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Re: [Freesurfer] FS-FAST modeling question
by Ben Deen 08 Sep '11

08 Sep '11

Hi, I have an update to this query. I tried using mkanalysis-sess instead of the ".new" version, and now I do seem to be able to get rid of intensity normalization and prewhitening (or at least, adding these flags now has an effect on betas/t-stats, and in the expected directions). The code I'm using is mkanalysis-sess -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -no-inorm -nowhiten -noautostimdur # mkcontrast stuff here... selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 However, I have a few remaining questions about the results. 1) When I look at the regressors used in the analysis, they have a surprisingly large magnitude -- the HRF peaks at a value of ~20. Is there any way to alter the analysis such that these peaks are comparable to the values used in FSL/SPM, which is around .8, so that beta values will be directly comparable across analyses? If not, I can just scale the betas by the relevant factor, but it would be nice if this were possible. 2) When I compare the results of this analysis to results obtained with FSL or SPM, I find that the spatial pattern of beta/t-stats is very similar, but the t-stats have a noticeably reduced magnitude across the brain. Is there anything that may differ about FS-FAST's implementation of the GLM, such that t-stats would differ? 3) I saw in a ppt presentation on FS-FAST that the option -hpf can be used to add a highpass temporal filter to the model. However, when I use this option with mkanalysis-new, the script says that the flag isn't recognized. Is there another way to add such a filter? Thanks in advance for any help. Cheers, Ben On Mon, Sep 5, 2011 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Message: 1 > Date: Sun, 4 Sep 2011 13:15:51 -0400 > From: Benjamin Matthew Deen <bdeen(a)mit.edu> > Subject: [Freesurfer] FS-FAST modeling question > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <D0755B22EA5ED64C941ED568237AEC8D1764DCC5E3(a)EXPO11.exchange.mit.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I'm trying to run a model in fs-fast using no intensity normalization and no autocorrelation correction, for the purpose of comparing results with other software packages, and comparing results with/without autocorrelation correction. However, I haven't been able to get this to work so far. I've tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but these don't seem to have any effect on the results: noinorm doesn't change the beta values, and nowhiten doesn't change either betas or t-stats, at all. The commands I'm using are: > > mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -noinorm -nowhiten > > mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 -a 1 -c 2 > mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 -a 2 -c 1 > mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 -a 1 -a 2 -c 0 > mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope4 -a 0 -c 1 -c 2 > > selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 > > Any idea what might be going wrong, or how I can get this to work? Thanks, > > Ben > >

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mri_convert: orientation issue
by Mohana Ramaratnam 08 Sep '11

08 Sep '11

Hello, I am using mri_convert to convert dicom image into analyze format using: mri_convert -i PATH_TO_DICOM_HERE --out_type analyze -o analyze.img The problem is: The hdr.hist.orient in the output file is set to 0, but the pixels in the analyze image are saggital. Does anybody have any suggestions as to what could be wrong? Regards Mohana Ramaratnam DIAGNOSTICS: mri_info on the dicom reports: Orientation : PIL Primary Slice Direction: sagittal and that on the analyze image reports: Orientation : LAS Primary Slice Direction: axial OUTPUT of mri_convert: INFO: Scanning for Series Number 4 INFO: found 176 files in series INFO: loading series header info. INFO: sorting. RunNo = 3 INFO: (256 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 0.038 -0.051 -2.542; -0.051 0.954 -0.294 -15.875; 0.038 0.296 0.954 -2.910; 0.000 0.000 0.000 1.000; FileName FILE_NAME_HERE Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName 65433 Date and time StudyDate 20110708 StudyTime 110252.125000 SeriesTime 111446.078000 AcqTime 110635.592500 Acquisition parameters PulseSeq tfl3d1_ns Protocol t1_mpr_1mm_p2_pos50 PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 3.16 InversionTime 1000 RepetitionTime 2400 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 104.6950 154.3827 112.3121 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 176 Vc -0.0493 -0.9976 0.0480 Vr -0.0403 -0.0460 -0.9981 Vs -0.9980 0.0511 0.0379 VolCenter 5.4129 25.2910 -5.9690 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00 i_ras = (-0.0492738, -0.997631, 0.0480037) j_ras = (-0.0402601, -0.0460391, -0.998128) k_ras = (-0.997974, 0.0511142, 0.0378956) writing to 110708_TC33875.img... Analyze Output Matrix -0.049 -0.040 -0.998 105.782; -0.998 -0.046 0.051 155.375; 0.048 -0.998 0.038 113.224; 0.000 0.000 0.000 1.000; -------------------- No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for FILE_NAME_HERE are: x_r = -0.0493, y_r = -0.0403, z_r = -0.9980, c_r = 5.4129 x_a = -0.9976, y_a = -0.0460, z_a = 0.0511, c_a = 25.2910 x_s = 0.0480, y_s = -0.9981, z_s = 0.0379, c_s = -5.9690 INFO: set hdr.hist.orient to 'transverse unflipped'

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Tracula - Bedpostx - missing output
by Judit Haasz 08 Sep '11

08 Sep '11

Hi, I am running bedpostx within Freesurfer Tracula with default settings. I got the following error message: Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. Below the individual slice folder I have the followings: dyads1.nii.gz, logfile, mean_f2samples.nii.gz, th2samples.nii.gz, dyads2.nii.gz, mean_S0samples.nii.gz ph1samples.nii.gz, f1samples.nii.gz, mean_dsamples.nii.gz, ph2samples.nii.gz, f2samples.nii.gz , mean_f1samples.nii.gz, th1samples.nii.gz. But I miss all the 3 and 4D volume below bedpostx dir. Is it possible that only the postprocessing step went wrong? Thanks for your help. Best regards, Judit Haasz, MD Neuroinformatics and Image Analysis Group, UiB, Norway

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v5.1, control points, and the aseg
by Nick Schmansky 07 Sep '11

07 Sep '11

Attention Freesurfer Users, If you are using v5.1, you should be aware of a new function in this version that wasn't fully documented in the Release Notes until recently. Beginning with v5.1, control points (added to fix white matter intensity issues, per normal procedures) are now used in the mri_ca_normalize stage which precedes the creation of the aseg. This functionality was added to v5.1 to help the aseg creation. However, we have discovered that it is possible for this normalization, making use of the control points, to adversely affect the subcortical segmentation, such that some structures differ in size when compared to processing without control points being used by mri_ca_normalize. This effect seems to occur only in instances where adding control points to regions where signal drop-off within white matter is dramatic (even while correcting the white matter intensity issue as intended). We did not observe this affect within our own test sets. The advice we give is to be sure that control points are not placed into regions which share or near voxel intensity values close to that of grey matter. If a control point is placed deep within a white matter strand (generally not recommended), an additional control point should be placed nearby outside of the strand (within white matter) to limit the spatial extent of the influence of those control points. An option is to disable the running of mri_ca_normalize when re-running the -autorecon2 or -autorecon2-cp stage after adding control points by adding the flag -nocanorm to the end of recon-all. The Freesurfer Team

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optimal sequence in a 1.5 T MR OPTIMA 450w GE MRI equipment...
by Gonzalo Rojas Costa 07 Sep '11

07 Sep '11

Hi: Which is the optimal parameters for a morphometric sequence in a 1.5 T MR OPTIMA 450w GE MRI equipment ?... Sincerely, Gonzalo Rojas Costa

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calculating GM and WM surface-based volumes
by Alexopoulos, Dimitrios 07 Sep '11

07 Sep '11

I have generated surfaces using the the centos4 build (version 5.0) and want to confirm that my surface-based GM and WM volumes are correct. For the surface-based GM calculation I originally used 'mris_anatomical_stats -l lh.cortex.label subjectID hemi' (run from within the 'label' subdirectory) and for WM i used 'mris_wm_volume subjectID hemi' (run from within the 'surf' subdirectory). When I add the calculated left/right cortical volumes, I get a total that is different from what is output in the 'aseg.stats' file, which in version 5.0 is noted to contain total surface-based GM volume (Cortex, CortexVol: Total cortical gray matter volume (based on surface-stream). What are the correct GM and WM surface-based volumes? Thanks. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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WM Parcellation - lobe mapping
by Brainiac . 07 Sep '11

07 Sep '11

Hi All, I need to classify WM into different lobes (temporal, parietal, frontal, occipital). I tried to do the lobe mapping using parcellations from wmparc.mgz. http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation My problem is the "unsegmented white matter" in wmparc.mgz. My understanding is that these unsegmented areas are classified so because they are beyond 5mm from any pre-classified cortex area. My questions: (1) So in order to classify "unsegmented WM" into lobes, do I need to take each voxel in the unsegmented WM region and then assign it to the closest cortex area to classify it into respective parcellations. Then re-group into lobes. Is this correct? (2) Are there any tailor made function or any other easier way to do this? Is there any easier way to segment WM into lobes directly that I have missed? Thanks, Brain

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Ubuntu / CentOS compatability
by Alexopoulos, Dimitrios 07 Sep '11

07 Sep '11

We have processed many of our datasets using the centos4, version 5.0.0 freesurfer build (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) on our 64-bit centos5.6 server. We would like to modify these datasets (i.e. modify segmentations, regenerate surfaces and cortical parcellations, etc.) on our stand-alone linux boxes running 32-bit Ubuntu 11.04. Can we install the 32-bit Centos4 build on Ubuntu (freesurfer-Linux-centos4-stable-pub-v5.0.0) and not have to worry with inconsistencies/incompatibilities between OSs and versions. Thanks. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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(newbie) recon-all error / result evaluation
by can atılgan 07 Sep '11

07 Sep '11

Hello, Firstly, I'm new to FreeSurfer. My objective is to get a thickness map of cerebral cortex. I converted a single slice of T1 dicom series in order to see whether i could get a proper result. I started the reconstruction progress simply with : recon-all -s 001 -all but after a long period of time the progress halted with a couple of error messages : ---------- unfolding failed - restoring original position -------------------- 0637: dt=0.000078, rms=0.365 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z GCAMwrite:: the popen error code is: 12 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Wed Sep 7 06:14:11 EEST 2011 /home/socat/Desktop/can/001/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux hstkaddogpc-160-75.ege.edu.tr 2.6.9-55.ELsmp #1 SMP Fri Apr 20 17:03:35 EDT 2007 i686 i686 i386 GNU/Linux recon-all -s 001 exited with ERRORS at Wed Sep 7 06:14:12 EEST 2011 before the error messages showed up that "ulfolding failed - restoring original position" steps were repeated 3 times. About result evaluation; I digged through fs wiki to find out how i can get a visual cortical thickness map but I couldn't find anything but only average thickness value using mris_anatomical_stats command. How can I see such a map for example of sample data "bert"? Thanks in advance. Regards, Can

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Re: [Freesurfer] Memory allocation problem with mri_robust_template
by Jeff Sadino 06 Sep '11

06 Sep '11

Hello, I am having a problem with mri_robust_template using too much RAM and causing my computers to freeze. I am using fs510. I think I would like to try to convert the inputs to uchar as Martin suggested, but I am not sure exactly where to do this. Would I issue this command: For each timepoint: mv tp1/mri/norm.mgz tp1/mri/norm.orig.mgz mri_convert -i tp1/mri/norm.orig.mgz -o tp1/mri/norm/mgz -odt uchar recon-all -base -tp 1 -tp 2 -all Also, my computers have two AMD processors and 4GB of DDR RAM running at 333MHZ. I dropped them down so they each only do one job, but they are still freezing. Besides upgrading the entire cluster to something more current, would doubling the RAM to 8GB be worthwhile? As always, thank you so very much! Jeff Sadino Mahen Fri, 11 Feb 2011 09:16:27 -0800 To Martin, Thanks a bunch. I haven't tested out all the recommendations, but at least I know what's going on. If I did want to convert to uchar, how would I go about this? Is there a function included in the Freesurfer package, or would I have to write my own function to do so? It's not a concern, as I'm probably not going to explore this avenue, but if I get time, I might enjoy trying to write such a function... Regards, Mahen On Wed, Feb 9, 2011 at 7:07 AM, Martin Reuter <mreu...(a)nmr.mgh.harvard.edu>wrote: > Hi Mahen, > > 4.5 is based on flirt registration which does a pairwise registration to > the first image. Since 5.0 we use the mri_robust_template tool (as it > can ignore outlier regions and produces more accurate registrations, see > Reuter et al Neuroimage 2010 "..robust registration"), but it is more > memory hungry and time consuming. > > If your input images are large, it can happen that mri_robust_template > uses a lot of memory. I tested that tool in the longitudinal stream > where I successfully ran it on > 10 images on a 4 gig machine (those > images are probably smaller than yours). > > So you have the following options: > > 1. use only the best 2 input images. This has been recommended in the > past, 5 inputs are usually not improving anything (see old emails on > this list from Bruce) > > 2. pass the flag -flirt-motioncor to recon-all and it will revert back > to using flirt (but accuracy of the registration might suffer, since the > inputs are full head images with potentially a lot of differences in > jaw, tongue, neck, eyes, scalp and cropping planes). > > Another option would be to convert the inputs to uchar and see if that > fits into the memory. They will be converted to uchar anyway in the > conform step. > > Best, Martin > > On Tue, 2011-02-08 at 23:21 +0800, Mahen wrote: > > Hi all, > > > > Since upgrading to Freesurfer v5.0, I have been unable to complete the > > first step of recon-all ('recon-all -autorecon1 -subjid ...') when > > using 5 anatomical datasets (our typical load for surface > > reconstruction). The problem seems to come when the third dataset is > > being registered, at which point recon-all exits with the following > > error message: > > ========================= > > Resolution: 0 > > Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536) > > malloc: *** mmap(size=921600) failed (error code=12) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th > > slice > > > > Cannot allocate memory > > /Users/mahen/fMRI/Surfaces/cck_kmu > > \n > > mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz > /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n > > mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz > /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform > > mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could > > not open file > > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > > reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz... > > Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version > > 10.6.0: Wed Nov 10 18:13:17 PST 2010; > > root:xnu-1504.9.26~3/RELEASE_I386 i386 > > > > recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST > > 2011 > > ===================== > > My machine has 4gb of RAM, and I've ssh'd into my advisor's machine > > (which has 16gb) and had the same problem. > > I tryed updating the binaries for recon-all and mri_robust_template > > (from > > > http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-in…) > but the problem remained unsolved. > > My advisor informs me that it is now running with version 4.5 (all 5 > > anatomicals); I'd still like to know what's going on. I have tried > > running it on version 5 with just 2 anatomical datasets, and it works > > just fine. > > > > Here is the output of bugr: > > > > FREESURFER_HOME: /Applications/freesurfer > > > > Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 > > > > Kernel info: Darwin 10.6.0 i386 > > > > Thanks in advance, > > Mahen > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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