Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Adding low-res T2 and PD images in the recon-all stream - any advantages?
by Nicola Toschi 18 Mar '13

18 Mar '13

Hello List, on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution. Would you recommend passing these (T2+PD) to the recon-all stream anyway - would they add value/accuracy to the segmentation/parcellation (or would they possibly decrease accuracy)? Thanks in advance, Nicola

5 9

A question regarding high FA values when running DTI script
by Rotem Saar 18 Mar '13

18 Mar '13

Hi all, I run into somthing that seems odd to me and wanted to consult - I run the following script for getting the FA values from my DTI scans: 1) dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec 2) tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii -fthresh 0.2 -fmax 1 4) mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s FOLDER-NAME --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat 5) tkregister2 --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_marsal.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg 6) mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii --sum /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME I got a table with all the FA values, for each segment, but I suspect a problem: I think that the values are too high (I set the threshold to 0.2-1), am I right ? I'm attaching the table I got, and to be specific, I'm very much interested in the Corpus-Colosseum values, which are high (not surprising) but when I wanted to validate with some other structures, like the "left putamen" I saw 0.53 which is to my opinion too high ? I would really appreciate if you can have a look at the table I attached here. Can u guide me regarding what I can do to solve the problem ? Is that any way to confirm that after the mask, I am left only with white matter ? Thanks ! Rotem

3 5

Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0
by Andrew Bock 08 Mar '13

08 Mar '13

Hello, I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/ subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock(a)u.washington.edu

4 8

QDEC - organization of folders for different projects
by Katharina Wittfeld 04 Mar '13

04 Mar '13

Dear FreeSurfer users, we started to analyze structural MRI data from two large cohorts (one with over 2100 and the other with over 1100 subjects). Preprocessing is completely done for all datasets and I've worked myself through this Qdec tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis) Everthing works fine but I would like to organize the output of qdec project-wise and not all together in the qdec folder in the subject directory. This is important because the qdec.table.dat file would be quite different for the various projects. Is there a way to organize the output like this: /project_1/analysis_1 ... /project_1/analysis_n /project_2/analysis_1 ... /project_2/analysis_n ... and the corresponding qdec.table.dat file in the project_x folder? I tried to run qdec with a qdec.table.dat file saved in another folder but the output is still saved in the subjects dir qdec folder. I would be very grateful for any hint or comment on this topic. Thank you in advance! Best regards, Katharina

2 2

Hippocampus volume calculations
by Garikoitz Lerma-Usabiaga 03 Mar '13

03 Mar '13

Hi, I am calculating hippocampus volumes with 5.2 in CentOS 4. I compare volumes (the same apply for lh and for rh) when calculating as: > Left.Hippocampus value in 1mm3 from aseg.stats > I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in order to get mm3, and sum every column except left_hippocampal_fissure. I obtain quite different values, for example: row.names lh.aseg lhHIP rh.aseg rhHIP 1S_00 4848.83828.187 4878.83767.7392 S_02 4153.83371.517 4547.63389.918 Am I doing anything wrong? Should I calculate the hippos subfields volumes differently? Many thanks! Gari

4 6

selxavg3-sess illconditioned error
by Katie Bettencourt 01 Mar '13

01 Mar '13

I am having a problem with selxavg3-sess (for FS 4.5) where it is giving me an Ill-conditioned error that I can't trace out. I have 8 runs that I am running separately (same basic analysis for each run, but each run gets it's own analysis for svm purposes). Originally for this subject, I created an analysis and it ran fine for all 8 runs. I went back and changed the timewindow on the analysis (and only the timewindow) and now, while it runs fine for 7 or the 8 runs, one of them gives me an ill conditioned error during selxavg3-sess. I double checked the paradigm file and all conditions are listed, and the only change between when the analysis ran fine and when it gave me this error was changing the timewindow. The mkanalysis commands I used both times are listed below. Original analysis (worked fine): foreach r (1 2 3 4 5 6 7 8) mkanalysis-sess -analysis grating_nodist_ld_run${r} -TR 2 -paradigm grating.dat -designtype event-related -funcstem fmc -motioncor -runlistfile nodist_run${r}.txt -inorm -tpexclude tpexclude.dat -nconditions 3 -timewindow 22 -TER 2 -noautostimdur -polyfit 2 end new analysis (illconditioned on one run only): foreach r (1 2 3 4 5 6 7 8) mkanalysis-sess -analysis grating_nodist_ld_34_run${r} -TR 2 -paradigm grating.dat -designtype event-related -funcstem fmc -motioncor -runlistfile nodist_run${r}.txt -inorm -tpexclude tpexclude.dat -nconditions 3 -timewindow 34 -TER 2 -noautostimdur -polyfit 2 end Katie

3 11

Question on stats analysis in Qdec
by Kristina Nalbandian 01 Mar '13

01 Mar '13

Hello, I am running qdec group analysis on my patient data. I am studying the differences between two Epilepsy onset types and have a few questions. 1) I select "subtype" as my discrete variable and "duration" as my continuous variable. In the display tab two questions appear. 1. Does the average thickness differ from zero? and 2. Does the average thickness differ between HYP and LVF (the two onset types)? What is the difference between these two questions? Mainly, can someone please explain question 1 and how that is calculated. 2) Are corrections for multiple comparisons already build into the qdec analysis? or is this something that needs to be run separately. Is permutation testing required to determine how likely the observed level of significant atrophy within each p-map would occur by chance? Thank you in advance, Kristina

2 1

RAS coordinates in tksurfer and matlab
by Brinkmann, Benjamin H., Ph.D. 01 Mar '13

01 Mar '13

Dear FreeSurfers, I am working on generating a functional map of electrophysiological activity on a freesurfer pial surface and I've come across something that has stumped me. I have the electrode coordinates in RAS space and I am trying to interpolate a value at each surface vertex for the color map using the RAS coordinate of each vertex. However, the RAS coordinates I read into matlab using freesurfer_read_surf.m are different from what is being displayed in tksurfer. (I'm comparing RAS coordinates by hovering the cursor in tksurfer.) Most of the time the differences are very small, but occasionally they can be large. I haven't been able to identify any kind of a constant offset or relationship between these coordinates. Should the RAS coordinates displayed in tksurfer be the same as what is read directly from the surface file? Is there a better way to approach this task? Thanks very much for any suggestions. Regards, Ben Brinkmann =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Benjamin H. Brinkmann, PhD Mayo Systems Electrophysiology Lab Alfred 9-441C, SMH 1216 Second St. SW Rochester, MN 55902

3 2

bbregister with SPM
by Chen, Xiaoyan 01 Mar '13

01 Mar '13

Dear freesurfer experts, I have a question regarding how to incorporating bbregister coregistered mean image into the SPM batch. After realignment step, I convert the mean functional image from the analyze format to nii format (to avoid flipping brain using bbregister) Then, I use bbregister to co-register the mean functional image to subjects' surfaces using following command bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold --reg register.dat -- spm-nii After this step, is the mean.nii the coregistered image already? If it is, in SPM, shall I skip the coregistration and segmentation step? If I do skip them, in the Normalization step, is the following correct? source image: mean.nii that has been coregistered in bbregister image to write: (Dependency) realigned session1 and realigned session2 template image: EPI Thank you very much for your help. Helen

2 2

Estimate of when "Download" section will re-open?
by DT 28 Feb '13

28 Feb '13

Went to download an updated version of Freesurfer today, and saw a posting on the site that says: > ALL DOWNLOADS ARE OFFLINE WHILE WE DEAL WITH STORAGE ISSUES Is there any estimate of when they might return? It looks like it's a fairly new issue, based on the wiki history on the download page, and I'm hoping it can be resolved quickly. thanks, - D

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Freesurfer February 2013