Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Talairach
by Wayne Su 10 Jul '07

10 Jul '07

I'm trying to use Flirt from FSL to get talairach.xfm. Here are the steps I took: 1) recon-all -autorecon1 -notalairach -subjid $subject 2) mri_convert $SUBJECTS_DIR/$subject/mri/nu.mgz $SUBJECTS_DIR/$subject/mri/nu.img 3) bet $SUBJECTS_DIR/$subject/mri/nu $SUBJECTS_DIR/$subject/mri/nu_brain 4) fsl_rigid_register -i $SUBJECTS_DIR/$subject/mri/nu_brain.img -r $FREESURFER_HOME/average/mni305_brain.cor.mgz -o $SUBJECTS_DIR/$subject/mri/nu_reged.img -dof 12 -cost corratio -xfmmat $SUBJECTS_DIR/$subject/mri/transforms/talairach.xfm The mni305_brain.cor.mgz is the skull-striped mni305.cor.mgz from average folder. The registered images from flirt is fine. However, when I checked the transform with the tkregister2: tkregister2 --mgz --s $subject --fstal It seems it's a bad transforms. I switched the input and ref volumes in step 4. The result is improved, but still not good. I tried to use orig.mgz instead of nu.mgz, the result is the same. Anything I missed? Thanks, Wayne

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sphere registration
by Leila BH 10 Jul '07

10 Jul '07

Hi I am using the freesurfer Parcellation, modify the obtained parcels to have a small rois. To validate my parcels subdivision into small rois, I need to know the variation of some roi_gravity_centers. Do you think that with the vertex number on the sphere of a subject (after parcellation) is it possible to know the corresponding vertex number in the template (Atlas) sphere ? In other words, from the annotatation file which is basically ?h.aparc.annot where I modified some labels is it possible to have the correspondence on the Atlas sphere (using the vertices and sphere.reg or other)? Thanks

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Talairach
by Sharon Ruso 10 Jul '07

10 Jul '07

Dear FreeSurfers I am pretty new to Freesurfer, and I'm using the workflows which are provided in your website; however, I was wondering If every time, I have to check my Talairach (i.e. and to fix it) Do I have to run the recon-all -autorecon1 ... Which takes hrs, or I have another short option which I can apply after correcting the Talairach transform? P.S following the workflow takes me almost 3-4 days for a subject (looking carefully and fixing everything,, am I on the right track? Help, Please Thank You Sharon

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Re: Freesurfer Digest, Vol 41, Issue 13
by Sebastian Moeller 09 Jul '07

09 Jul '07

Hi, not being an expert, please take my rambling with a grain of salt. But I am somewhat curious to learn better ways ;) On Jul 9, 2007, at 11:03 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 9 > Date: Mon, 9 Jul 2007 17:01:42 -0400 > From: "Wang, Xin" <Xin.Wang2(a)utoledo.edu> > Subject: [Freesurfer] add the gray matter > To: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <B8C005270B26F04CAA5A0F779FD8DEBD056A85(a)MSG02CV04.utad.utoledo.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, Group > > I need to edit the pial surface. I learned to remove points with > tkmedit from the tutorial. But how to add gray matter in the pial > surface? 1) If you have nothing where gray matter should be, then check brainmask.mgz, if this is missing gray matter, around where your problems occur edit the bainmask.mgz volume and pick up your reconstruction from there. (IIRC there is something in the tutorial about this) 2) If there is white matter where gray matter should be, be sure to to check nu.mgz and brainmask.mgz at the critical parts for too high intensity in the supposed gray matter. Either control points might helo (unlikely) or redoing the intensity correction (and then starting again from that point). At least for my data, acquired with surface coils, sub-optimal intensity correction is really annoying. ahoi & good luck Sebastian > > Thank you in advance. > > Xin >

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Is converting to mgz conducive for 16-bit files?
by Greg Soltis 09 Jul '07

09 Jul '07

Greetings, The data at this lab initially comes in a RAW data format. When converted to 16-bit TIFF files, the quantitative data is retained. I recognize that, in order for FreeSurfer to be of use, this data must be converted to mgz files. However, does the process of converting this information into the mgz format allow me to maintain quantitative data that is retained when converting to 16-bit TIFF files? Or does this process of converting to mgz files only ensure proper retention of data for 8-bit files? Thank you for your time and advice. Greg _________________________________________________________________ http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migrati…

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between group contrast using glmfit
by Robert Levy 09 Jul '07

09 Jul '07

Hello, I ran a group contrast in an ROI, correcting for multiple comparisons using the cluster size threshold method. It seems to have worked, however the one element that I don't understand as well is the basic between group contrast using an fsgd file, so I'm wondering if my commands really do what I want them to do. Is the below a correct usage to accomplish that? (apologies again for average7, it is because the data is relatively old.) The output looks very similar to the results of the contrast using intergroup_avg so that is promising. The main thing I'm uncertain about is how the fsgd file specifes that the two classes are to be contrasted. Thanks, Rob # perform the actual contrast mri_glmfit \ --really-use-average7 \ --y rh.ASvfix_8s_BwGroupError5.fsfast.mgh \ --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ --glmdir rh.ASvfix_8s_BwGroupError5.fsfast.glmdir \ --pca \ --surf average7 rh \ --C fsgd_and_contrast_files/BwGroupError5.mat \ --label average7/label/dACC_rACC_final-rh.label \ --fwhm 13.488420 Contents of matfile: [levy@vantz fsgd_and_contrast_files]$ cat BwGroupError5.mat +1 -1 Contents of fsgd file: [levy@vantz fsgd_and_contrast_files]$ cat BwGroupError5.fsgd GroupDescriptorFile 1 Title HCvASD Class Normals Class ASD Input mano001 Normals Input mano002 Normals Input mano004 Normals Input mano005 Normals Input mano007 Normals Input mano008 Normals Input mano009 Normals Input mano010 Normals Input mano011 Normals Input mano012 Normals Input mano013 Normals Input mano014 Normals Input mano016 Normals Input mano025 Normals Input manoA02 ASD Input manoA03 ASD Input manoA04 ASD Input manoA05 ASD Input manoA07 ASD Input manoA08 ASD Input manoA09 ASD Input manoA10 ASD Input manoA11 ASD Input manoA13 ASD And just for the sake of completenes, here is a sample of what I ran after that: # monte carlo simulation data mri_glmfit --really-use-average7 \ --y rh.ASvfix_8s_BwGroupError5.fsfast.mgh \ --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ --glmdir rh.ASvfix_8s_BwGroupError5.fsfast.glmdir \ --surf average7 rh \ --C fsgd_and_contrast_files/BwGroupError5.mat \ --sim mc-full 1000 2 BwGroupError5_ASvfix_8s_rhMCSIM01 \ --fwhm 13.488420 \ --label average7/label/dACC_rACC_final-rh.label ( x10 ) # apply simulation data to show significant clusters mri_surfcluster \ --src rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh \ --csd BwGroupError5_ASvfix_8s_rhMCSIM01-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM02-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM03-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM04-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM05-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM06-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM07-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM08-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM09-BwGroupError5.csd \ --csd BwGroupError5_ASvfix_8s_rhMCSIM10-BwGroupError5.csd \ --sum rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM.sum \ --ocp rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM.mgh \ --thmax infinity -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Retinotopic mapping: fMRI analysis help?
by McLean John (NHS Greater Glasgow & Clyde) 09 Jul '07

09 Jul '07

Hi, I am hoping to perform a retinotopic mapping fMRI study. My paradigms consist of a reversing checkerboard annulus which increases and decreases in size and a reversing checkerboard wedge which moves clockwise dor 180 degrees and then anticlockwise. I am struggling to correctly perform the fMRI analysis. I hope to use FSL so that i can then overlay the functional data on the flattened visual cortex using freesurfer. My problem is that i do not know how to correctly model the fMRI data using FSL, i believe i should use a sinusoid model but i am unsure of how to proceed. Would anyone with experience in this area be willing to discuss these issues with me? Thanks for your help, John ********************************************************************** This message may contain confidential and privileged information. If you are not the intended recipient please accept our apologies. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. NHSmail is used daily by over 100,000 staff in the NHS. Over a million messages are sent every day by the system. To find out why more and more NHS personnel are switching to this NHS Connecting for Health system please visit www.connectingforhealth.nhs.uk/nhsmail **********************************************************************

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mean thickness of whole cortex
by Wang, Xin 09 Jul '07

09 Jul '07

Hello, Group Could anybody please tell me how to get the mean thickness of whole cortex? I got only the average thickness of each hemisphere with mris_anatomical_stats -a subject/lable/lh.aparc.annot -b subject lh Thank you in advance, Xin Wang

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installing FreeSurfer on Mandrake 10.2
by Narly A Golestani 09 Jul '07

09 Jul '07

Hello, I would like to install FreeSurfer on Mandrake 10.2 (Mandriva), and would like to know which version I should download. The available versions appear to be for: CentOS 4, CentOS 4 x86_64, or Red Hat 9. Also, posts to the archive seem to suggest that Mandrake may not be an optimal platform for Freesurfer, and that it may be necessary to compile tk8.3. Unfortunately I am not a unix expert and do not know exactly how to proceed. I would appreciate any guidance / suggestions. Thanks, Narly.

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mri_convert: Dicom to 4D Niftii
by Gallo, Antonio (NIH/NINDS) [F] 06 Jul '07

06 Jul '07

Hello all Is there an option in mri_convert to create 4D niftii from Dicom diffusion files? Thanks Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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