Freesurfer

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30132 discussions

mkanalysis.sess versus mkanalysis.sess.new
by Maryam Vaziri Pashkam 14 Apr '11

14 Apr '11

Hi Everyone, Two beginner question again. 1. What is the difference between mkanalysis-sess and mkanalysis-sess.new? which one should be preferably used and why? 2. What is the best way to exclude trials from the analysis: a) in the paradigm file define them as a separate condition and this way include them in the GLM analysis and later on ignore them in the contrast analysis? b) exclude the time points of that trial in the tpexclude.dat using the tpexclude flag? c) another way that I have not thought of? Thanks, Maryam

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high resolution segmentation
by Jonathan A Winawer 14 Apr '11

14 Apr '11

I recently started using freesurfer for gray-white segmentation with great success. However, I have had one problem I cannot solve myself: I have been unable to create a ribbon file at the native resolution of my T1 scans (0.7 mm isotropic voxels), and I am puzzled by the result. My strategy was as follows: 1. standard recon all (this works nicely) 2. resample aseg.mgz to match the slicing of rawavg.mgz 3. create new ribbon file using mris_volmask The standard recon at 1x1x1 mm resolution produces a nice ribbon file: http://white.stanford.edu/~winawer/brain/2011/axial_ribbon_1mm.tiff The hires recon after steps 2 and 3 above fails: http://white.stanford.edu/~winawer/brain/2011/axial_ribbon_hires.tiff If anyone knows why this is, I would greatly appreciate the help. For details, see below. Many thanks, Jon The hires t1 I started with is here: http://white.stanford.edu/~winawer/brain/2011/t1.nii.gz and the code I used for the initial recon and the creation of the new ribbon is here: # give the subject a name subj=homer # recon all using hires t1 (0.7 mm isotropic voxels) recon-all -i ~/t1.nii.gz -all -subjid $subj -all # define the working directory d=$SUBJECTS_DIR/$subj/mri # back up original ribbon and aseg files mkdir $d/1mm; mv $d/*ribbon* $d/aseg.mgz -t $d/1mm ## Create Hi-Res Ribbon##################### # reslice the aseg file to the size and resolution of rawavg mri_convert $d/1mm/aseg.mgz -o $d/aseg.mgz --reslice_like $d/rawavg.mgz --resample_type nearest # re-create surface at resolution of rawavg mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance $subj ##################################### # back up high-res files mkdir $d/hires; cp $d/*ribbon* $d/aseg.mgz $d/hires/ # Compare the two ribbon files. Original (1x1x1 mm) looks good: tkmedit $subj 1mm/aseg.mgz -segmentation 1mm/ribbon.mgz # HiRes looks bad: tkmedit $subj hires/aseg.mgz -segmentation hires/ribbon.mgz ******************************* Jonathan Winawer Stanford University Department of Psychology Jordan Hall, Building 01-420 450 Serra Mall Stanford, CA 94305 Phone: 650-725-1255 winawer(a)stanford.edu http://www-psych.stanford.edu/~winawer/

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Re: [Freesurfer] creating labels in tksurfer
by Ilana Hairston 14 Apr '11

14 Apr '11

Thanks Bruce, It seems there are some display bugs on the server running freesurfer. In addition to the vanishing label (the label option was on), the scatter plots were messed up. After transferring the data to a different server it seems to be ok. Not sure what the issue is. ilana ______________________ If you can't be kind, be vague •••••••••••••••••••••••••••••••••••• Sent from my iPhone On Apr 4, 2011, at 10:23, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Ilana, > > it looks fine to me. Is it a left hemisphere label? If so, it looks like superior temporal gyrus. Make sure that label display is turned on in the tksurfer interface (the default may be off). It's one of the buttons on the top right. > > cheers > Bruce > > > On Sat, 2 Apr 2011, Ilana Hairston wrote: > >> sorry for the delay (can't ftp from the server). the file is attached >> >> On 2 April 2011 12:33, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> >>> can you email us the label? >>> >>> On Sat, 2 Apr 2011, Ilana Hairston wrote: >>> >>> sorry, i probably should have said that this was on the fsaverage, after >>>> glmfit. >>>> basically i wanted to create a VOI and extract a stats table for it. >>>> >>>> >>>> On 1 April 2011 22:33, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>>> >>>> Hi Ilana, >>>>> >>>>> usually a bizarre labeling means the annot is out of date. Try running >>>>> recon-all with -make all on that subject and see if it needs to recreate >>>>> anything. >>>>> >>>>> Not sure what's up with your label, but things can act strangely when the >>>>> surfaces are out of date >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> On Fri, 1 Apr 2011, Ilana Hairston wrote: >>>>> >>>>> Hi there, >>>>> >>>>>> I'm having difficulty creating labels in tksurfer (v4.5). I followed >>>>>> the >>>>>> "Creating Labels" instructions on the Wiki, however clicking Fill on the >>>>>> closed path didn't seem to do anything. I used save label anyway, and >>>>>> tried >>>>>> to load this new label again, and even though it says "7681 nonzero >>>>>> vertices >>>>>> found", again i see nothing. >>>>>> Not quite sure what i'm doing wrong. >>>>>> >>>>>> Also - which LUT file is the correct one to go with aparc.annot? i get >>>>>> the >>>>>> most bizarre labeling with FreeSurferColorLUT >>>>>> Thanks >>>>>> ilana >>>>>> >>>>>> >>>>>> >>>>>> >>>>> 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 at >>>>> http://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. >>>>> >>>>> >>>>> >>>> >>>> >>>> >> >> >>

2 1

?h.aparc.stats file question
by Tetiana Dadakova 14 Apr '11

14 Apr '11

Dear list, I was trying to find the values of volumes for different cortical regions. What I found is the 4th column (called GrayVol) in ?h.aparc.stats file. Although, the values don't really seem to be what I look for, as values are too small (e.g. 0.5 mm^3 for cuneus). Could you please guide me where I should look for these values, or probably how should I interpret the values in ?h.aparc.stats file. Thank you, Tanja.

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create summary images
by McLean John (NHS Greater Glasgow & Clyde) 14 Apr '11

14 Apr '11

I'd like to create some summary images (.tiff, .png ) so that I can quickly inspect subcortical structure segmentation quality on a large number of subjects. I know I can open tkmedit and extract a series of tiff images, I've also been playing with Slicer3 but again I have to load the data for each subject. I'd also like to hone in on particular structures, for example, to extract images only showing the hippocampus (whole segmentation or outline) on the T1 3D backdrop, does anything exist in Freesurfer to do this from the command line? Essentially I'm looking for something similar to the first_roi_slicerdir command in FSL as I found this a really quick way of visually checking segmented data. Any advice around this would be a great help, Thanks John ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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Visualizing Subcortical Volume Differences
by Jeff Sadino 14 Apr '11

14 Apr '11

Hello, I am interested in a way to visualize the differences in the volume in subcortical structures, preferably in 3D. For example, I would like to view the Thalamus of controls. And then I would like to overlay a color-coded map that shows the difference between the volume of the Control Thalamus and the Study Thalamus. I have seen a couple of different ways to do this, but they all seem rather clunky. Can anyone recommend a method for this? Thank you very much, Jeff Sadino

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bert functional data set
by Palzes, Vanessa 13 Apr '11

13 Apr '11

Hi, I'm trying to go through this tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AutomaticRegistratio nSpm I have already downloaded/unpacked the buckner_data-tutorial-subjs.tar.gz, and also set up the correct SUBJECTS_DIR as: setenv TUTORIAL_DATA /Applications/freesurfer/subjects cd $TUTORIAL_DATA/buckner_data/tutorial_subjs setenv SUBJECTS_DIR ${PWD} But, when I try to run the following command, it tells me it cannot find bert-brf... spmregister --s bert-brf --mov f001.img --reg register.dat Any suggestions on how I can locate and use this tutorial data? Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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Smoothing & ROIs
by pikase＠tin.it 13 Apr '11

13 Apr '11

Dear FS experts, I'm quite sure this is a very trivial question since apparently it hasn't been posed previously. I'm performing a CT analysis with the aim to compare two groups of subjects, which are different regarding the degree of expertise in a given area (experts vs non experts) and using as covariates age and gender. The total number of subjects is 21 for the expert group and 20 for the naive subjects. At first I performed a whole brain analysis both via qdec and command-based, wich reveal substantially no differences between the two groups. Now, I also have some a-priori ROIs I would like to test. I went several times through the steps suggested in the tutorial, but still something is not clear to me. Do I need to apply a smoothing on the ROI I want to draw? I would assume so. How can I do that? Is it possible to extract ROIS from previously smoothed data? (All my datas have been passed through -qcache). Thanks so much for your time and help! Best regards, Laura

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Bug in mri_info?
by Scott Burns 13 Apr '11

13 Apr '11

Freesurfers -- This morning, I was trying to convert a 4 frame MPRAGE scan into a 1 frame RMS image. I wrote my own matlab code to do it ... function err = rms_mprage(old,new) %convert 4-frame mprage into 1 frame mprage by taking RMS of voxels old_hdr = load_nifti(old); new_hdr = old_hdr; new_hdr.vol = sqrt((old_hdr.vol(:,:,:,1).^2+old_hdr.vol(:,:,:,2).^2+old_hdr.vol(:,:,:,3).^2+old_hdr.vol(:,:,:,4).^2)/4); err = save_nifti(new_hdr,new); So I ran >>> rms_mprage('MPRAGE1.nii','MPRAGE_new.nii') Also, Bruce said I could do this ... mri_average -noconform -sqr MPRAGE1.nii#0 MPRAGE1.nii#1 MPRAGE1.nii#2 MPRAGE1.nii#3 MPRAGE_rms.nii However... kerryave:002 $ ls -l -rw-rw-r-- 1 sburns lingua 92275040 Dec 21 12:27 MPRAGE1.nii -rw-rw-r-- 1 sburns lingua 24340 Dec 20 15:17 MPRAGE1.nii-infodump.dat -rw-rw-r-- 1 sburns lingua 23069024 Apr 12 13:29 MPRAGE_new.nii -rw-rw-r-- 1 sburns lingua 46137696 Apr 12 13:35 MPRAGE_rms.nii So I was curious why the _rms.nii was twice as big. Probably a datatype issue, right? kerryave:002 $ mri_info MPRAGE_new.nii Volume information for MPRAGE_new.nii type: nii dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.0055, y_r = 0.0068, z_r = -1.0000, c_r = -0.9523 : x_a = -0.9719, y_a = 0.2354, z_a = -0.0037, c_a = 2.8859 : x_s = -0.2354, y_s = -0.9719, z_s = -0.0079, c_s = 0.8822 Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.0055 0.0068 -1.0000 85.4734 -0.9719 0.2354 -0.0037 97.4806 -0.2354 -0.9719 -0.0079 156.1061 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: 0.0055 -0.9719 -0.2354 131.0176 0.0068 0.2354 -0.9719 128.1845 -1.0000 -0.0037 -0.0079 87.0654 0.0000 0.0000 0.0000 1.0000 And... kerryave:002 $ mri_info MPRAGE_rms.nii Volume information for MPRAGE_rms.nii type: nii dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.0055, y_r = 0.0068, z_r = -1.0000, c_r = -0.9523 : x_a = -0.9719, y_a = 0.2354, z_a = -0.0037, c_a = 2.8859 : x_s = -0.2354, y_s = -0.9719, z_s = -0.0079, c_s = 0.8822 Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.0055 0.0068 -1.0000 85.4734 -0.9719 0.2354 -0.0037 97.4806 -0.2354 -0.9719 -0.0079 156.1061 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: 0.0055 -0.9719 -0.2354 131.0176 0.0068 0.2354 -0.9719 128.1845 -1.0000 -0.0037 -0.0079 87.0654 0.0000 0.0000 0.0000 1.0000 Weird that mri_info shows the datatype for both images as float. fslhd shows different things... kerryave:002 $ fslhd MPRAGE_new.nii filename MPRAGE_new.nii sizeof_hdr 348 data_type INT16 dim0 4 dim1 256 dim2 256 dim3 176 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units ms datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.0000000000 pixdim4 2530.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 0.000000 0.000000 -1.000000 87.473366 qto_xyz:2 -0.976296 0.216439 -0.000000 100.261627 qto_xyz:3 -0.216439 -0.976296 -0.000000 153.275482 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Anterior-to-Posterior qform_yorient Superior-to-Inferior qform_zorient Right-to-Left sform_name Aligned Anat sform_code 2 sto_xyz:1 0.005469 0.006804 -0.999962 85.473358 sto_xyz:2 -0.971887 0.235419 -0.003714 97.480621 sto_xyz:3 -0.235385 -0.971870 -0.007900 156.106079 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Anterior-to-Posterior sform_yorient Superior-to-Inferior sform_zorient Right-to-Left file_type NIFTI-1+ file_code 1 descrip FreeSurfer Dec 18 2010 aux_file kerryave:002 $ fslhd MPRAGE_rms.nii filename MPRAGE_rms.nii sizeof_hdr 348 data_type FLOAT32 dim0 3 dim1 256 dim2 256 dim3 176 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 16 nbyper 4 bitpix 32 pixdim0 0.0000000000 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.0000000000 pixdim4 2.5299999714 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 0.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 0.005469 0.006804 -0.999962 85.473358 qto_xyz:2 -0.971887 0.235419 -0.003714 97.480621 qto_xyz:3 -0.235385 -0.971870 -0.007900 156.106079 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Anterior-to-Posterior qform_yorient Superior-to-Inferior qform_zorient Right-to-Left sform_name Scanner Anat sform_code 1 sto_xyz:1 0.005469 0.006804 -0.999962 85.473358 sto_xyz:2 -0.971887 0.235419 -0.003714 97.480621 sto_xyz:3 -0.235385 -0.971870 -0.007900 156.106079 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Anterior-to-Posterior sform_yorient Superior-to-Inferior sform_zorient Right-to-Left file_type NIFTI-1+ file_code 1 descrip FreeSurfer Mar 19 2011 aux_file fslhd shows different data types, which explains the difference in size. I think there's a bug in mri_info that is incorrectly reading MPRAGE_new.nii as float data. Not an earth shattering bug by any means, but I thought I'd let you know anyways. Scott Burns Kuperberg Lab Martinos Center for Biomedical Imaging sburns(a)nmr.mgh.harvard.edu 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 at http://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.

2 1

Checking correct hemisphere in tksurfer
by Ed Gronenschild 13 Apr '11

13 Apr '11

Dear FreeSurfer developers, With tksurfer you have to watch out to select the correct hemisphere when loading an overlay or annotation. My suggestion to the developers is to implement an easy check since it is known to which hemisphere the displayed surface belongs. As far as I know, the only file for which such a check would fail is sig.mgz, the result of a statistical analysis. Kind regards, Ed

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