Freesurfer January 2024

freesurfer@nmr.mgh.harvard.edu

70 participants
111 discussions

[FreeSurfer] Lesion detection at different thresholds
by Krystal Xiwing Yau 18 Apr '24

18 Apr '24

External Email - Use Caution Dear FS experts, I am testing out which threshold works the best for the image. As I tested 0.3 and 0.9, the lesion masks do show the difference but the measurement is the same. Please see below for your information: [cid:abc00aac-cc49-4ef4-9cca-50c4bf72188b] Fig 1. Lesion.mgz with a threshold of 0.3 applied to FLAIR image [cid:7e206b3b-741a-497a-aec8-5bef569267b7] Fig 2. Lesions.mgz with a threshold of 0.7 applied to FLAIR image Do the volume of lesions supposedly different with threshold adjustments? The following code is what I used for running samseg: run_samseg --input $FREESURFER_HOME/${i}.nii $FREESURFER_HOME/${i}_flair_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 --output $SUBJECTS_DIR/${i}_samsegOutput_thold0.7/ --save-posteriors --threads 8 Thank you for your attention. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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xhemi
by Joost Janssen 06 Mar '24

06 Mar '24

External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The following commands work without error but are they correct for meeting my objective? Thanks. surfreg --s $subject --t fsaverage_sym --lh --no-annot surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg $subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg $subject/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg $subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg $subject/xhemi/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0 $subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o $subject/surf/li.thickness.lh.fsaverage_sym.mgh mri_segstats --annot fsaverage lh aparc --i $subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum $subject/stats/li.thickness.aparc.stats -joost

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Re: [Freesurfer] Subject does not have a bstampfile
by fsbuild 04 Mar '24

04 Mar '24

External Email - Use Caution   Let me add that it will not work to use shared mount point from the Windows filesystem as you list below, /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri - for your SUBJECTS_DIR when running a recon-all command.  The command will fail because the Windows file system does not support soft-links.   Any SUBJECTS_DIR used for recon-all needs to be inside the Linux OS image running freesurfer.  You could however copy the files from that mount point to create another SUBJECTS_DIR somewhere inside your Linux image, e.g., under your home directory in linux. .... in your linux terminal window ... $ cd$ mkdir subjects$ export SUBJECTS_DIR=$HOME/subjects$ cd $SUBJECTS_DIR$ cp -p -f -R /mnt/c/Users/GCM/Desktop/subjects/NowakG . - R. On Jan 8, 2024, at 16:10, Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:You need to specify the input files to process. Here is the wiki page for recon-all -  https://secure-web.cisco.com/1hqVY7QioPnD85rxOcGMUcCuynnW47DWZwkPX0Z-CZpPZhsuOE3Dqq56yZOR48pnqlARbSGSU1uJNTssTzOLeJZDej-4B4APtXHQmIDTAeNiz6injsGyGghBE4szgzC-CIvlktYVKAeIFD9vBNBZGTgRtRAfcxOZTJJXzk0kPtE9fSY8vo9o05Q8Lf5La4t7Av6IvB6hkO3ZqlfaDGIxlZfRhNJC0f5oWDNXpfp8nYykG-egLh8zOuhOsHSbWCac7UKV67GamZPc5FS5KwH3vo_4_Omj5v0dIRxZ5O4d9WtJGN0f3IkrLaqnXHmnqhmI4YmYtNQmp-0UBF38a-xfw4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-allBest,Yujing-----Original Message-----From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Joanna KidonSent: Monday, January 8, 2024 3:33 PMTo: freesurfer(a)nmr.mgh.harvard.eduSubject: [Freesurfer] Subject does not have a bstampfile       External Email - Use Caution        Hello FreeSurfer Developers,I'm attempting to compute Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal), as described on the https://secure-web.cisco.com/1JRIAQtmLphlXIykU3RsSWy2GeEv_y0Em3hHjyX02njKQR… I get the following error when I run the recon-all -all -s command:Subject does not have a bstampfile, copying /usr/local/freesurfer/7.3.2/build-stamp.txtSubject FS Version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version DoneINFO: SUBJECTS_DIR is /mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux#--------------------------------------------#@# MotionCor Sun Jan  7 20:48:46 CET 2024ERROR: no run data found in/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume called 001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig.If you have a second run of data call it 002.mgz, etc.See also: http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwu… LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s NowakG exited with ERRORS at Sun Jan  7 20:48:46 CET 2024I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the scripts/recon-all.log in case it's of any use.Best regards,Joanna------------------------------------------------------------------------------------dr n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w KatowicachPhD, specialist in medical physics, neurobiologist Chairwoman of the Diagnostic Imaging Section of the Polish Society of Medical Physics Department of Invasive Cardiology and Electrocardiology, 3rd Department of Cardiology, Medical University of Silesia in Katowice Head of the Medical Physics Department, Coordinator for Radiological Protection, Deputy Head of the Department of Diagnostic Imaging Leszek Giec Upper-Silesian Medical Centre of the Medical University of Silesia in Katowice_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon all with optiBET brain mask
by BALBONI Irene 27 Feb '24

27 Feb '24

External Email - Use Caution Hello, I would like to run recon all on a batch of subjects using 2 inputs (mprage and mp2rage). I would also like to run recon all using as brain mask not the standard brain mask generated by recon-all itself but a previously created optiBET. Would you have any suggestion on how to proceed? I tried simply replacing the brainmask file with the optiBET but it did not work. Just for context all my participants (150) have been already segmented using recon-all but we noticed during quality control that we still have skull stripping and pial surface errors for the majority of them and that is why we would like to implement the optiBET mask. Thanks for your help, Irene Balboni PhD student She/Her Institute de plurilinguisme<https://secure-web.cisco.com/1pftPU5_0h0FupMF_jZDy_UxBYrJAQ-AW89umP7RzP_duH…> | Université de Fribourg & Brain and Language Lab<http://secure-web.cisco.com/1GVUYNYViIIVEm2bvje-SiFox0WAIrWlf7gC0y8Dy1Yk6xj…> | Université de Genève c/o Campus Biotech Chemin des Mines 9 – 1202 Université de Genève, CH +41(0)223790141 Twitter<https://secure-web.cisco.com/17WKW8eFYGf6kC7ikhhz87_g3_OExqqtlPMTRdUfjaGR0u…> | ResearchGate<https://secure-web.cisco.com/17QR3OuPCdu6j4aAtW1iy0qnt2WV8MA0yHG3gonUNgbpno…> | Linkedin<https://secure-web.cisco.com/10d7bSA4mUh4az6x-hBwYc5c1373f-jWI1YMV5SjB-YHxE…>

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Manual/reproduce conform
by Dipterix Wang 23 Feb '24

23 Feb '24

External Email - Use Caution Dear FreeSurer Wizards, I'm trying to run the recon-all command on one of my template brains such that the resulting Norig and Torig are identical. I understand that fs always conforms the MRI to 256^3 before segmentation. I wonder if there is any way that I can resample the original MRI to achieve the same Norig and Torig? More specifically, currently the Torig (vox to tkrRAS) is [,1] [,2] [,3] [,4] [1,] -1 0 0 128 [2,] 0 0 1 -128 [3,] 0 -1 0 128 [4,] 0 0 0 1 If I resample the input image such that Norig (vox to scanRAS) equals this matrix, can I expect that "conform" does not change the orientation? Alternatively, is there any method I can use to "predict" or reproduce the Torig from the original MRI outside of FreeSurfer? Thanks, - Dipterix

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Fixing intensity normalization issue which leads to gray matter classified as WM
by Maya Yablonski 23 Feb '24

23 Feb '24

External Email - Use Caution Hello, I am running freesurfer v7.3.2 reconall with -synthseg on a pediatric sample, and for one specific subject I keep getting a lot of gray matter classified as white matter, which leads to the ?h.white surfaces being too close to the pial surface. I have tried running with and without the --robust option but the issue recurs. Are there any expert options that I can play with before manually editing the WM.mgz? The issue is pervasive throughout the brain so will require heavily editing every single slice. The values for the misclassified gray matter are 85-97 in the brainmask.mgz and 100-110 in the WM.mgz and the T1 image looks ok by eye. When trying to run the same subject with the default pipeline (no synthseg), it crashes with the following error: reading 1 input volumes... logging results to talairach.log reading '/share/software/user/open/freesurfer/7.3.2/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... error: mghRead(/MYPATH/freesurfer/sub-2341/mri/brainmask.mgz, -1): could not open file error: mri_em_register: could not open mask volume brainmask.mgz. I wonder if there's any parameter I can tweak in the expert.opts? Thanks for any leads, Maya

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Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 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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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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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 January 2024