Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

Project full annotation files from one subject to another
by mbrickho＠nmr.mgh.harvard.edu 12 Sep '11

12 Sep '11

Hi FS team, Is it possible to project an entire annotation file from one subject's surface to another? I haven't been able to find a command for this, but I might just not be looking hard enough. My intent is to project an annotation I've made on fsaverage to every member of a cohort of 500+ subjects, and then extract thickness data from each newly created annotation file. Currently, I do mri_annotation2label to split the original annotation into its individual labels. Then I project each label, one at a time, with mri_label2label. Then, I combine them back into an annotation with mri_label2annot for every subject. While this method works fine, it seems like it's more cumbersome than it has to be. Any help/advice would be appreciated. Thanks! Mike

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mri_vol2vol
by Constantin Anastasopoulos 12 Sep '11

12 Sep '11

Hellom I coregistered manually a aparc+aseq.nii file to my DWI-space with tkregister2. I saved the .dat file and applied it later to the T1 image in order to apply the same spatial coregistration as to the aparc+aseg. For woth the aparc+aseg and the T1 I used the command mri_vol2vol --mov was the b0image --targ was the aparc+aseg and T1 respectively --o was the output (a .nii in both cases) --reg was the .dat file and at the and --inv. While the aparc+aseg registration to the b0 worked, the T1-registration gave a false result (altough it had the same dimensions and was in the same space with the aparc+aseg). What am I doing wrong? Is the mri_vol2vol command the wrong one? I want to apply the same changes as to the aparc+aseg, as they are saved in the .dat file. Thanks a lot, Constantin

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some very basic Recon-all questions
by Martijn Cloos 10 Sep '11

10 Sep '11

Hi, When running something like: "recon-all -autorcon1 -i file1.nii.gz -s subject" it first converts the nifti file to the mgz format (orig.mgz, i think). In the proses the data appears to get converted to 8bit integers. Starting with float data how does this impact the analysis? It seems to me that the range selected in "orig.mgz" is not optimal and this appears to be resampled in T1.mgz. Are there ways to use a higher dynamic range, by forcing it to use floats or 16bit/32bit integers? Or should I just manually optimize/verify "orig.mgz" before running recon-all? Also, are there ways to use the original resolution instead of resampling to 1mm iso? Thanks! Martijn

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bedpostx changes in past 2 years?
by swoodman＠nmr.mgh.harvard.edu 09 Sep '11

09 Sep '11

Hi all, We always run bedpostx in the developement (nmr-dev-env) environment, and after some digging around, we've noticed some differences in outputs between 2008 and now. Has anything changed with bedpostx in dev environment since 2008, that would effect data and/or analysis? There seem to be more log files in the bedpostx log directory in the sessions that were run more recently. So this is mainly why we are wondering if something has changed in the bedpostx program between October 2008 and October 2009 that affects the tractography data. Thank you! Sandra

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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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Freesurfer September 2011