Freesurfer

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30089 discussions

Surface number of vertices mismatch
by Pablo Polosecki 26 Jul '12

26 Jul '12

Dear List, I am trying to show my results on Caret's F99 atlas, in Caret. For this I already managed to take my anatomical (white, pial etc) surfaces and register them to F99 in Caret, which works fine. I am trying now to get my functional p-map (initially a nifti volume) into Caret too to overlay them on my anatomical surface together with the atlas information. For this my plan s the followign 1-Convert my nifti p-map volume into a surface using mri_vol2surf 2-Convert the resulting surface into caret surface using caret_command tools. 3-Apply to the resulting surface the same transformation I applied to my anatomical surfaces to have them all in register with Caret's F99 atlas. It seems like step 1 works fine, but when I try to run step too, Caret complains that my anatomical surface doesn't have the same number of vertices as my functional surface. Indeed, when opening the anatomical surface in maltab with read_surf, it seems to have exactly twice the number of vertices that my functional surface has (I cannot open it with read_surf for some reason but I see the number when I open it with a text editor or when I look at the output of mri_vol2surf). Would anyone have a suggestion as to why this is the way it is and how I could have my 2 surfaces have the same number of nodes? Thank you very much, Pablo

4 7

FW: bringing surfaces from different subjects into the same space in matlab
by Rebelo Ferreira Marques Jose Pedro 26 Jul '12

26 Jul '12

Dear freesurfer experts, I would like to know how to have paint surfaces (.w) from different subjects into a common surface (fsaverage for example) and/or would like to know if my current approach is correct: I have first used the general "recon-all" step on some T1-w images. Subsequently I used "mris_expand" to create the different surfaces at different depths. with "mri_vol2surf" I was able to obtain the T1-w images in the various surfaces. At that moment my different subjects surfaces had different number of vertices and I would like to average them together. Using matlab, read_surf, I loaded the coordinates in the sphere of the subject data and of the fsaverage data. Subsequently I used the matlab function distributed with freesurfer, mesh_vertex_nearest, to find the nearest vertices of the subject sphere surface to those of the fsaverage surface. I then created a new paint surface where only those vertices were taken into account. Could I say that now all my subjects are co-registered and that I can use the PALS12.annot distributed with fsaverage to extract the properties of the different Brodmann areas? Is there a better way to do this? Thanks in advance, Jose Marques

3 2

CSF segmentation and cortical ribbon
by Christopher Coello 26 Jul '12

26 Jul '12

Dear Freesurfer users, I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels. Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned. My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ? Thanks a lot in advance, Best, -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516 -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516

2 5

recon-all error
by Yigal Agam 25 Jul '12

25 Jul '12

Hi, We're getting the following error from recon-all: command line: pbsubmit -m etanski -c 'recon-all -s DODASD012 -all -i /cluster/archive/300/siemens/TrioTim-35006-20120718-151622-227000/391000-000015-000001.dcm -mail etanski(a)nmr.mgh.harvard.edu' output: ... ... mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14699/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/manoach/dod/subjects/DODASD012/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14699/ones.mgz sysname Linux hostname compute-0-88 machine x86_64 user etanski input ./tmp.mri_nu_correct.mni.14699/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.14699/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/input.mean.dat $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/input.mean.dat sysname Linux hostname compute-0-88 machine x86_64 user etanski Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.14699/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/output.mean.dat $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/output.mean.dat sysname Linux hostname compute-0-88 machine x86_64 user etanski Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz Loading ./tmp.mri_nu_correct.mni.14699/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.14699/output.mean.dat (standard_in) 1: syntax error mris_calc -o ./tmp.mri_nu_correct.mni.14699/nu2.mnc ./tmp.mri_nu_correct.mni.14699/nu2.mnc mul Linux compute-0-88 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 18:58:52 BST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DODASD012 exited with ERRORS at Wed Jul 25 12:27:28 EDT 2012 For more details, see the log file /autofs/cluster/manoach/dod/subjects/DODASD012/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any suggestions? Thanks, Yigal

2 1

non-stationarity in CTh maps
by Hugo Baggio 25 Jul '12

25 Jul '12

Dear all, I have been performing cortical thickness analyses and as far as I understand the thickness maps are non-stationary (please correct me if I'm wrong). I have two questions: 1. How susceptible is Monte Carlo clusterwise correction to this (should I expect clusters at smoother areas to be bigger?)? 2. Does FS perform some sort of correction to this non-stationarity or are images assumed to be stationary at statistical analyses? Thanks a lot for your help! Hugo

2 1

MRIread on matlab
by Kevin Chen 25 Jul '12

25 Jul '12

Hi all, I am a beginner to FreeSurfer, and have been experimenting with the MRIread function on MATLAB. I am able to load .nii files using MRIread, but is there a way to display a particular slice from a nifti file on MATLAB using MRIread and its related functions? Thanks in advance, Kevin

2 1

Re: [Freesurfer] Freesurfer Question
by Alexandra Tanner 25 Jul '12

25 Jul '12

Hi Doug, Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well. We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are? Thanks so much! Alex > Hi Alexandra, what structure are you looking to analyze? Ie, the volume > of what? The volume of cortex? > doug > ps. In the future, please post such questions to the freesurfer list as > it gives others the opportunity to answer and to learn. thanks! > > On 07/23/2012 12:03 PM, Alexandra Tanner wrote: >> Hi Mr. Greve, >> >> My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain >> Genomics Lab. I had a question regarding conducting volume analyses. On >> the freesurfer wiki there are commands that show how to conduct Paired >> Analyses to look at average surface, and I was curious if it was >> possible >> to do a paired analysis looking at volume instead. >> Any information you have would be very helpful. >> >> Thanks so much! >> >> Best, >> >> Alexandra Tanner >> Clinical Research Coordinator >> Laboratory for Brain Genomics >> Division of Psychiatric Neuroimaging >> Massachusetts General Hospital >> 149 13th Street >> Charlestown, MA 02129 >> (p) 617.643.3215 >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > >

2 4

Recon-all -qcache curvature error & recon-all make -all
by Gibbard, Clare 25 Jul '12

25 Jul '12

Hello, I have run several scans using recon-all -all -subjid subject_no -expert expert.opts where my expert.opts file changes the parameters for the mri_normalize step (this works well in my scans). I then had to edit a few of the scans by adding in more white matter and a few control points. I re-ran them to incorporate the edits using recon-all -s subject_no -make all -xopts-use. This worked well. I then ran recon-all -s subject_no -qcache ready for doing a group analysis. I got an error reading the curvature file in those subjects I had edited. I can see from the mailing list that others have had this error previously and ran recon-all -s subject_no -make all to fix it. I tried this, but I got a message saying that there was nothing to be done for all. Are you able to advise me on what I can try now? Do I need to go back a step? Thank you very much, Clare

2 1

Paired t-test with independent samples
by Jürgen Hänggi 24 Jul '12

24 Jul '12

Dear statistic experts We have done statistics between two independent groups using an independent t-test. One group consistent of 13 male patients and the other group consistent of 13 male control subjects who were matched to the patients with respect to age and education (in years). The reviewer proposed that it might be more appropriate to use a paired t-test. However, we can imaging a design where such an approach is adequate e.g. monozygotic twins reared in shared environments who are discordant for a particular trait. In our opinion, the matching of only age and education is not sufficient in order to apply a paired t-test. In addition, the paired t-test is more anti-conservative than the independent t-test and therefore advantages our hypothesis and this might be identified as a statistical "trick" by other reviewers. Any comment about whether or not the suggested paired t-test is appropriate in our study is highly appreciated. Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

4 3

tracula RAM memory ?...
by Gonzalo Rojas Costa 24 Jul '12

24 Jul '12

Hi: How much memory needs tracula to process a DTI study ?... Because my PC (Ubuntu Linux, 4GB RAM) exit because it can't allocate memory in trac-preproc... There exist any tip & trick in such a case?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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