Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] Freesurfer passowrd
by fsbuild 31 May '22

31 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 31, 2022, at 05:38, nairulislam(a)tutamail.com wrote:        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._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Virtual Box Password
by fsbuild 31 May '22

31 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 31, 2022, at 00:56, Wojciech Górecki <goorec83(a)gmail.com> wrote:        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 RegardsW. Górecki_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_surf2surf error: No such file or directory (but file exists)
by Salma Salhi 31 May '22

31 May '22

External Email - Use Caution Hello FreeSurfer Developers, I am trying to run the mri_surf2surf command as shown in this MRtrix tutorial on page 35 (https://secure-web.cisco.com/1IRfOd9DbtoZ73ePUy1kNxDjehQaayodvb_Pq3LttY1M2Y…) in order to map the annotation files of the HCP MMP 1.0 atlas. I keep running into a “No such file or directory” error when the code tries to read the “lh.orig” file, but the file is clearly in the required directory. Below is the output of my code: (base) salmasalhi@SalmasMacbookAir 100307_F26-30 % mri_surf2surf --srcsubject fsaverage --trgsubject subject_100307 --hemi lh --sval-annot $SUBJECTS_DIR/fsaverage/label/lh.glasser.annot --tval $SUBJECTS_DIR/subject_100307/label/lh.hcpmmp1.annot Setting mapmethod to nnf 7.2.0 setenv SUBJECTS_DIR /Users/salmasalhi/my_code/HumanBrain_v2/reconall cd /Users/salmasalhi/my_code/HumanBrain_v2/100307_F26-30 mri_surf2surf --srcsubject fsaverage --trgsubject subject_100307 --hemi lh --sval-annot /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/label/lh.glasser.annot --tval /Users/salmasalhi/my_code/HumanBrain_v2/reconall/subject_100307/label/lh.hcpmmp1.annot sysname Darwin hostname SalmasMacbookAir.local machine x86_64 user salmasalhi srcsubject = fsaverage srcval = (null) srctype = trgsubject = subject_100307 trgval = /Users/salmasalhi/my_code/HumanBrain_v2/reconall/subject_100307/label/lh.hcpmmp1.annot trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/surf/lh.sphere.reg Loading source data Reading surface file /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/surf/lh.orig error: No such file or directory error: could not read annot file /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/label/lh.glasser.annot If I cd into the surf directory and check the files, this is the output: (base) salmasalhi@SalmasMacbookAir surf % ls lh.area lh.sphere.reg rh.inflated_avg lh.avg_curv lh.sphere.reg.avg rh.inflated_pre lh.avg_sulc lh.sulc rh.orig lh.avg_thickness lh.thickness rh.orig.avg.area.mgh lh.cortex.patch.3d lh.white rh.orig_avg lh.cortex.patch.flat lh.white.avg.area.mgh rh.pial lh.curv lh.white_avg rh.pial.avg.area.mgh lh.fsaverage_sym.sphere.reg lh.white_avg.H rh.pial_avg lh.inflated lh.white_avg.K rh.pial_semi_inflated lh.inflated.H mris_preproc.surface.lh.log rh.smoothwm lh.inflated.K mris_preproc.surface.rh.log rh.sphere lh.inflated_avg rh.area rh.sphere.reg lh.inflated_pre rh.avg_curv rh.sphere.reg.avg lh.orig rh.avg_sulc rh.sulc lh.orig.avg.area.mgh rh.avg_thickness rh.thickness lh.orig_avg rh.cortex.patch.3d rh.white lh.pial rh.cortex.patch.flat rh.white.avg.area.mgh lh.pial.avg.area.mgh rh.curv rh.white_avg lh.pial_avg rh.fsaverage_sym.sphere.reg rh.white_avg.H lh.pial_semi_inflated rh.inflated rh.white_avg.K lh.smoothwm rh.inflated.H lh.sphere rh.inflated.K (base) salmasalhi@SalmasMacbookAir surf % pwd /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/surf The “lh.orig” file is clearly in the right place. I tried to check the format of the file by typing mri_info lh.orig but the output was “ERROR: could not determine type of lh.orig”. Below are more details about my setup: 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: macOS Monterey 12.3.1 (M1 chip) Thank you very much for your help, I greatly appreciate it. Salma Salhi

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Password for 7.2.0 VM box virtual machine
by niels.foit＠gmx.de 31 May '22

31 May '22

Dear all I require the password to unzip the above named archive. Since at least 10 people have asked this in the past hours, You might wanna reconsider the necessity of a password. Cheers niels External Email - Use Caution

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load PET.reg.lta freesurfer corregistration file in 3D slicer 4.11
by Gonzalo Rojas Costa 31 May '22

31 May '22

External Email - Use Caution Hi: I coregistered a PET file to a freesurfer data using mri_coreg command. I imported the freesurfer-generated data to 3D Slicer. How can I import the PET.reg.lta file in 3D Slicer? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1e17f0KeEx1uku6w91Y5lIGB5srmBKu9TQ3WRtpCV4CmGc… https://secure-web.cisco.com/1cs2LDGSTCr6GnV5Rq-K7aFHHjdJcgniT_IPajEDX9qitb… https://secure-web.cisco.com/1c3Ub-NigVjcMlUsRtymIbNmw_2reyZp6e5kdQWcxIjWpR… http://secure-web.cisco.com/1ptxxoRnoGXKniE15hzEh72mpWXmTkdcqzTdZL3sLc-LQjZ… https://secure-web.cisco.com/1V3s1u1ecjyempv27N_dkVM0NX2R9IvzTwxF-bXTbBaHXD…

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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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