Freesurfer

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30132 discussions

E-TIV and Linux version: Some quick questions
by Jeff Crawford 07 Jun '18

07 Jun '18

External Email - Use Caution Dear Freesurfer Experts, I have two questions that I hope are easy to answer. 1. Would the calculation for E-TIV change if I edited the pial and reran recon-all as in this tutorial below? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview My understanding is that E-TIV should not change after minor edits to the pial segmentation, because the transform happens before these edits even happen. We start the at autorecon2-pial for the pial correction, which is after the Talairach transform computation. 2. I have two different windows computers with two VMware workstations running what I thought were the same versions of CentOS. They are both CentOS 6, but one is 6.5 and the other is 6.9. If both VMware workstations run the exact same versions of Freesurfer 6 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c), is it a problem if the CentOS versions are slightly different? I know the FS wiki says "it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS.", but would there be enough of a difference between CentOS 6.5 and 6.9 to cause major discrepancies in Freesurfer T1 processing? Thanks so much, Jeff

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poor anterior lobe surfaces
by Meaghan Perdue 07 Jun '18

07 Jun '18

External Email - Use Caution Hello Freesurfer experts, I have come across a problem with several subjects in which the pial surface fails to adequately capture the anterior temporal lobes. This occurs despite accurate brainmask and wm volumes. I have included a screen shot below, in this case, the wm surface is also affected, but this is not always the case. This is pediatric data that was acquired on a 1.5T scanner and processed in Freesurfer v 5.3. The following expert options have been employed to try to improve surface rendering: mris_make_surfaces -max_gray_at_csf_border 80 -max_csf 30 -min_gray_at_csf_border 35 Please let me know how I can solve this issue. As a second question, I've heard that segmentation and surface rendering is improved with v 6.0, and I'm wondering if subjects that have been initially run through v. 5.3 and had manual edits made can then have autorecon run through v 6.0 for improvement of surfaces? Please let me know if this would be a reliable/recommended approach to improving surfaces. Thank you, Meaghan Perdue -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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Matrix ill-conditioned
by Guillaume Bellanger 06 Jun '18

06 Jun '18

External Email - Use Caution Hello Freesurfer people, I am having an issue with my matrix using QDEC (ERROR: matrix is ill-conditioned or badly scaled, condno = 10880.8), I have 2 discrete variables (Sex, Cognition) and I want to regress against 2 continuous variable (Age, Education). My outcome: is there a relation between cortical thickness and Cognition (yes/no), accounting for Sex, Age and Education. I attached my FSGD file and matrix. Thanks a lot. Guillaume

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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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