Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30064 discussions

make_average_subject command error
by Asuka Toyofuku 09 Feb '24

09 Feb '24

External Email - Use Caution Dear Freesurfer experts, We're trying to make an average subject for group analysis using Freesurfer 7.1, but the make_average_subject command exits with errors after calling make_average_surf: MakeAverageSurf(): 129 lh pial sphere.reg talairach.xfm 1 1 It appears to be trying to find the lh.pial surface for the first participant, but this file is named "lh.pial.T1". (In FS 5.3 and 6.0, this file was labelled "lh.pial", but with FS7.1, it seems to be named lh.pial.T1). Does anyone have a suggestion for how to fix this problem? (We want to avoid changing all the file names to "lh.pial" from "il.pial.T1") Should we call make_average_subject again with -no-surf-to-surf ? Best regards, Asuka

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Re: [Freesurfer] Synthsr command !
by fsbuild 08 Feb '24

08 Feb '24

External Email - Use Caution The python distribution in the 7.4.1 release cannot run all the python based tools on a Silicon Mac (M1, M2, M3 chip) because at that time we did not have a python distribution that was completely compatible with the arm64 architecture. We currently have a development build for the Silicon Mac, and you can download/try the installer package from: https://secure-web.cisco.com/1iKFStD8SwFv0R2HIbwHmO8r1CRu1iDcQPEOYPG7jJvIjr… But we cannot recommend this build for ongoing work as it is currently unstable and not a tested release. - R. On Feb 7, 2024, at 17:05, Martin Juneja <mj70481(a)gmail.com> wrote:        External Email - Use Caution        Dear Juan and FreeSurfer developers,I am trying to run the mri_synthsr command on a MacPro M2 Max chip (OS 13.6.4) - but somehow, I am getting the following error when I try to run this command. I am using FreeSurfer's 7.4.1 version.Illegal instruction: 4I would greatly appreciate any help in getting this resolved.Thanks._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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if: Expression Syntax - preproc-sess with -nomc option
by Stefano Delli Pizzi 08 Feb '24

08 Feb '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run preproc-sess with -nomc option preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -force if: Expression Syntax. This error occurred before to create the file with slice timing correction The error did not occur when I run the preproc-sess command line without the -nomc option. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Platform: Darwin Kernel Version 21.6.0

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[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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