Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Re: [Freesurfer] FreeSurfer relevance for studying structures other than the bra
by Greg Soltis 11 Jul '07

11 Jul '07

Howdie Doug, We are interested in studying not the ventricles, per say, but the actual cells and components of the cells that comprise these ventricles. For example, cells from a heart, spleen, sperm, or cochlea. Since we are not using an MRI machine to obtain the images, is FreeSurfer of no use to us? (You said it handles only TI-weighted MRI data). Additionally, you mentioned in a previous correspondence that as our files traverse along the data stream in FreeSurfer, they will ultimately be converted into 8-bit format. However, since we need the files in 16-bit format, would this be a deal-breaker as well? Thanks. Greg _________________________________________________________________ http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migrati…

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FreeSurfer relevance for studying structures other than the brain
by Greg Soltis 10 Jul '07

10 Jul '07

Greetings, I am attempting to use FreeSurfer/Slicer to study data from a mass sprectrometer. To be of use, the segmentation capability of FreeSurfer/Slicer has to be based on quantitative data, not morphology. It appears as if FreeSurfer uses a generic mapping of the brain's structure as a starting point for the model it generates. However, for one seeking to study a structure other than the brain, this can be a concern. Can FreeSurfer/Slicer accommodate data whose source is not an MRI and or of the brain? This concern also stems from the file entitled "SlicerTraining06_vtkFreeSurferReaders.ppt" provided on a Slicer site that has about a dozen tutorials for Slicer 2.6 (this is one of them). On Slide #25, entitled 'Determining label numbers in an ASEG file', there is a list of the first 30 sections created and various parameters. The names of these sections seem to be predetermined (i.e., Left Cerebral-Exterior, Left Cerebral-White-Matter, Left Cerebral-Cortex, etc.). This seems to imply that FreeSurfer/Slicer know what to look for from the onset and thus the segementation is not based solely on quantitative data. Please let me know if these conclusions are warranted. If I am mistaken, please advise as to why. Thanks for your time and advice, Greg _________________________________________________________________ Need a brain boost? Recharge with a stimulating game. Play now! http://club.live.com/home.aspx?icid=club_hotmailtextlink1

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smoothing and monte carlo sim
by Robert Levy 10 Jul '07

10 Jul '07

Hi Doug, As you suggested, I ran mc simulation data with a threshold taken from fwhm.dat so that the smoothing on the simulation matches the smoothing on the real data. What I was wondering is, if I use the same simulation data for several contrasts (they have the same fsgd, so this seems like a valid thing to do), it becomes less clear how to choose the smoothing. Or maybe it is not possible to use the same mc simulation data, because the smoothing turns out to be different. Should I instead use an average of the smoothing values, or maybe use the lowest one? Conceptually it seems like this might make the results less accurate, but in practice is there a certain level of slack in smoothing without sacrificing accuracy? If not, it makes a big difference, because the full simulation will take 6 days instead of 2. The z simulation, which at at least with the level of smoothing we have applied, showed results being much less significant, which is why I'm trying the full mc simulation. Thanks, Rob Just to give you an idea of the variance in the smoothing reported in fwhm.dat for the three contrasts: lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 17.128043 rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 16.675573 lh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 15.202638 rh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 15.771982 lh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 14.438915 rh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 15.766636 -- 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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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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