Freesurfer July 2007

freesurfer@nmr.mgh.harvard.edu

61 participants
99 discussions

mri_motion_correct.fsl problems
by Catherine Hartley 10 Jul '07

10 Jul '07

Hi, I'm still having problems with the rawavg.mgz volume being generated with incorrect orientations. I gave Jenni two 00?.mgz volumes and she was able to generate a correctly-oriented rawavg. Our two log files look very different, but I'm not able to figure out the problem by looking at them. To start with, the i_ras, j_ras, and k_ras value for the 00?.mgz volumes are different in each of our log files. Mine also has several warnings in which it says that it cannot read a matfile, and that the hist.orient value is not valid. I've attached the log files. Any suggestions would be very very welcome. Thanks in advance, Cate

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MR to MGZ
by Jerry Yeou-Wei Chen 10 Jul '07

10 Jul '07

Hello, We have been having difficulties importing GE .MR files into FreeSurfer. We have tried a number of methods: 1) directly importing .MR 2) converting to .IMG via BrainVoyager, then importing .IMG with .HDR 3) converting to .IMG via BrainVoyager and creating .MAT using SPM99, then importing .IMG with .HDR and .MAT 4) renaming .MR to .DCM, then importing .DCM Here is a summary of our problems: 1) autorecon1 exits with error 2) orig.mgz is in wrong orientation; T1.mgz is in correct orientation but a "cosine info" error arises when loading in tkmedit; brainmask.mgz is in wrong orientation; reconstructed surface is in wrong orientation (i.e. not actually a hemisphere; appears oblique) 3) orig, T1, and brainmask are all in wrong orientation 4) autorecon1 exits with error (in all cases except reconstructed surface, "wrong orientation" means: C = axial with anterior to the left and right to the top H = sagittal upside-down S = coronal with superior to the left ) Here is a summary of what seems to be the source of our errors, from corresponding recon-all.log files (I have attached .doc and .txt files with longer excerpts) 1) mri_convert /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig.mgz --conform MRIresample(): source matrix has zero determinant; matrix is: -0.000 0.000 -0.000 0.000; 0.000 0.000 0.000 -15877550310885762478336514187067392.000; 0.000 -0.000 -0.000 -2013832203448376356765696.000; 0.000 0.000 0.000 1.000; 2) mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz ----------------------------------------------------------------- INFO: could not find /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file 3) reading from /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.img... WARNING: analyzeRead(): matfile /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat file 4) mri_convert /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm /home/omid/freesurfer/subjects/IBS_renamed/c1/mri/orig/001.mgz reading from /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm... genesisRead(): can't determine file name format for We are now in the thick of attempting to manually import the volume from .MR to .MGZ by using the load_mgh.m, load_mgh2.m, save_mgh.m, and save_mgh.m scripts, but before pursuing that avenue further we would like to seek some expert advice. Any thoughts or suggestions would be greatly appreciated. Please let me know if I can provide any more necessary information. Thank you for your time, - Jerry ============================================================================= 1) IBS_raw -> autorecon1 exit with error ============================================================================= /home/omid/freesurfer/subjects/IBS_raw/csd mri_convert /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz mri_convert /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz reading from /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR... freadShort: fread failed No such file or directory freadShort: fread failed No such file or directory fname_format : /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I%d.MR fname_format2 : /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I%03d.MR zero frames specified in file - setting to 1 TR=811509.69, TE=811509.69, TI=811509.69, flip angle=0.00 i_ras = (-0, 1, 1.01471e-34) j_ras = (0, 0, -1) k_ras = (-0.997933, 0, -0.0642636) writing to /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Jul 10 11:53:26 EDT 2007 Found 1 runs /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_raw/csd mri_convert /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig.mgz --conform mri_convert /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig.mgz --conform MRIresample(): source matrix has zero determinant; matrix is: -0.000 0.000 -0.000 0.000; 0.000 0.000 0.000 -15877550310885762478336514187067392.000; 0.000 -0.000 -0.000 -2013832203448376356765696.000; 0.000 0.000 0.000 1.000; reading from /home/omid/freesurfer/subjects/IBS_raw/csd/mri/rawavg.mgz... TR=811509.69, TE=811509.69, TI=811509.69, flip angle=0.00 i_ras = (-0, 1, 1.01471e-34) j_ras = (0, 0, -1) k_ras = (-0.997933, 0, -0.0642636) Original Data has (4.6006e-41, 4.6006e-41, 4.6006e-41) mm size and (256, 256, 124) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation Linux omid-laptop 2.6.17-10-386 #2 Tue Dec 5 22:26:18 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Tue Jul 10 11:53:34 EDT 2007 ============================================================================= 2) IBS_fromBV -> mri_convert cosine error: ============================================================================= mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz ----------------------------------------------------------------- INFO: could not find /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.mat file ----------------------------------------------------------------- reading from /home/omid/freesurfer/subjects/IBS_fromBV/_orig_/c1/sd0823iso.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed May 30 12:51:21 EDT 2007 Found 1 runs /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig/001.mgz /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV/c1 mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz --conform mri_convert /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz --conform reading from /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz... mri_add_xform_to_header -c /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/transforms/talairach.xfm /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz /home/omid/freesurfer/subjects/IBS_fromBV/c1/mri/orig.mgz INFO: extension is mgz ============================================================================= 3) IBS_fromBV_reO -> mri_convert .MAT, cosine error ============================================================================= mri_convert /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig/001.mgz mri_convert /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.img /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig/001.mgz matfile: only read 476 bytes of name (1768711468 specified) MatlabRead: readHeader returned NULL reading from /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.img... WARNING: analyzeRead(): matfile /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/omid/freesurfer/subjects/IBS_fromBV_reO/_orig_/c1/sd0823iso.mat file ----------------------------------------------------------------- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed May 30 14:51:26 EDT 2007 Found 1 runs /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig/001.mgz /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1 mri_convert /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz --conform mri_convert /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/rawavg.mgz /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz --conform reading from /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz... mri_add_xform_to_header -c /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/transforms/talairach.xfm /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz /home/omid/freesurfer/subjects/IBS_fromBV_reO/c1/mri/orig.mgz INFO: extension is mgz ============================================================================= 4) IBS_renamed -> autorecon1 exit with error ============================================================================= mri_convert /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm /home/omid/freesurfer/subjects/IBS_renamed/c1/mri/orig/001.mgz mri_convert /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm /home/omid/freesurfer/subjects/IBS_renamed/c1/mri/orig/001.mgz reading from /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm... genesisRead(): can't determine file name format for /home/omid/freesurfer/subjects/IBS_renamed/_orig_/c1/anat_1.dcm Linux omid-laptop 2.6.17-10-386 #2 Tue Dec 5 22:26:18 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Thu Jun 28 13:00:47 EDT 2007

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

2 1

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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Freesurfer July 2007