cvalencia-Precision-WorkStation-T3400 2.6.35-30-generic-pae #54-Ubuntu SMP Tue Jun 7 20:28:33 UTC 2011 i686 GNU/Linux recon-all -s hptu_vol04 exited with ERRORS at Thu Jul 7 11:03:21 COT 2011 is possible to process it in automated fashion? Thanks, Best regards, Carolina

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Matlab and FS
by Carolina Valencia 07 Jul '11

07 Jul '11

Hello FS'users, I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, where can I find the cortical thickness in each regions (Brodmann areas, gyrus or sulci) of the brain in order to compare a normal patient with a patiwnt who has a cortical dysplasia ? Thanks a lot for your help, Carolina

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tracula bvecs problem
by Franz Liem 07 Jul '11

07 Jul '11

Dear Freesurfers. I am trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don't have the same number of entries. I checked the dmri/bvals and dmri/bvecs. There seems to be a problem at the -corr stage (-corr alone finishes without error). My input file is one 4d .nii.gz file (with a total of 33 images, with the first being a b0 image). (I have attached the files from the dmri folder) The dmri/bvecs file only contains: 0,0000000 0,0000000 0,0000000 The original bvecs contains 3 columns and 33 lines. The dmri/bvals seems to be ok (1 column and 33 lines). eddy_correct processes 33 files (dmri/dwi_tmp0000 ... dmri/dwi_tmp0032). I am running FSL(4.6.1) and Freesurfer v5.1.0 on Mac (10.6.4) (although the recon was done with 5.0.0, but I guess this not important at this stage, is it?) ******* My Configuration File: set dtroot = $SUBJECTS_DIR/DTI set subjlist = (s02x) set dcmroot = $SUBJECTS_DIR/DTI set dcmlist = (s02x/dti4d.nii.gz) set bvalfile = /Users/.../DTI/bvals/bvals set bvecfile = /Users/.../DTI/bvals/bvecs set nb0 = 1 set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 ******* Thanks, Franz

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QDEC table
by Ignacio Letelier 07 Jul '11

07 Jul '11

Hi freesurfers Do anyone know if it's possible to automatically enter in the QDEC table the gray matter volume of every subject in the study, to avoid entering this item manually for each one ? Best regards. -- Ignacio.

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bbregister - Are 6 dof enough for MNI305?
by Joao Pereira 07 Jul '11

07 Jul '11

Dear Freesurfers, I was wondering if you could help me clarify one question I have re the recommended use of bbregister to register PET data. If I want to register my PET data to MNI305 space used in Freesurfer, is a 6 dof rigid registration enough? I notice that the tailarach function used within autorecon1 is a 12 dof affine, so I'm guessing that bbregister is unlikely to fully register the PET data to the template space in the same way that (eg) brain.mgz is registered. Thank you very much! Best, Joao Pereira

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