Freesurfer May 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

mris_flatten distortions
by Alberto Pisoni 31 May '22

31 May '22

External Email - Use Caution Hi all, I am trying to flatten a whole hemisphere, and i created the cut patch following the tutorials. see the result here. https://secure-web.cisco.com/1xjf27LYk5Ie25CTk51Q3cPiwVe-uMjYXB4V0ViZqlanRh… Then I run the command mris_flatten <input patch> <output patch> from the surf dir and it works, but when I visualize the patch it is distorted, like if I did not cut the inflated surface. https://secure-web.cisco.com/128ktBKDV9wlBus-Bu1XsphHIMQpHtnuoTRQ6748JzsrgK… What am I missing? The Freesurfer version is 7.2.0 (although I also tried with 6.0) and the system is a OS 11.6.1 BigSur Macbook Pro with M1 chip. Thanks Alberto ------------------------------------------------------ Alberto Pisoni, PhD Associate Professor Department of Psychology University of Milano-Bicocca Building U6 ~ Room 3139 piazza dell'Ateneo Nuovo 1 20126, Milano, Italy

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(no subject)
by Alberto Pisoni 31 May '22

31 May '22

External Email - Use Caution Hi all, I am trying to flatten a whole hemisphere, and i created the cut patch following the tutorials. see the result here. https://secure-web.cisco.com/1yFIFkAQ7JVCxQ9XtdXA16rgidANEj5tq1VECDMPQ70qTM… Then I run the command mris_flatten <input patch> <output patch> from the surf dir and it works, but when I visualize the patch it is distorted, like if I did not cut the inflated surface. https://secure-web.cisco.com/1tWLYU7SKnF0l2rwCeoMbCKMijBrdYwXtLipGGQBhN40aO… What am I missing? The Freesurfer version is 7.2.0 (although I also tried with 6.0) and the system is a OS 11.6.1 BigSur Macbook Pro with M1 chip. Thanks Alberto

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Freesurfer version 6.0 and 7.2
by Lexuri Fernández de Gamarra Oca 31 May '22

31 May '22

External Email - Use Caution Good afternoon, I have both versions (i.e., version 6.0 and 7.2) downloaded and for the analyses to run only with the newer version I was typing the following command: export FREESURFER_HOME=/usr/local/freesurfer_7.2.0 export FSFAST_HOME=/usr/local/freesurfer_7.2.0/fsfast export MNI_DIR=/usr/local/freesurfer_7.2.0/mni I have compared my volumetrics and thickness analyses with a colleague who only has version 7.2 and they are totally different. Does it have something to do with the versions? Does it have something to do with the fact that she is using Mac and I am using Linux? Thanks in advance, Lexuri -- Lexuri Fernández de Gamarra Oca Osasun Zientzien Fakultatea Deustuko Unibertsitatea Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3212) <%2B34%20944139000>

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Error with mri_ca_register
by Brett Green 31 May '22

31 May '22

External Email - Use Caution Hello, My recent attempt to run recon-all on one of my MRIs was unsuccessful. I ran the command as: recon-all -subjid ${subject} -all -time -log logfile -nuintensitycor-3T -sd $SUBJECTS_DIR -parallel About 37 minutes into running, the process terminated with the following error: ERROR: mri_ca_register with non-zero status 9 This is my first time using FreeSurfer, so it's very possible that I've made a mistake. However, the issue may also be that atlas-based segmentation is not a good choice for my brain. I have a magnetically-adjusted VP shunt that produces an artifact 3.5 cm in diameter on the top of my right frontal lobe of which I anticipate would make registration with a normal brain difficult. Please let me know whether this sounds like an error in my input, in which I will be happy to produce more information, or whether I should seek an alternative solution for segmenting my brain from an MRI. Thank you!

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Overlapping label files and issue with --ldir in mris_label2annot
by Deck,Benjamin 31 May '22

31 May '22

External Email - Use Caution Hi there, Thanks for putting together FS, great software! I am having trouble running mris_label2annot Currently I have extracted individually estimated .mgh overlay files from Li 2019 et a., Performing group-level functional image analyses based on homologous functional regions mapped in individuals, software suite in matlab. These individual .mgh files are for every ROI from every one of Yeo 2011's 17 network parcellation scheme. I then take the .mgh files and convert them into label files with the following script. if [[ $# -lt 1 ]]; then cat <<USAGE $0 <inDir> <subjects> <SUBJECTS_DIR> inDir - input directory --path to matchrate folder from li 2019 subjects - list of subjects to run SUBJECTS_DIR - Freesurfer SUBJECTS_DIR USAGE exit 1 fi # echo inputs echo "input 1 is ${1}" echo "input 2 is ${2}" echo "input 3 is ${3}" # parse inputs inDir=$1 subjects=$2 subDir=$3 networks='Net_10 Net_11 Net_12 Net_13 Net_14 Net_15 Net_16 Net_17 Net_18 Net_19 Net_2 Net_3 Net_4 Net_5 Net_6 Net_7 Net_8 Net_9' export SUBJECTS_DIR=${subDir} # gather the freesurfer subjects directory # loop over subjects for sub in ${subjects}; do for net in ${networks}; do # extract networks masks masks=$(find ${inDir}/Indi_Matched_ROIs/${net}/${sub} -iname '*Net_*.mgh') # extract confidence masks echo echo -------------------------------------------- echo -- START: creating .cor files ${sub} -- echo -------------------------------------------- echo # loop over masks for mask in ${masks}; do netMaskName=$(basename ${mask} .mgh) # gather mask name by network number (Yeo 2011) hemi=$(echo ${mask} | grep -Eo '[lr]h') # designate the hemisphere # resample to native mri_surf2surf --srcsubject fsaverage4 \ --srcsurfval ${mask} \ --trgsubject ${sub} \ --trgsurfval ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${netMaskName}.mgh \ --hemi ${hemi} \ --cortex mri_vol2label --i ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${netMaskName}.mgh \ --id 1 \ --l ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${netMaskName}.label \ --surf ${sub} ${hemi} white echo echo -------------------------------------------- echo -- START: creating label files ${sub} -- echo -------------------------------------------- echo mri_label2label --srclabel ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${netMaskName}.label \ --s ${sub} \ --hemi ${hemi} \ --dilate 2 \ --trglabel ${subDir}/${sub}/label/${sub}_${netMaskName}_dil2.label \ --regmethod surface done done done After this script runs to completion, I then run mris_label2annot with the following command mris_label2annot --s sub-DAEK --hemi rh \ --ctab /mnt/c/Users/Ben/Documents/GitHub/parcellationPipeline/li2019_to_dti/yeo2011nodesLUT.txt \ --a yeo2011nodes \ --surf orig \ --maxstatwinner \ --l Net_10_ROIs_1_rh.label --l Net_11_ROIs_1_rh.label --l Net_12_ROIs_1_rh.label --l Net_12_ROIs_2_rh.label \ --l Net_13_ROIs_1_rh.label --l Net_13_ROIs_2_rh.label --l Net_13_ROIs_3_rh.label --l Net_13_ROIs_4_rh.label \ --l Net_14_ROIs_1_rh.label --l Net_14_ROIs_2_rh.label --l Net_14_ROIs_3_rh.label --l Net_14_ROIs_4_rh.label \ --l Net_14_ROIs_5_rh.label --l Net_15_ROIs_1_rh.label --l Net_16_ROIs_1_rh.label --l Net_16_ROIs_2_rh.label \ --l Net_16_ROIs_3_rh.label --l Net_17_ROIs_1_rh.label --l Net_17_ROIs_2_rh.label --l Net_17_ROIs_3_rh.label \ --l Net_17_ROIs_4_rh.label --l Net_18_ROIs_1_rh.label --l Net_18_ROIs_2_rh.label \ --l Net_18_ROIs_3_rh.label --l Net_18_ROIs_4_rh.label --l Net_19_ROIs_1_rh.label --l Net_2_ROIs_1_rh.label \ --l Net_2_ROIs_2_rh.label --l Net_3_ROIs_1_rh.label --l Net_3_ROIs_2_rh.label --l Net_3_ROIs_3_rh.label \ --l Net_4_ROIs_1_rh.label --l Net_5_ROIs_1_rh.label --l Net_5_ROIs_2_rh.label --l Net_6_ROIs_1_rh.label \ --l Net_6_ROIs_2_rh.label --l Net_6_ROIs_3_rh.label --l Net_7_ROIs_1_rh.label --l Net_7_ROIs_2_rh.label \ --l Net_8_ROIs_1_rh.label --l Net_8_ROIs_2_rh.label --l Net_8_ROIs_3_rh.label --l Net_8_ROIs_4_rh.label \ --l Net_8_ROIs_5_rh.label --l Net_8_ROIs_6_rh.label --l Net_9_ROIs_1_rh.label --l Net_9_ROIs_2_rh.label \ --l Net_9_ROIs_2_rh.label --l Net_9_ROIs_3_rh.label --l Net_9_ROIs_4_rh.label --l Net_9_ROIs_5_rh.label \ --l Net_9_ROIs_6_rh.label --l Net_7_ROIs_3_rh.label However, the label files are overlapping. Is there a way to fix this, perhaps with some thresholding scheme? Finally, I also noticed that the -ldir argument from mris_label2annot doesn't seem to be working. Here is my LUT: # #No. Label Name: R G B A # 0 Unknown 0 0 0 0 1 Net_2_ROIs_1_lh 25 5 25 0 2 Net_2_ROIs_1_rh 25 100 40 0 3 Net_2_ROIs_2_lh 70 130 180 0 4 Net_2_ROIs_2_rh 125 100 160 0 5 Net_3_ROIs_1_lh 196 58 250 0 6 Net_3_ROIs_1_rh 100 25 0 0 7 Net_3_ROIs_2_lh 120 70 50 0 8 Net_3_ROIs_2_rh 220 20 10 0 9 Net_3_ROIs_3_lh 220 20 100 0 10 Net_3_ROIs_3_rh 180 40 120 0 11 Net_4_ROIs_1_lh 122 186 220 0 12 Net_4_ROIs_1_rh 140 20 140 0 13 Net_5_ROIs_1_lh 12 48 255 0 14 Net_5_ROIs_1_rh 20 30 140 0 ............. Etc etc Thanks, Ben

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How to create white.deformed file in longitudinal pipeline
by 정범석 31 May '22

31 May '22

External Email - Use Caution Dear Freesurfer experts, I'm running GenericfMRIVolumeProcessingPipeline of HCP pipeline in longitudinal dataset(T1w and fMRI). After running longitudinal pipeline in freesurfer, I'd like to run script like below. bbregister --s ses-01 --mov Scout_gdc_undistorted2T1w_init.nii.gz --surf white.deformed --init-reg ./mri/transforms/eye.dat --bold --reg ./rfMRI_REST1_PA_fmap/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/EPItoT1w.dat --6 --o ./rfMRI_REST1_PA_fmap/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted2T1w.nii.gz However, "white.deformed" file in surf directory is not found in .long directory but in cross-section one. When I use "white.deformed" file in cross-section directory, an error message was occurred "  ERROR: number of vertices in ./surf/lh.thickness does not match surface (132608,133203)" How to create white.deformed file, appropriately, in the line of the longitudinal pipeline? Bumseok

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Request for password for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Arjun Singh 31 May '22

31 May '22

External Email - Use Caution Hello, Please provide me with the password for the virtual machine file for freesurfer (FS_7_2_0_Ubuntu_18_04_06.ova.7z) Thank you Regards, Arjun Singh

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pw for fs vm edition
by Niels Foit 31 May '22

31 May '22

External Email - Use Caution Hi guys, i require the unzip pw for fs vm on windows. Best niels

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Freesurfer passowrd
by nairulislam＠tutamail.com 31 May '22

31 May '22

External Email - Use Caution Hi there, I just downloaded the Freesurfer zip file that is meant to be used with the virtual box. I need the password of that zip file.

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Virtual Box Password
by Wojciech Górecki 31 May '22

31 May '22

External Email - Use Caution Hello I wanted to ask whether you can send me the pass code for VB image: FS_7_2_0_ubuntu_18_04_06.ova.7z Regards W. Górecki

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Freesurfer May 2022