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issue merging label files
by Nicholas Blauch 06 Jun '18

06 Jun '18

External Email - Use Caution Hello freesurfer experts, I wrote some matlab functions for merging surfaces, overlays, curvature, annotations, and curvature across hemispheres for easier viewing in Freeview and in preparation for multiple comparisons correction. It all works with the exception of merging the labels. It is odd, because out of 4 labels I've tried, 1 worked perfectly, and the others did not work at all. I cannot see any reasons why this would be the case. I wanted to see if anybody might have some insight as to what's going wrong. The function is below. x_shift is so that the hemispheres do not overlap (not sure why its necessary since when plotted separately the hemispheres do not overlap, but it is). I also attached two output merged label files, one working (mh.STS.label), and one not working (mh.FFA.label), along with a surface to view on (apologies if it is too big and doesn't send; it is just a merged partially inflated fsaverage with x_shift = 90 applied to right hemisphere). When the label function is fixed, I'd be happy to share the collection of functions with others who are interested. thanks for any help, Nick function merge_fs_hemi_labels( exp, subname, labname) %MERGE_FS_HEMI_LABELS( exp, subname, labname) % % merge freesurfer labels across hemispheres % requires freesurfer % % inputs: % % exp: experiment name under bids/ directory % subname: subject name % labname: base label name, e.g., 'OFA'. hemis will be preprended to this % using standard format, e.g. 'lh.OFA', 'rh.OFA', 'mh.OFA' % % x_shift = 90; bids_dir = get_bids_dir(exp); setenv('SUBJECTS_DIR',[bids_dir,'/derivatives/freesurfer']) fs_sub_dir = [bids_dir,'/derivatives/freesurfer/',subname]; surf_L = read_surf([fs_sub_dir,'/surf/lh.white']); n_nodes_L = length(surf_L); %check for which hemispheres label exists try lab_L = read_label(subname, ['lh.',labname]); use_L = 1; catch use_L = 0; end try lab_R = read_label(subname, ['rh.',labname]); use_R = 1; catch use_R = 0; end % determine how to create lab_M and do it if use_L && use_R lab_R(:,1) = lab_R(:,1) + n_nodes_L; lab_R(:,2) = lab_R(:,2) + x_shift; lab_M = [lab_L;lab_R]; elseif use_L && ~use_R lab_M = lab_L; elseif ~use_L && use_R lab_M = lab_R; lab_M(:,1) = lab_R(:,1) + n_nodes_L; lab_M(:,2) = lab_R(:,2) + x_shift; end %first two lines standard for FS label files line_1 = ['#!ascii label , from subject ',subname,' vox2ras=TkReg coords=white']; line_2 = num2str(length(lab_M)); %create file, write first two lines fname_M = [fs_sub_dir,'/label/mh.',labname,'.label']; if exist(fname_M) delete(fname_M) end fid = fopen(fname_M,'w'); fprintf(fid,'%s\n%s\n', line_1, line_2); fclose(fid); %write the tab delimited data dlmwrite(fname_M,lab_M,'-append','delimiter','\t','precision','%10.5f','newline','unix'); end

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Re: [Freesurfer] pcc.mgh file missing
by jahanvi patel 06 Jun '18

06 Jun '18

External Email - Use Caution Hello, thank you, we are using FS 5.3 virtual box, is there a version of 6.0 for the virtual box too? About the correlation, we meant to obtain the r-value (pearson correlation coef) from each significant cluster we got after running Monte Carlo simulation. So we didn't want to correlate only one cluster because we had correlate the whole brain thickness with the scores first, and we got the results from freesurfer, but it shows only the p-value, there was no r-value shown in the files. Hope it is correct to do in this way? Best, Jahanvi > Message: 2 > Date: Tue, 5 Jun 2018 12:55:23 -0400 > From: Douglas Greve <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] pcc.mgh file missing > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <4a311f78-3567-8817-f500-8bac737fa1af(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > Which version of FS are you using? I don't think it was in 5.3, so you > might have to use 6.0 version of mri_glmfit. Also, before you compute > and report the mean correlation inside of a significant cluster, you > might want to read this paper: > Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, > and Social Cognition > https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web& > cd=2&cad=rja&uact=8&ved=0ahUKEwj6wuqb_rzbAhVnslQKHa4tAAkQFggzMAE& > url=https%3A%2F%2Fwww.edvul.com%2Fpdf%2FVulHarrisWinkielmanPashler- > PPS-2009.pdf&usg=AOvVaw0C6XKQkj4hypGKRIaZFLc0 On 6/5/18 10:24 AM, jahanvi patel wrote: > > > Hello together, > > We used the following command to perform correlation analysis. But we > didn't obtain the "pcc.mgh" file which we want to extract the > correlation coefficient?from the significant cluster. > > Is there a command or way to generate the pcc.mgh file? > > Thank you in advance > > > > mri_glmfit \ > --glmdir GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2 \ > --y lh.testretest_only_TP2.thickness-pc1.stack.fwhm15.mgh \ > --label lh.testretest.fsaverage.cortex.label \ > --fsgd GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/TP1_TP2.fsgd \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/main.mtx \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_age.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_CesD_score.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_STATI_state.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_STATI_trait.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_total_medi_min.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_FFMQ_f1.mtx > \ > --C > GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_FFMQ_f2.mtx > \ > --surf fsaverage lh > > > Best, > Jahanvi > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Correction for multiple comparisons
by Yann Quidé 06 Jun '18

06 Jun '18

External Email - Use Caution Dear all, Using Freesurfer 5.3, I would like to limit my whole-brain analyses to a mask I already defined (ie, small volume correction-like analysis). To correct for multiple comparisons, I want to use the mri_glmfit-sim option. As I am looking within my own mask, I understand I need to run my own Monte-Carlo simulation. Would 10,000 permutations be sufficient? Also, I am a bit confused on what is best practice when setting the cluster forming threshold. Should I use the mc-z=3 (that is p=0.001) or mc-z=1.3 (that is p=0.05)? Here is an exemple of what I’m doing so far: mri_glmfit-sim \ --glmdir $STATS_DIR/lh.my_analysis.glmdir \ --sim mc-z 10000 3 mc-z.abs.3 \ --sim-sign abs Thanks for your time. Yann

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5th order polynomial
by Piero Chiacchiaretta 06 Jun '18

06 Jun '18

External Email - Use Caution Hi list, FS-FAST guidelines reports this example for seed-based FC analayis: mkanalysis-sess -analysis fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR <TR> You suggest a 5th order polynomial. Thus, I wonder to know which is the rationale to use this option and which is the advatage to use it then defaut option (1st or 2nd order). Thanks

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creating a mask for the thalamus parcellations
by Erik O'Hanlon 06 Jun '18

06 Jun '18

External Email - Use Caution Dear FS Experts, Is it possible to use the labels found in the FreesurferColourLUT.txt for the Thalamus parcellations (8001-8014) using the mri_extract_label command? If so, what is the correct input file to use ? mri_extract_label <input file????> 8001 L_Ant_thalamus.mgz Thanks Cheers Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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ERROR: mpr2mni305 failed
by Fernanda Hansen P. de Moraes 06 Jun '18

06 Jun '18

External Email - Use Caution Dear FreeSurfer experts, I am having some trouble to understand this error that showed up in some subjects that my group is processing. The recon-all log shows that message: *ERROR: mpr2mni305 failed, see transforms/talairach_avi.log * All talairach_avi.log shows the same error message: *imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 3335' failed! status=254 ERROR: mpr2mni305 execution aborted * I believe it happened the same in this thread: *https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37685.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37685.html>* but it seems that here the solution is to use .nii images. We are already doing this. Do you have any tip on what to do to solve it? Thank you very much in advance, Fernanda Hansen P. de Moraes -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

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Resampling cerebellum atlas to fmriprep outcome
by zuxfoucault Wong 06 Jun '18

06 Jun '18

External Email - Use Caution Hi Freesurfer experts, I am trying to resample the cerebellum atlas Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz to fmriprep output volume ${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz. I was wondering if the following 3 procedures are equivalent (if not what’s the difference?)? 1. mri_vol2vol --mov ${FREESURFER_HOME}/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --s ${sub} --targ ${project_path}/fmriprep/${sub}/func/${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz --o ${output_file_path}/Buckner2011_17Networks_MNI152NLin2009cAsym_brainmask.nii.gz --nearest 2. mri_vol2vol --mov ${project_path}/fmriprep/${sub}/func/${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz --s ${sub} --targ ${FREESURFER_HOME}/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --o ${output_file_path}/Buckner2011_17Networks_MNI152NLin2009cAsym_brainmask.nii.gz --nearest --inv 3. mri_vol2vol --mov ${FREESURFER_HOME}/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --s ${sub} --reg register.dat --o ${output_file_path}/Buckner2011_17Networks_MNI152NLin2009cAsym_brainmask.nii.gz --nearest where register.dat was generated by the following: bbregister --s ${sub} --mov ${FREESURFER_HOME}/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --int ${project_path}/fmriprep/${sub}/func/${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz --init-coreg --reg register.dat --t2 Thank you for your time! Regards, Foucault

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ROI extraction using functional masks
by Yann Quidé 06 Jun '18

06 Jun '18

Dear FS experts, I am trying to extract values for cortical thickness, surface area and volumes, from different functional ROIs. These cortical ROIs have been defined using SPM tools, and are in .nii format. My scans have been processed using FS v5.3. Although the conversion seems to go well, the “end product” does not really look good, some of the extracted ROI for some subjects are empty. Does anyone have a clue of why? Here is what I have done: 1) transform .nii file to .mgz file $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/L_ROI.mgz $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/R_ROI.mgz 2) to make sure our masks from SPM will match fsaverage templates, I did tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/L_ROI.mgz -fthresh 0.5 tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/R_ROI.mgz -fthresh 0.5 It was fine. 3) I created a .dat file containing the registration matrix from avg152T1 onto fsaverage cd $SUBJECTS_DIR/fsaverage/surf spmregister --s fsaverage --mov $MASKS_DIR/avg152T1.nii --reg $REG_DIR/avg152T1_to_fsaverage.dat 4) Visualisation of the registration tkregister2 --mov $MASKS_DIR/avg152T1.nii --targ $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg $REG_DIR/avg152T1_to_fsaverage.dat --surf orig The registration was bad, so… I manually relocate the TAL template onto the fsaverage template and saved a new avg152T1_to_fsaverage.dat file called avg152T1_to_fsaverage_edited.dat. This file is used for the next steps. 5) Visualisation of the registration of our mask onto fsaverage T1 cd $SUBJECTS_DIR/fsaverage/surf tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/L_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/R_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white Up to this sep, everything looks good. 6) Transformation of the ROI mask to surface and thickness mri_vol2surf --src $MASKS_DIR/L_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi lh --o $MASKS_DIR/L_ROI.mgh mri_vol2surf --src $MASKS_DIR/R_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi rh --o $MASKS_DIR/R_ROI.mgh mri_cor2label --i $MASKS_DIR/L_ROI.mgh --surf fsaverage lh --id 1 --l $MASKS_DIR/L_ROI.label mri_cor2label --i $MASKS_DIR/R_ROI.mgh --surf fsaverage rh --id 1 --l $MASKS_DIR/R_ROI.label 7) Extraction of the ROI surface and thickness for analyses mris_anatomical_stats -l $MASKS_DIR/L_ROI.label -f $OUT_DIR/results_L_ROI_SubjID SubjID lh mris_anatomical_stats -l $MASKS_DIR/R_ROI.label -f $OUT_DIR/results_R_ROI_SubjID SubjID rh Thanks to anyone who will be able to help me with that! Yann

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slice timing correction with mulit-band
by Xu, Yaoda 06 Jun '18

06 Jun '18

Dear all, I am trying to do slicing timing correcting with Siemens’s 3T Prisma data at acceleration 3. I am told that I can use “-ngroups” when running "preproc-sess”. How do I use the “-ngroups” flag? Should I do “-ngroups 3”? Would fs-fast automatically compute the slice timing file and apply it accordingly? I have the actual slice timing file. I tried to use "-sdf slicedelayfile”, but it does not seem to be a recognized flag. It appears that fs-fast does slice timing correction after motion correction. If the volume is going to be resliced after motion correction, thus each slice will no longer have its original timing, shouldn’t slice timing correction be done before motion correction? Is there a way in fs-fast to run slice timing correction before motion correction? I guess instead of running “preproc-sess”, I could first run “sts-sess” and then “mc-sess”? Any suggestions would be greatly appreciated. Thank you! - Yaoda Xu

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selxavg3-sess /tmp dir out of space
by Jiahe Zhang 06 Jun '18

06 Jun '18

External Email - Use Caution Dear Freesurfer experts, While running selxavg3-sess on a large functional scan (7 Tesla, 768 time points), I got these errors gzip: stdout: No space left on device ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected 3257077248 It sounds like there wasn't enough space on /tmp for an intermediate file to be written. Is there any way I can override the default so the intermediate file gets written to a location that does have enough storage space? Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649

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