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30132 discussions

autorecon1 output is just a white block
by Christopher Luna 09 Sep '11

09 Sep '11

Hello, After running an *.img file through autorecon1. Freesurfer says it finishes with errors, but I cannot find any error messages in the command line output. Checking the tkregister2 of the output shows that the "Target" is just a white box, while the "Moveable" stills eems like a typical image that I would find in any other output. Are there some settings I need to alter for mri_convert? The IMG file looks fine before running autorecon1. Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT

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Ventricular structures - exact definitions
by mschwei1＠gwdg.de 09 Sep '11

09 Sep '11

Hello, as I am interested in the volume of ventricular structures in the brain, I would like to more precisely understand the labels given by /stats/aseg.stats in Freesurfer. Most importantly, what is the precisely defined difference between Left-Lateral-Ventricle and Left-Inf-Lat-Vent? Would you always combine these two in a volumetric study? Why are they separately segmented? And what exactly is the 5th-Ventricle? Less importantly, how exactly do you define CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, and CC_Anterior? Is there a paper or homepage defining these exactly? Any help appreciated! Thanks a lot, Meike

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structure volume
by Adil Javed 09 Sep '11

09 Sep '11

Hi, After running dti_recon and recon_all, I noticed that they produce different volumes of structures for the same brain. Just trying to understand why that is? best, AJ

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refeventdur in mkanalysis-sess
by Maryam Vaziri Pashkam 08 Sep '11

08 Sep '11

Hi, I am making an analysis in freesurfer 5.1 using mkanalysis-sess and I am a bit confused about the flag refeventdur. In the help it is said that it should be set to the event duration if the events have similar durations. I have four conditions that last for 16 second each in a block design paradigm, but my fixation condition lasts for 8 second. What should I set the refeventdur to? Also I have an event related design with variable fixation durations. what should it be in that condition? How about if I have an event related design with variable stimulus durations? How does this value influence the design matrix? Thanks, Maryam

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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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