Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

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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Recon-all exited with errors
by Hanna Vasilevskaya 05 Jun '18

05 Jun '18

External Email - Use Caution Good afternoon all, I am new to Freesurfer (using version 6.0) and trying to run recon-all on multiple subjects. Every subject exited with errors. Specifically, a number of surfaces are missing from the "surf" subject's folder (only 30 files instead of 80). Would you happen to know how to fix it? Taken from the recon-all status log: #@# Smooth2 lh Mon Jun 4 16:26:27 DST 2018 #@# Smooth2 rh Mon Jun 4 16:26:31 DST 2018 #@# Inflation2 lh Mon Jun 4 16:26:35 DST 2018 #@# Inflation2 rh Mon Jun 4 16:27:02 DST 2018 #@# Curv .H and .K lh Mon Jun 4 16:27:29 DST 2018 Linux Laptop 4.4.0-43-Microsoft #1-Microsoft Wed Dec 31 14:42:53 PST 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1062_2 exited with ERRORS at Mon Jun 4 16:27:32 DST 2018 I have also attached a recon-all.log for your convenience. Thank you, Anna

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pcc.mgh file missing
by jahanvi patel 05 Jun '18

05 Jun '18

External Email - Use Caution 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

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PROBLEM DOWLOAD LINUX VERSION
by Davide Momi 05 Jun '18

05 Jun '18

External Email - Use Caution Dear Freesurfer expert, I'm not able to download the Linux version of Freesurfer by your website. For some reason it doesn't open the page. Could you please send me an another link or the version? Thanks in advance Davide

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Freesurfer June 2018