Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

tkregister-sess errors
by Gold, Andrea 24 Oct '05

24 Oct '05

Hi all, I am having errors with the tkregister-sess command. I tried re-doing stages 1 & 2 of recon-all, but still get the same errors (see log window below)running the NMR standard environment on Kermit. It can't seem to open the structural even though the image files seem to be present in the structural directory (DCS_recon). Thanks!!!!! Functional data located in /space/phrenic/6/users/wright/studies/DCS Structural data located in /space/phrenic/6/users/wright/studies/DCS_recon [kermit:DCS] (nmr-std-env) tkregister-sess -sf sessid_all -df sessdir -------------------------------------------------------------- tkregister-sess logfile is /autofs/space/phrenic_006/users/wright/studies/DCS/log/tkregister-sess.log -------------------------------------------------------------- Session: /autofs/space/phrenic_006/users/wright/studies/DCS/dcs1.1 ---------------- Mon Oct 24 14:34:51 EDT 2005 INFO: anatdir set to /space/phrenic/6/users/wright/studies/DCS_recon//dcs1/mri/T1 ---------------------------------------------------- INFO: surface white does not exist for dcs1, so it will not be loaded into the display. This may be because the subject's anatomical data has not been processed with FreeSurfer in order to reconstruct the surface. You can change the surface from white with the -surf option (followed by the name of the surface. Continuing... ---------------------------------------------------- ________________________________________________ /autofs/space/phrenic_006/users/wright/studies/DCS/dcs1.1/bold/010 tkregister2 --targ /autofs/space/phrenic_006/users/wright/studies/DCS_recon/dcs1/mri/T1 --mov ./f bshort --reg ../register.dat --plane cor --title dcs1--dcs1.1--010 --volview targ ________________________________________________ target volume /autofs/space/phrenic_006/users/wright/studies/DCS_recon/dcs1/mri/T1 movable volume ./f reg file ../register.dat LoadVol 1 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.001 -0.002 -0.001 -1.863; -0.002 -1.001 -0.000 -91.365; 0.001 -0.000 1.001 -10.891; 0.000 0.000 0.000 1.000; float2int = 2 --------------------------------------- INFO: loading target /autofs/space/phrenic_006/users/wright/studies/DCS_recon/dcs1/mri/T1 INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ./f INFO: bvolumeRead: min = 0, max = 1295 INFO: changing move type to float Tmov: -------------------- -3.125 0.000 0.000 100.000; 0.000 0.000 3.300 -49.500; 0.000 -3.125 0.000 100.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 2 INFO: making tkreg matrix compatible with round ---- New registration matrix -------- 1.001 -0.001 -0.001 -0.304; -0.002 -1.001 -0.000 -93.078; 0.001 -0.000 1.001 -12.428; 0.000 0.000 -0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.001 -0.001 -0.001 -0.304; -0.002 -1.001 -0.000 -93.078; 0.001 -0.000 1.001 -12.428; 0.000 0.000 -0.000 1.000; subject = dcs1 Zoom Factor = 2 FOV = 256 Opening window dcs1

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Re: Freesurfer Digest, Vol 19, Issue 49
by Blaise Frederick 24 Oct '05

24 Oct '05

On Sep 27, 2005, at 3:06 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Message: 2 > Date: Tue, 27 Sep 2005 13:42:02 -0400 > From: Keith Schneider <ks(a)rcbi.rochester.edu> > Subject: [Freesurfer] mri_convert doesn't recognize DICOM files > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <1F6EBE81-3EC6-41F9-840C-1C2E8B4C05A6(a)rcbi.rochester.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > I installed Freesurfer on a G5 Tiger Mac, but mri_convert and > mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a > Siemens Trio 3T) as DICOM files. Has anyone else encountered this? > > Other programs can read the DICOM files just fine. > > keith > > > ------------------------------ I have found exactly the same thing. The thing is, it _used_ to work... Using a G5 with 10.4.2, in a directory with DICOM files pulled off a Siemens Trio using Osirix, I execute the following: /usr/local/freesurfer/bin/Darwin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hoot I get the following error (many, many times) mri_convert(1841) malloc: *** Deallocation of a pointer not malloced: 0xd10ea0; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment variable MallocHelp to see tools to help debug However, when all is said and done, I get a correct analyze file. The binary in question is: -rwxr-xr-x 1 frederic frederic 2034036 Feb 18 2004 /usr/local/ freesurfer/bin/Darwin/mri_convert However, if I execute: /Users/Shared/freesurfer/bin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hoot2 it returns with: no DICOM files found. Exit This binary is from the newest distribution that I have: -rwxr-xr-x 1 frederic wheel 6236540 Jul 7 21:23 /Users/Shared/ freesurfer/bin/mri_convert So it looks like something broke. Unfortunately, I don't want to just use the old binary, because it is missing many output formats (particularly nii) Blaise Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and/or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, PHI by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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RE: [Freesurfer] Anatomical parcellation in patients
by Bagnato, Francesca (NIH/NINDS) 21 Oct '05

21 Oct '05

Thanks Bruce, I was wondering if you have noted differences between 1.5 and 3T images as far as it concerns this issue. Indeed, the MS cortical lesions are definitely visible on a 3T anatomical RMI but barely detectable in 1.5T SPGRs. Thanks, -francesca Francesca Bagnato, 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 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, October 21, 2005 7:39 PM To: Bagnato, Francesca (NIH/NINDS) Cc: Goulven Josse; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Anatomical parcellation in patients Hi Francesca, this is tough to answer as it depends on the exact location of the cortical lesion, and the thickness of the underlying white matter. As you know, we have done a fair number of MS subjects, so in general it's okay, but I can certainly imagine scenarios in which things fail. sorry I can't be more help. Bruce On Fri, 21 Oct 2005, Bagnato, Francesca (NIH/NINDS) wrote: > Dear Josse and all: > Before posing the parcellation problem with respect to patients with > cortical lesions, I was wondering to ask if anybody has a clue on how > the segmentation of the cortex/WM might work in patients with > juxtacortical/cortical lesions. > > In other words: how the drop of the signal given by cortical lesions > affects the segmentation of the cortex? Also, how much partial (CSF) > volume voxels due to the empty space left by cortical lesions may affect > the cortical thickness measurements? > > Thanks, > -francesca > > > Francesca Bagnato, 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 > > > -----Original Message----- > From: Goulven Josse [mailto:goulven@uchicago.edu] > Sent: Friday, October 21, 2005 6:29 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] Anatomical parcellation in patients > > Dear freesurfers, > > We are trying to analyse data from patients who had an early stroke. > I did one automated parcellation (Fischl et al, 2004) in a patient with > a peri-ventricular enlargement associated with a large overall atrophy > of the injured hemisphere. I was pleased to find out that, even in the > injured hemisphere, the anatomy was -apparently- well parcellated. I am > now thinking of applying the parcellation to other subjects with a > similar lesion and, possibly, to subjects with a much bigger, cortical, > lesion. > > Before going ahead, I am wondering if anyone had an opinion about > whether it makes sense to use this parcellation in patients, while it > was (i think) originally designed for normal brains. Variability is > huge in normals but still ... > > thanks ! > Goulven Josse > (Brain Research Imaging Center, U of Chicago) > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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RE: [Freesurfer] Anatomical parcellation in patients
by Bagnato, Francesca (NIH/NINDS) 21 Oct '05

21 Oct '05

Dear Josse and all: Before posing the parcellation problem with respect to patients with cortical lesions, I was wondering to ask if anybody has a clue on how the segmentation of the cortex/WM might work in patients with juxtacortical/cortical lesions. In other words: how the drop of the signal given by cortical lesions affects the segmentation of the cortex? Also, how much partial (CSF) volume voxels due to the empty space left by cortical lesions may affect the cortical thickness measurements? Thanks, -francesca Francesca Bagnato, 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 -----Original Message----- From: Goulven Josse [mailto:goulven@uchicago.edu] Sent: Friday, October 21, 2005 6:29 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Anatomical parcellation in patients Dear freesurfers, We are trying to analyse data from patients who had an early stroke. I did one automated parcellation (Fischl et al, 2004) in a patient with a peri-ventricular enlargement associated with a large overall atrophy of the injured hemisphere. I was pleased to find out that, even in the injured hemisphere, the anatomy was -apparently- well parcellated. I am now thinking of applying the parcellation to other subjects with a similar lesion and, possibly, to subjects with a much bigger, cortical, lesion. Before going ahead, I am wondering if anyone had an opinion about whether it makes sense to use this parcellation in patients, while it was (i think) originally designed for normal brains. Variability is huge in normals but still ... thanks ! Goulven Josse (Brain Research Imaging Center, U of Chicago) _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Anatomical parcellation in patients
by Goulven Josse 21 Oct '05

21 Oct '05

Dear freesurfers, We are trying to analyse data from patients who had an early stroke. I did one automated parcellation (Fischl et al, 2004) in a patient with a peri-ventricular enlargement associated with a large overall atrophy of the injured hemisphere. I was pleased to find out that, even in the injured hemisphere, the anatomy was -apparently- well parcellated. I am now thinking of applying the parcellation to other subjects with a similar lesion and, possibly, to subjects with a much bigger, cortical, lesion. Before going ahead, I am wondering if anyone had an opinion about whether it makes sense to use this parcellation in patients, while it was (i think) originally designed for normal brains. Variability is huge in normals but still ... thanks ! Goulven Josse (Brain Research Imaging Center, U of Chicago)

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good news and bad news
by Bruce Fischl 21 Oct '05

21 Oct '05

Hi All, I'll start with the good: thanks to Anders Dale (UCSD), Howard Pinsky (CorTechs) and Christian Euseman (MGH), we have finally signed an open source agreement for FreeSurfer. We will be posting a "read-only" tarball on the website in the next couple of weeks, and anyone is free to download it and look at it. We will *not* be supporting a make/configure type env for people to download and build, as we simply aren't ready to do so. We plan to implement such a procedure, but it will be a while. Instead of waiting until that was ready, I thought people would like to have access to the source to at least see what things are doing, and be able to see file formats and such. Now the bad news. I know we've been promising a new release, but it is being delayed for another month or two. Partially this is due to the opensourcing, which has taken our time and resources, but it is also because we *really* don't want to release something that is half broken. There are also a number of features that we want to get into the release, and not have updates to it right away. We have continued to post current versions on the website as prereleases, but *please* be aware that we can't guarantee that these versions will be compatible with the one we ultimately release. I think they will be, but can't say for sure. Our hope is that datasets processed with the prerelease versions can be rerun automatically with recon-all --rerun or something like that, but again, no guarantees. cheers, Bruce

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FS-FAST Registration Question: registration across sessions within subjects
by Tommi Raij 20 Oct '05

20 Oct '05

Hi Doug/All, This is a question about registering several functional scans from the same subject in the same space. The functional scans are from different sessions, so even if the slice recording parameters are identical, the head will inavoidably be in different locations and with different rotation. The data have already been collected, so we cannot use any on-line corrections. Four different techniques come to mind that could be used to achieve this, but I would expect that the accuracy of the methods varies a lot. Optimally IMHO one should register the different functional runs with respect to each other directly, simply because the EPI images are very similar with respect to each other (or at least their T1 contrast is). The high-resolution structural image is very different compared to the EPI images so functional-to-structural registration is expected to be much more inaccurate. Here are the four different techniques (please tell me if you can think of more): 1. One possibility would be to use mc-sess for all runs from the same subject (place all the runs from the different sessions in a single "bold" directory and just run mc-sess). Possible problem: If I have understood correctly, mc-sess only corrects for motion within slices. Therefore the different head rotations would make this technique very inaccurate. Or does there exist an updated version of mc-sess that could handle even large displacements and rotations? 2. A second possibility would be to use one of the automatic functional-to-structural registration programs and register each functional run to the same hires structural image. However, based on the discussion above, there are expected to be inaccuracies in the functional-to- structural registration that could be large enough to make comparisons across the functional sessions meaningless (i.e., the differences would mainly be driven by inaccuracies in the registration). 3. A third possibility would be to use the same technique as for registration across subjects, i.e., resampling the different runs from the same subject into a spherical space calculated from this specific subject. Again this is just as variety of registration from functional to structural, and would be expected to provide suboptimal results. 4. A fourth possibility would be to find a method for registering all the functional images in a single space with respect to each other, e.g. by picking one of the functional sessions as the target space and resampling all other functional sessions from this subject into this space (without using the hires structurals at all). I guess this would be kind of motion correction but capable of handling rotations. If such a tool exists, it might be more accurate than any of the methods above, simply because the functional images are more similar compared to each other than compared to the subject's hires structural image. Any ideas/suggestions which method would give the most accurate result? And what kind of tools currently exist? Thanks, Tommi --- Tommi Raij MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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mris_glm
by antao＠itsa.ucsf.edu 20 Oct '05

20 Oct '05

Hi, I processed all data in older version (20040218). Can I do group comparison with mris_glm? I just wanted to try, I got the following error message: gdfReadHeader: reading ./ad_cn_fsgd.txt INFO: ignoring tag vs. INFO: ignoring tag SomeTag INFO: gd2mtx_method is doss INFO: Normalized Design Matrix Condition Number is 18.894 INFO: found 3 elements in group contrast vector 1.000 -1.000 0.000; $Id: mris_glm.c,v 1.43 2005/08/17 22:19:35 greve Exp $ setenv SUBJECTS_DIR /home/antao/freesurfer/subjects /home/antao/freesurfer/subjects/stats mris_glm lh --trgsubj average_ftd --fsgd ./ad_cn_fsgd.txt doss --beta_in ./lh_beta_ad_cn.mgz --var_in ./lh_var_ad_cn.mgz --gcv 1 -1 0 --ces ./lh_ces_ad_cn.mgz --t ./lh_t_ad_cn.mgz --sigt ./lh_sigt_ad_cn.mgz Design Matrix ------------------------------------ 1.000 0.000 71.000; 1.000 0.000 63.000; 1.000 0.000 60.000; 1.000 0.000 63.000; 0.000 1.000 62.000; 1.000 0.000 51.000; 0.000 1.000 77.000; 0.000 1.000 60.000; 0.000 1.000 57.000; 0.000 1.000 65.000; Design Covariance Matrix ------------------------------------ 5.000 0.000 308.000; 0.000 5.000 321.000; 308.000 321.000 40027.000; Contrast Matrix: ----------------------------- 1.000 -1.000 0.000; DOF = 7 INFO: loading surface /home/antao/freesurfer/subjects/average_ftd/surf/lh.sphere.reg nvertices = 163842 surface nvertices 163842 surface area 125674.750000 INFO: loading beta_in ./lh_beta_ad_cn.mgz ERROR: number of components in input beta does not match the number of regressors in the design matrix [antao@freesurfer stats]$ Thanks, Antao

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determining significance levels
by d.g.lawyer＠medisin.uio.no 20 Oct '05

20 Oct '05

Hi, We've been having alot of discussion in our group regarding how one should set significance levels. Since you include FDR in the newer releases, I take it that is your current reccomendation (see also Doug's slides: http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsfsl-mris_glm.pdf) Correct? Put very roughly, the FDR rate controls the (expected) percent of your positive results that are false. So what level is appropriate? All that Genovese says is that "it is common to set q to conventional levels ...(e.g. 0.01-0.05) ... values in the range of 0.10-0.20 are reasonable in many problems (Benjamini, personal communication)" [quote from pg 872, 2nd column]. What sort of rates do you think are reasonable, and under what conditions? +glenn

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mapping left hemi into right hemi coordinates
by Irina Sigalovsky 19 Oct '05

19 Oct '05

Hi, I was wondering if there is a way to map one hemisphere onto the other (e.g., left on right) so that I could average data from the two hemispheres. Thank you. Irina

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