Freesurfer

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18 participants
30131 discussions

Periaqueductal gray (PAG) volume
by Alan Francis 27 Aug '21

27 Aug '21

External Email - Use Caution Hi Doug et al, I know that this question may have been asked before, but does the latest version of FS segment/ parcellate the volume of the periaqueductal gray (PAG? Thank you, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

2 1

Error in the final step of the longitudinal pipeline
by Robin Kämpe 27 Aug '21

27 Aug '21

External Email - Use Caution Hi Freesurfer Community and developers! First time poster here! I am running freesurfer version 7.1: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b We have 2 sessions of MRI-data from each participant, separated with about 1-2 months. We don't want to compare Freesurfer parcels, but we use Freesurfer to get good parcelations which we later use as masks in the fMRI-analysis. Since we do have two T1w images per subject, I thought to use the longitudinal pipeline to get more stable results as per: https://secure-web.cisco.com/1C82j67WZziPcBPH-8KbA5rOwb-isVXVvr87pgVrBwGd2M… "...a longitudinal design can significantly reduce the confounding effect of inter-individual morphological variability by using each subject as his or her own control" I know this gude is for FS <= 6.0 but I could not find any specfic instructions for FS 7.1, which meant that I used an old script from when I did this sucessfully in the past with FS6.0. The pipeline is basically: TP1=/path_to_timepoint1/1_sT1W_3D.nii TP2=/path_to_timepoint2/2_sT1W_3D.nii #Run each TP seperatley #TP1 recon-all -all -s TP1 -i $TP1 -sd $subject_dir -parallel & PIDT1=$! #TP2 recon-all -all -s TP2 -i $TP2 -sd $subject_dir -parallel & PIDT2=$! wait $PIDT1 wait $PIDT2 #Wait until TP 1-2 are done and create template recon-all -base ${subject}_Template -tp TP1 -tp TP2 -all -sd $subject_dir -parallel These two steps generates, in each subject-dir, the directories TP1, TP2 and subX_Template. The recon-all.log files under scripts say all these processes finished without errors (TP1+TP2+Template), which is really good. Then comes the final step: #TP1 recon-all -long TP1 ${subject}_Template -all -sd $subject_dir & PIDT1=$! #TP2 recon-all -long TP2 ${subject}_Template -all -sd $subject_dir & PIDT2=$! wait $PIDT1 wait $PIDT2 Which generates the dirs TP1.long.subX_Template TP2.long.subX_Template So far so good. But these two finished WITH ERRORS. When searching the recon-all.log files under TP1.long.subX_Template/scripts and TP2.long.subX_Template/scripts it is the same error for both TPs: Half way through the recon-all.log file: SUBJECTS_DIR /home/robka/BG_FS_temp/sub102 FREESURFER_HOME /usr/local/freesurfer Loading source label. error: Invalid argument error: mri_label2label: could not open label file /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label\00 ERROR reading /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label Command exited with non-zero status 1 @#@FSTIME 2021:08:20:16:47:37 mri_label2label N 12 e 0.00 S 0.00 U 0.00 P 100% M 5672 F 0 R 202 W 0 c 0 w 1 I 0 O 0 L 12 4 44 @#@FSLOADPOST 2021:08:20:16:47:37 mri_label2label N 12 12 4 44 Linux maul 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:21:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TP1.long.sub102_Template exited with ERRORS at fre 20 aug 2021 16:47:37 CEST And at the very bottom: SUBJECTS_DIR /home/robka/BG_FS_temp/sub102 FREESURFER_HOME /usr/local/freesurfer Loading source label. error: Invalid argument error: mri_label2label: could not open label file /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label\00 ERROR reading /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label Command exited with non-zero status 1 @#@FSTIME 2021:08:20:19:47:29 mri_label2label N 12 e 0.00 S 0.00 U 0.00 P 100% M 5680 F 0 R 203 W 0 c 0 w 1 I 0 O 0 L 93 2 97 @#@FSLOADPOST 2021:08:20:19:47:29 mri_label2label N 12 93 2 97 Linux maul 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:21:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TP1.long.sub102_Template exited with ERRORS at fre 20 aug 2021 19:47:29 CEST To report a problem, see http://secure-web.cisco.com/15tLPkzOOjinGp7ztirAETf15D3Q8ETWtMs3R1sqMS9rpNU… Output of TP2s recon-all.error log (sampe for TP1): ------------------------------ SUBJECT TP2.long.sub102_Template DATE fre 20 aug 2021 19:47:02 CEST USER robka HOST maul PROCESSOR x86_64 OS Linux Linux maul 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:21:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b) /usr/local/freesurfer/bin/recon-all PWD /home/robka/BG_FS_temp/sub102/TP2.long.sub102_Template/label CMD mri_label2label --srcsubject fsaverage --srclabel /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label --trgsubject TP2.long.sub102_Template --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface Output of unknown-args.txt (same for both TPs): -long TP1 sub102_Template -all -sd /home/robka/BG_FS_temp/sub102 Only warning I can see is that TP1 and TP2 has different resolutions. Both have exactly the same matrix dims but differ a little in mm resolution: 1x1x1 mm vs 0.9999x0.99999x1 mm. I.e. minor difference. I also ran the script with the two commands using -parallel: #TP1 recon-all -long TP1 ${subject}_Template -all -sd $subject_dir -parallel & PIDT1=$! #TP2 recon-all -long TP2 ${subject}_Template -all -sd $subject_dir -parallel & PIDT2=$! This also failed but only with one error that I could not figure out. Any ideas of how to find the problem here? =) The two images don't have apparent issues: [cid:ceb92c6f-2d9d-484a-8221-71760fdcca23] Thanks! Robin Kämpe Research engineer CSAN, Center for Social and Affective Neuroscience Department of Clinical and Experimental Medicine, IKE Phone: +4673-8005561

2 1

Run script
by Haley Park 27 Aug '21

27 Aug '21

External Email - Use Caution Hello, I got a response to a question I asked earlier to run the following script: mri_convert lh.Yeo2011_17NetworksConfidence_N1000.mgz --reorder 2 1 3 lh.Yeo2011_17NetworksConfidence_N1000.reordered.mgz How would I run this? I tried running freesurfer in terminal and typing the above in but got an error, ":could not open file" Maybe I can compile an .sh file and run it but I'm not sure what to write in it Thank you for the help! Haley

2 1

please remove me from this mailing list
by Michele Lee Fullilove 27 Aug '21

27 Aug '21

External Email - Use Caution Thank you very much!

1 0

Re: [Freesurfer] Password
by fsbuild 26 Aug '21

26 Aug '21

External Email - Use Caution Sending the info to your email shortly … - R. On Aug 26, 2021, at 18:19, mahmood mohammadisadr <mahmoodasdfzjy(a)gmail.com> wrote:        External Email - Use Caution        I am attempting to use FreeSurfer on Windows via VirtualBox following this tutorial: https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZ… I ask for the password that is required to log in Ubuntu when using the /Ubuntu_710_clone-disk1.vdi /disk image provided in the tutorial?Thank you very much_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Password
by mahmood mohammadisadr 26 Aug '21

26 Aug '21

External Email - Use Caution I am attempting to use FreeSurfer on Windows via VirtualBox following this tutorial: https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZCnfUSNQq80weZWA… < https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZCnfUSNQq80weZWA… >Can I ask for the password that is required to log in Ubuntu when using the /Ubuntu_710_clone-disk1.vdi /disk image provided in the tutorial? Thank you very much

1 0

recon-all ends in 4 seconds without error!!
by vin rasa 25 Aug '21

25 Aug '21

External Email - Use Caution Dear Freesurfer Experts, Greetings! I am trying to run freesurfer on Synthetic T1 data (see in snapshot: *''Simulated T1 image', last sentence in the snapshot*') from Brainweb ( https://secure-web.cisco.com/1M8y2jTKqcaZLr3pWIX9ajloxBQ00by9kyM5AmTJvStE6d…) . After i run recon-all, freesurfer ends without any error in 4 seconds. ###### >recon-all -i $data_dir/$i/mT1t.nii.gz -sd $rdir/results/freesurfer -s $i Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /results/freesurfer Actual FREESURFER_HOME /FreeSurfer/freesurfer-linux-centos8_x86_64-7.1.1 mri_convert /data/subject54_t1w_p4/mT1t.nii.gz /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz mri_convert /data/subject54_t1w_p4/mT1t.nii.gz /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz reading from /data/subject54_t1w_p4/mT1t.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz... @#@FSTIME 2021:08:25:16:50:08 mri_convert N 2 e 3.56 S 0.08 U 2.84 P 82% M 53580 F 0 R 12154 W 0 c 1228 w 1454 I 83632 O 83736 L 3.30 2.59 1.96 @#@FSLOADPOST 2021:08:25:16:50:12 mri_convert N 2 3.27 2.59 1.97 /results/freesurfer/subject54_t1w_p4/mri/transforms /results/freesurfer/subject54_t1w_p4 /results/freesurfer/subject54_t1w_p4 Started at Mi 25. Aug 16:50:07 CEST 2021 Ended at Mi 25. Aug 16:50:13 CEST 2021 #@#%# recon-all-run-time-hours 0.002 recon-all -s subject54_t1w_p4 finished without error at Mi 25. Aug 16:50:13 CEST 2021 done ###### Please help! Thanks! [image: image.png]

2 2

matlab fatal error macOS query
by Szulia Agata 24 Aug '21

24 Aug '21

External Email - Use Caution Hi, I see that others have posted on this but not necessarily the fix. I'm happy to test anything out that I can with it. I'm using MacOS running 11.5.1, freesurfer 7.2.0 with added Matlab 2014B files. Every time I try to run a recon-all'd scan through matlab, I end up gettin a MATLAB fatal error. Any subsequent run also failed. Crash dumps and script is enclosed if they can be of any help. I welcome any suggestions that you may have - thank you for your help with this. Kind regards, Agata Klauzula poufno?ci. Ta wiadomo?? pocztowa i wszelkie za??czone do niej pliki s? poufne i podlegaj? ochronie prawnej. Je?li nie jeste? jej prawid?owym adresatem, jakiekolwiek wykorzystanie w tym zapoznanie si? z tre?ci? przes?anych informacji, jej ujawnienie, reprodukcja, dystrybucja lub inne rozpowszechnienie, s? ?ci?le zabronione. Je?li otrzyma?/a Pan/i niniejszy przekaz wskutek b??du, prosz? o niezw?ocznie powiadomienie nadawcy i usuni?cie otrzymanych informacji. Kontakt: Uniwersytet Medyczny w ?odzi, 90-419 ??d?, Al. Ko?ciuszki 4, Rektorat - Centrala, Tel. 42 272 59 66 umed.lodz.pl Confidentiality Notice - This e-mail is confidential, may be legally privileged. If you are not the intended recipient, you may not use, disclosure, distribute, copy, print or rely on this e-mail. If you received this e-mail in error, please notify the sender and delete the material from any computer.Contact:Medical University of Lodz, 90-419 Lodz, POLAND, 4 Kosciuszki Avenue, Rector's Office, phone 0048 42 272 59 66 umed.lodz.pl

1 0

Re: [Freesurfer] Password request for the Windows VM Install
by fsbuild 24 Aug '21

24 Aug '21

External Email - Use Caution Sending the password to your private email shortly. - R. On Aug 24, 2021, at 11:11, Philémon Roussel <philemon.roussel(a)inserm.fr> wrote:        External Email - Use Caution        Dear FreeSurfer team,I am attempting to use FreeSurfer on Windows via VirtualBox following this tutorial: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1vYFHOaHbz-1NQJncypAbnT3tEhuBgp9s66RiL… I ask for the password that is required to log in Ubuntu when using the Ubuntu_710_clone-disk1.vdi disk image provided in the tutorial?Thank you very much,Philémon Roussel_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Password request for the Windows VM Install
by Philémon Roussel 24 Aug '21

24 Aug '21

External Email - Use Caution Dear FreeSurfer team, I am attempting to use FreeSurfer on Windows via VirtualBox following this tutorial: https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZCnfUSNQq80weZWA… <https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZCnfUSNQq80weZWA…> Can I ask for the password that is required to log in Ubuntu when using the /Ubuntu_710_clone-disk1.vdi /disk image provided in the tutorial? Thank you very much, Philémon Roussel //

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