Freesurfer February 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
83 discussions

[TRACULA] how to setup with opposite phase-encoding
by Fahad Hannan 07 Feb '24

07 Feb '24

External Email - Use Caution Hi, I've been trying to use TRACULA on my data, trying to setup a configuration file but I am having some difficulty on how to incorporate my data. I have a DWI scan with 65 volumes (1 b0 image, 64 with b = 1000) I also have separate volumes for b0 pairs having opposite phase-encoding directions. I am not sure how to incorporate these into the configuration file. I can do it with using just the one b0 image, but I'd like to use the opposite phase-encoding as well. How would I go about this in the configuration file? Thanks, Fahad Hannan

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Calculation of MRI intensity
by ERNEST KISSI 07 Feb '24

07 Feb '24

External Email - Use Caution Hi Freesurfer Team, Please I want to calculate the mean intensity of a skullstripped MRI image. I do not want to use recon-all because I do not want to parcellate or segment it. Is there such utility or function in freesurfer? Thank you. Sincerely, Ernest Kissi Kontor.

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Re: [Freesurfer] No ROI name in summary of MNI305 group analysis
by wangzhiwei3233 07 Feb '24

07 Feb '24

External Email - Use Caution Dear Gouglas,Thank you for your replay. There is still no ROI name in the summary after adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat. My updated command is as followed: mri_volcluster --in ./sig.${sigFormat} --thmin ${thvoxel} --sign ${sigsignTemp} --cwpvalthresh 0.05 --minsize 273 --fwhm 6 --no-adjust--sum ${nameout}.cluster.summary --out ${nameout}.cluster.nii.gz --ocn ${nameout}.ocn.nii.gz --labelbase $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label --reg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat--mask ${SUBJECTS_DIR}/fsaverage/mri.2mm/subcort.mask.mgz Best, zhiwei ------------------------------------------------------------------------------------------------------------------------------------------------------- Date: Sat, 25 Nov 2023 14:04:08 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] No ROI name in summary of MNI305 group analysis To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <af2e6147-e3d1-4146-b6f9-b685d6899eb7(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Try adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat On 11/23/2023 2:32 AM, wangzhiwei3233 wrote: > > ????????External Email - Use Caution > > Dear Freesurfer Experts, > I did group-level analysis in MNI305 space.? Then I output the summay > via command 'mri_volcluster' as follows: > /*mri_volcluster --in* ./sig.nii.gz *--thmin* ${thvoxel} *--sign* > ${sigsignTemp} *--cwpvalthresh* 0.05 *--minsize* 273 *--fwhm 6* > *--no-adjust --sum* ${nameout}.cluster.summary*--out* > ${nameout}.cluster.nii.gz *--ocn* ${nameout}.ocn.nii.gz *--labelbase* > $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label > *--mask* > /mnt/hgfs/G/work/MetaCog/Human/subjects/fsaverage/mri.2mm/subcort.mask.mgz/ > / > / > the output is as follows. there are no ROI names in the table. Is it > because I missed the option '--reg' in the command line? Which > register file shoul I use if I should add it? I can't find the > 'register.dat' file in fsaverage folder. > > Very appricated if you can help me. > > Best, > zhiwei

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T1 maps longitudinal data
by AJ 07 Feb '24

07 Feb '24

External Email - Use Caution Hi, I have T1 relaxation maps over 4 time points. In terms of longitudinal analysis, could these maps be fed into Freesurfer longitudinal pipeline to control for intersubject variability of signal intensity? Any other method you would recommend? Many thanks AJ

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Freesurfer Intensity representation
by ERNEST KISSI 07 Feb '24

07 Feb '24

External Email - Use Caution Hi, Please I made an initial enquiry about using freesurfer for MPF maps. The feedback was that I register the MPF maps on their corresponding T1 images using multimodal registration. I used FSL to do the multimodal registration and then use recon-all in freesurfer. Now I want to know what the intensity and the volume of the output in the aseg file represent. Is it the intensity of the MPF or the TI and MPF?

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Recon-all Longitudinal Talairach issue
by Kapteijns, Kirsten 07 Feb '24

07 Feb '24

External Email - Use Caution Dear all, I have run recon-all successfully on multiple subjects on multiple timepoints. If I open the mri folder, it shows the correct talairach files and no issues arose during processing. However, when I then run the longitudinal pipeline (first base, which also shows correct files) on the subjects (recon-all -long SUBJXXtp1 SUBJXXbase -all) the talairach shows an failure detection and the subsequent file is talairach.invalid.mgz. The actual segmentation etc. seems fine when inspecting, but when I then want to run segmentBS.sh on these processed folders, it gives an error. I have run this a few month back without issue, and had just a few subjects left, but now all of them show this same error. Any idea how this could be caused? Kind regards, Kirsten De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kopi?ren en verspreiden van deze e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaande schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 80262783. The content of this message is intended solely for the addressee. No rights can be derived from this message or its attachments. If you are not the intended recipient, we kindly request you to delete the message and inform the sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, without a written consent from the sender. Radboud university medical center is registered with the Dutch Chamber of Commerce trade register with number 80262783.

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MRIread and RAS orientation
by Fotiadis, Panagiotis 07 Feb '24

07 Feb '24

External Email - Use Caution Hello, I have two nifti files that are both in the same MNI space, the former of which is saved in LAS orientation while the other in RAS orientation (as showcased by the “Orientation” field of mri_info). I just wanted to verify: When loading both on MATLAB using MRIread, both of their volumes are automatically loaded (or transformed in the case of the first file) in the same RAS orientation, right (using the vox2ras transformation)? Thanks in advance! Best, Panos ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Create a Binarized ROI for Surface
by Na, Xiaoxu 07 Feb '24

07 Feb '24

External Email - Use Caution Dear Freesurfer Expert, We would like to extract mean Cth values for each subject within a own-creaded ROI (surface defined), using freeview (for instance). Is it possible to create a ROI (i.e. spherical surface) surrounding a particular vertex of an sig.mgh file? (and then extract its mean Cth values for each subject)? I think this is not a new question, and it was posted somehow on https://secure-web.cisco.com/15jmZMEaxCepVMfyQImwGR_dFusKbz7ObR8zcE3AMwMwg6…, and https://secure-web.cisco.com/1nS4AASSkp9fTCLDzqspNVvBf35PGarlPS708pOXtzpIMD…, but I'm still encountering questions. These commands did run, but together they didn't create a binarized mask with 1 for the sphere around the coordinates, and 0 for the other voxels. Would you recommend what I should change? Thank you so much! $mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf sphere --sphere-center -7.4 67.22 60.27 --radius 5 --o delta.sm00.mgh $mris_fwhm \ --smooth-only \ --subject fsaverage \ --hemi lh \ --i delta.sm00.mgh \ --niters 10 \ --o delta.sm10.mgh $mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Freesurfer recon-all qcache partial failure
by Asuka Toyofuku 07 Feb '24

07 Feb '24

External Email - Use Caution Dear Freesurfer researchers, I have an issue with recon-all-qcashe results. (please find the recon-all.log attached.) The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but it did not create fsaverage files with different smoothing levels (e.g., lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh, lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf" folder. I used the command below: for d in Te* te* EPK* epk* do recon-all -s $d -qcache done (Subjects names start from either Te, te, EPK or epk) For several subjects with failed recon-all commands, I re-ran the command individually: recon-all -s subjectname -qcashe (output from the terminal window) It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /media/m-proc/Vol03/FREESURFER7_SUBJECTS/teen_subject_name/scripts/IsRunning.lh+rh **Try to copy the line and then rerun again with the quche code. I'm currently using freesurfer-x86_64-redhat-linux-gnu-dev4-20090216. Do you have any ideas why the command did not produce different fwhm files? I'm thinking about re-running the recon-all again, so I would appreciate it if you could help me modify the commands. Thank you very much in advance. Best regards, Asuka

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Command terminated by signal 11 when execute mris_place_surface
by Yp Ben 07 Feb '24

07 Feb '24

External Email - Use Caution Hello FreeSurfer Developers, I'm want to run HCP T1W data of recon-all , but it always failed on step " WhitePreAparc lh", below is my run information: OS: Ubuntu 22.04.2 LTS MEM: 32G CPU: 16 Freesurfer Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Command: export SUBJECTS_DIR=$(pwd) nohup recon-all -s $1 -i $(ls *${1}*) -all -qcache -3T -parallel -openmp 16 -threads 200 > nohup_${1}.log 2> nohup_${1}.log & Error messages as below: mris_autodet_gwstats done @#@FSTIME 2024:02:06:05:28:14 mris_autodet_gwstats N 8 e 5.75 S 1.02 U 8.70 P 169% M 277604 F 3 R 131626 W 0 c 403 w 6466 I 0 O 8 L 1.96 14.01 13.54 @#@FSLOADPOST 2024:02:06:05:28:20 mris_autodet_gwstats N 8 1.96 13.81 13.47 #-------------------------------------------- #@# WhitePreAparc lh 2024年 02月 06日星期二 05:28:20 CST cd /home/tben/ds000102/HCA6139970_V1_MR/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.4.1 7.4.1 cd /home/tben/ds000102/HCA6139970_V1_MR/mri setenv SUBJECTS_DIR /home/tben/ds000102 mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 200 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Command terminated by signal 11 @#@FSTIME 2024:02:06:05:28:20 mris_place_surface N 18 e 24.22 S 4.47 U 1.71 P 25% M 185596 F 9 R 46047 W 0 c 184 w 12734 I 1296 O 0 L 1.96 13.81 13.47 @#@FSLOADPOST 2024:02:06:05:28:44 mris_place_surface N 18 69.96 28.86 18.46 Linux tben-dev-server 6.5.0-15-generic #15~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 12 18:54:30 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HCA6139970_V1_MR exited with ERRORS at 2024年 02月 06日星期二 05:28:45 CST For more details, see the log file /home/tben/ds000102/HCA6139970_V1_MR/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1gYb-2hE-QjkoVlTlGmx1IVV7-IUAB7paWJo1QUb0Vj4eza… Check the core dump file under /var/crash vim _opt_freesurfer_bin_mris_place_surface.1000.crash ProcStatus: Name: mris_place_surf Umask: 0002 State: S (sleeping) Tgid: 23410 Ngid: 0 Pid: 23410 PPid: 22657 TracerPid: 0 Uid: 1000 1000 1000 1000 Gid: 1000 1000 1000 1000 FDSize: 64 Groups: 4 24 27 30 46 122 134 135 1000 NStgid: 23410 NSpid: 23410 NSpgid: 23410 NSsid: 22657 Kthread: 0 VmPeak: 10878292 kB VmSize: 10394436 kB VmLck: 0 kB VmPin: 0 kB VmHWM: 185500 kB VmRSS: 185500 kB RssAnon: 179356 kB RssFile: 6144 kB RssShmem: 0 kB VmData: 2068316 kB VmStk: 132 kB VmExe: 3084 kB VmLib: 3820 kB VmPTE: 1772 kB VmSwap: 0 kB HugetlbPages: 0 kB CoreDumping: 1 THP_enabled: 1 untag_mask: 0xffffffffffffffff Threads: 200 SigQ: 0/128234 SigPnd: 0000000000000000 ShdPnd: 0000000000000000 SigBlk: 0000000000000000 SigIgn: 0000000000000000 SigCgt: 0000000100000000 CapInh: 0000000000000000 CapPrm: 0000000000000000 CapEff: 0000000000000000 CapBnd: 000001ffffffffff CapAmb: 0000000000000000 NoNewPrivs: 0 Seccomp: 0 Seccomp_filters: 0 Speculation_Store_Bypass: thread vulnerable SpeculationIndirectBranch: conditional enabled Cpus_allowed: ffff Cpus_allowed_list: 0-15 Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003 Mems_allowed_list: 0-1 voluntary_ctxt_switches: 21 nonvoluntary_ctxt_switches: 17 Signal: 11 Uname: Linux 6.5.0-15-generic x86_64 UserGroups: adm cdrom dip lpadmin lxd plugdev sambashare sudo CoreDump: base64 I use 3 different VMs to run the same sample with different freesurfer versions , 2 are 7.4.1 and another one is 7.2 , but always failed on this step , I don't know what's the reason cause this failed , can you please help to have a look ? Thanks a lot .

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Freesurfer February 2024