Freesurfer April 2016

freesurfer@nmr.mgh.harvard.edu

122 participants
173 discussions

Lme matlab tools lhstats
by Patrizia Dall'Acqua 20 Apr '16

20 Apr '16

Dear FS-Group I am attempting to use the lme matlab tools for my longitudinal analysis. My dataset consists of 2 time-points and 2 groups (patients and controls). I will not use covariates since the groups are well matched for age, gender and education. I am trying to adapt the wiki instructions of the mass-univariate model to our data. Our design matrix X contains 4 columns: 1. intercept 2. time 3. group 4. interaction group*time Our Cmd history: [Y,mri] = fs_read_Y('lh.thickness_sm15.mgh'); lhsphere = fs_read_surf('/subjects/average_LTHV_long_all_49/surf/lh.sphere'); lhcortex = fs_read_label('/subjects/average_LTHV_long_all_49/label/lh.cortex.label'); Qdec = fReadQdec('qdec.long.table_4columns.txt'); Qdec = rmQdecCol(Qdec,1); sID = Qdec(2:end,1); Qdec = rmQdecCol(Qdec,1); M = Qdec2num(Qdec); [M,Y,ni] = sortData(M,1,Y,sID); X = [ones(length(M),1) M M(:,1).*M(:,2)]; lhstats = lme_mass_fit_vw(X, [4], Y, ni, lhcortex) I am mainly interested in comparing longitudinal changes between groups (group*time interaction) but also interested in the main effect of group and time. I have two questions: 1. I am not sure about my „interpretation“ of random and fixed effect. Since I am interested in the group*time interaction (4. column), does it make sense to use a single random effect for this interaction or should I take a second random effect for time (2. column)? 2. If a model with two random effects make sense (2. and 4. column), should I compare the model including two random effects with a model with a single random effect to test which one is significantly better? Thank you for your help! Patrizia

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how to add skull and scalp and how to convert RAS coordinates
by Chiara Bulgarelli 20 Apr '16

20 Apr '16

Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data. After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues: 1. How can I add the CSF, the skull and the scalp in my model? I know that with FS you can get just WM and GM. 2. How can I convert the RAS coordinates to MNI ones? I have been trying to look at these topics on line and on the FreeSurfer website, but I haven’t find anything useful so far. Many thanks in advance for your help! Best Regards Chiara ---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01(a)mail.bbk.ac.uk // bulgarelli.chiara3(a)gmail.com

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entorhinal & temporal pole thickness measurements
by Mihaela Stefan 20 Apr '16

20 Apr '16

Dear Freesurfers, We noticed that some subjects in our study have the average cortical thickness values in entorhinal and temporal pole above 4 mm. They are adolescent girls so they're pretty young but we wonder if these values are accurate. Visually, their segmentations seem good. In an older email, Bruce was recommending using _exvivo.stats instead of aparc for entorhinal measurements: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26364.html Is there a similar recommendation for the temporal pole? There doesn't seem to be any stats files apart from aparc concerning this region. Thanks! Mihaela

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Convert retenotopic areas from brainvoyger to Freesurfer
by Lilia Jorge 19 Apr '16

19 Apr '16

Hello I intend to compute cortical thickness in retinotopic areas. However retinotopic areas were delimited in BrainVoyager and the cortical thickness maps with FreeSurfer. There are any way to reconcile data from the two softawares? -- Com os melhores cumprimentos, Lília Jorge

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fcseed-sess ERROR: could not determine file for .../fmcpr
by Julio Alberto González Torre 19 Apr '16

19 Apr '16

Hi Freesurfer users. I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject. In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields): fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg > mean.L_CA1.config In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why: fcseed-sess -s con_algon -cfg L_CA1.config ERROR: could not determine file for > /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr > stem2fname > /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr I've checked the "009" folder and there isn't any file with the name "fmcpr". Does someone have any idea how could I resolve this? Thanks!

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Re: [Freesurfer] PET voxelwise & Segmentation Fault during mri_glmfit-sim
by Elijah Mak 19 Apr '16

19 Apr '16

No, more like running the voxelwise comparisons only on voxels that have positive BP between 2 group. Is that possible? On another note, I am running into a puzzling "Segmentation fault" error with the following command: mri_glmfit-sim --glmdir lh_ad_hc.glmdir --cache 2 neg --cwp 0.05 --2spaces ================================================ Reading source surface /Users/MacPro/Documents/NIMROD_DTI//fsaverage/surf/lh.white Done reading source surface Reading annotation /Users/MacPro/Documents/NIMROD_DTI//fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Segmentation fault ================================================ Strangely, I can't seem to reproduce this error consistently too. Sometimes, after a pause of few minutes, the exact same command works! This happens on smoothed and non-smooth PET data. I have attached the text outputs resulting from both scenarios 1) seg_fault and 2) no_seg_fault (about 10 minutes between each execution). The mri_glmfit-sim version is v .53.2.2 2015/08/28 19:00:13 I am running this on a Mac Pro with 64 GB RAM. Thanks again Best Wishes, Elijah

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mkanalysis-sess stimulusdelay parameter
by Joseph Dien 19 Apr '16

19 Apr '16

I’m taking a look at the effects of stimulus delay settings in one of my datasets so I was surprised to notice that the default setting of mkanalysis-sess is a delay of -TR/2 seconds. What is the reasoning for this? If, as I expect, it was just empirically found that it worked better than without, my question is whether this decision was made on the basis of all the event-related options or just some subset of them? I’m worried that this might be an optimization that isn’t appropriate for my particular parameter choices (FS 5.3, spmhrf0). Any comments would be appreciated. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park http://joedien.com

2 1

CA2 hippocampal subfield in FS6.0
by Patrick Sezen 19 Apr '16

19 Apr '16

Dear FreeSurfers, I was running the FS 6.0 hippocampal subsegmentation and was wondering where the CA2 subfield disappeared to. Version 5.3 had a CA2-3 label, but in 6.0 I can only find CA3, is it implicated that CA2 is part of CA3 as well in 6.0? Sincerely, Patrick Sezen

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Re: [Freesurfer] preproc-sess error opening tmp brain_mask
by Mcnorgan, Christopher 19 Apr '16

19 Apr '16

du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is the “not found” error telling me that a binary is not found, or that some expected output file is not found? I was looking for /bin/imtest and /bin/remove_ext, and those binaries indeed do not exist, but we’ve run Freesurfer on another dataset (but on another workstation, but neither were those two binaries to be found on that workstation). Is your /tmp space full? On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote: > > I was hoping the developers might be able to help with a problem I'm > having with a sub-step of preproc-sess. > I executed the following: > > preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold > > In the relevant output, I see mktemplate-sess completed, followed by a > call to mkbrainmask-sess, which eventually reported: > > # ---------- Using FSL's BET to Extract Brain------------------ # > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold > bet.fsl /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1 > /usr/local/freesurfer/bin/bet.fsl: 1: > /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found > /usr/local/freesurfer/bin/bet.fsl: 1: > /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found > /usr/local/freesurfer/bin/bet.fsl: 1: > /usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found > /usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator > /usr/local/freesurfer/bin/bet.fsl: 231: > /usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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(no subject)
by macara.p＠libero.it 19 Apr '16

19 Apr '16

Dear all, I need to compute the geodesic distance (i.,e. the distance on the cortical surface) between a series of vertices. Specifically, I want to compute the distance between all the vertices in the right hemisphere (>100000) and a series of vertices of interest (around 20000), always located in the right hemisphere. Ideally, my output should be a matrix right_verticesXvertices_of_interest where in each entry there is the geodesic distance between the pair of vertices. And I need to do this for hundreds of subjects! I tried to use mris_pmake: for i = right_vertices; for j=vertices_of_interest; command1 = ['/Applications/freesurfer_v5.3/bin/mris_pmake --subject 001 --hemi rh --surface0 white --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:' num2str(i) ',' 'endVertex:' num2str(j)] T(i)=evalc('system([command1])') end end But the problem is that it is way too much time consuming and it is difficult to store the results in a matrix. Is there a way to adapt this command for such high computations? I Are there other ways to obtain the geodesic distance between vertices, either than mris_pmake (for example a matlab function)? Thank you in advance,Marica

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Freesurfer April 2016