Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

PCA
by stdp82＠virgilio.it 27 Aug '21

27 Aug '21

External Email - Use Caution Dear list, is possible to do a whole-brain, voxel-wise PCA analysis by FS-FAST? Thanks Stefano

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Isolate Function Error
by A.R. Sekar 27 Aug '21

27 Aug '21

External Email - Use Caution Hello Experts, Hope you are well! I am trying to extract ROIs from the aparc+aseg file after running recon all however, I am getting the following result for all my images: ciddrg@CIDDRGs-MacBook-Air C961060 % cd /Volumes/Akila/Cambridge/C961022 ciddrg@CIDDRGs-MacBook-Air C961022 % isolate_labels.csh --vol aparc+aseg.nii --outprefix aparc+aseg_labels --L $label 7 Input file: aparc+aseg.nii Output prefix: aparc+aseg_labels mri_convert aparc+aseg.nii aparc+aseg.nii.gz reading from aparc+aseg.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to aparc+aseg.nii.gz... Label of interest: 7 Number of voxels and volume for label 7 is = (0, 0.000000mm^3) mri_binarize --i aparc+aseg.nii.gz --match 7 --o aparc+aseg_labels_label7.mgz 7.1.1 cwd /Volumes/Akila/Cambridge/C961022 cmdline mri_binarize --i aparc+aseg.nii.gz --match 7 --o aparc+aseg_labels_label7.mgz sysname Darwin hostname CIDDRGs-MacBook-Air.local machine x86_64 user ciddrg input aparc+aseg.nii.gz frame 0 nErode3d 0 nErode2d 0 output aparc+aseg_labels_label7.mgz Binarizing based on matching values nMatch 1 0 7 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Count: -1 -1.000000 16777216 -0.000006 mri_binarize done ciddrg@CIDDRGs-MacBook-Air C961022 % Could you help me with where the error might be? I would really appreciate your help, thank you! Regards, Akila

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Error messages when trying to start Qdec
by inbal paran 27 Aug '21

27 Aug '21

External Email - Use Caution Dear FreeSurfer experts, I recently started to work with freesurfer and I am now trying to perform my analysis with Qdec. I tried to open it and *the following error message came up: * qdec: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory After a quick search, I* tried to solve it using*: sudo apt-get install libjpeg62 Next, I tried starting qdec again, *but received another error message *: "Tcl_Init error: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 /home/inbal/freesurfer/lib/tcl8.4 /home/inbal/lib/tcl8.4 /home/inbal/freesurfer/library /home/inbal/library /home/inbal/tcl8.4.6/library /home/tcl8.4.6/library /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly." How can I solve this? Kind regards, Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1OuQr7d_D0M3pPog2BDevo1f-1Hb2hjTzySqc-z7bj2Pk0p…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

2 1

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.*

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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

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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]

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