Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Password for virtual machine
by Ogier, Stephen E. (Assoc) 01 Apr '22

01 Apr '22

External Email - Use Caution Hi, I'm getting started with FreeSurfer, and I was wondering if I could be sent the passcode to unzip the virtual machine? Thanks, Stephen Stephen Ogier, PhD Postdoctoral Associate, Magnetic Imaging Group, Applied Physics Division National Institute of Standards and Technology

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license text
by krystaly 01 Apr '22

01 Apr '22

External Email - Use Caution Dear Free Surfer experts, I just downloaded the newest version of Free Surfer. The system says FS_LICENSE=/home/developer/license.txt set in /home/developer/.bashrc does not point to a freesurfer license. Freeview will not run w/o a license - edit FS_LICENSE to point to your license file. Would you please send the license key to me? Thanks! Best regards, Krystal

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WM error near the right putamen
by Gabor Perlaki 01 Apr '22

01 Apr '22

External Email - Use Caution Dear all, fswiki suggests that " There are regions where the surfaces are not intended to be accurate that you should be aware of: Areas around the hippocampus and amygdala. " I also found inaccuracy of the WM surface near the putamen and accumbens regions. WM surface goes into the putamen (please see the attached picture). Do I need to fix this error or is it normal? Are the thickness of ctx-rh-medialorbitofrontal and the volume of right putamen valid in this case? Thank you in advance, Gabor

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Re: [Freesurfer] illegal instruction 4 Mac M1
by fsbuild 31 Mar '22

31 Mar '22

External Email - Use Caution Hello Miriam, I can reproduce your error running mri_sclimbic_seg on an M1 Mac running MacOS BigSur with the latest freesurfer development build.  We will look into this and see what can be done. - R. On Mar 31, 2022, at 16:14, Miriam Taza <miriam.taza(a)mail.mcgill.ca> wrote:        External Email - Use Caution        Hello,I am trying to run mri_sclimbic_seg command using dev version of freesurfer on my macbook pro m1 max (monterey version 12.2.1) and I keep getting illegal instruction: 4 (here is the output)/Applications/freesurfer/python/scripts/mri_sclimbic_seg --i Desktop/doc/corlab/sub-121123/anat/sub-121123_T1w.nii.gz --o Desktop/doc/derivatives/MT/corlab/sclimbic_output/sub-121123/anat/rois/sub-121123_atlas-sclimbic_dseg.niiExcluding seg [853]Using CPUIllegal instruction: 4I am very new to coding and first time using freesurfer. Unfortunately, my lab mates have not had a similar problem as they all have intel-based macs. Thanks!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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illegal instruction 4 Mac M1
by Miriam Taza 31 Mar '22

31 Mar '22

External Email - Use Caution Hello, I am trying to run mri_sclimbic_seg command using dev version of freesurfer on my macbook pro m1 max (monterey version 12.2.1) and I keep getting illegal instruction: 4 (here is the output) /Applications/freesurfer/python/scripts/mri_sclimbic_seg --i Desktop/doc/corlab/sub-121123/anat/sub-121123_T1w.nii.gz --o Desktop/doc/derivatives/MT/corlab/sclimbic_output/sub-121123/anat/rois/sub-121123_atlas-sclimbic_dseg.nii Excluding seg [853] Using CPU Illegal instruction: 4 I am very new to coding and first time using freesurfer. Unfortunately, my lab mates have not had a similar problem as they all have intel-based macs. Thanks!

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Tracula fsl commands fail in Freesurfer docker
by Clément Nicolas Graffard 31 Mar '22

31 Mar '22

External Email - Use Caution Hi, I am trying to use tracula within the freesurfer docker (freesurfer:7.2.0) but some commands related to fsl fail because the fsl script is not found. For example, within the trac-preproc command, the subcommand bet /input/inputData/sub-010017/dmri/lowb.nii.gz /input/inputData/sub-010017/dmri/lowb_brain.nii.gz -m -f 0.3 is launched but this script is named bet.fsl instead of just bet in the folder /usr/local/freesurfer/bin inside the docker. This causes the command to fail. Have I missed some initialization steps ? Many thanks, Clément Nicolas--Graffard

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bedpostx error inside trac-all
by Mirro, Amy 31 Mar '22

31 Mar '22

External Email - Use Caution Hello, I am trying to run trac-all -bedp and I am running into the following error: /opt/freesurfer/bin/bedpostx_mgh: 128: /opt/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected Others have encountered this error previously, and you had advised running bedpostx locally (as oppsoed to bedpostx_mgh). I was wondering, however, if there is a way to still run bedpostx inside trac-all. I was looking at the source code for trac-all in your github (branch 7.2), and I noticed that line 611 calls bedpostx_mgh despite being within the "if (! $onpbs)" conditional. Would changing line 611 from: set cmd = (bedpostx_mgh -n $nstick -model 1 $dtdir/dmri) to set cmd = (bedpostx -n $nstick -model 1 $dtdir/dmri) fix the problem? If it's helpful: I am running on centos7 and my build stamp is: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Thanks, Amy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] mri_vol2vol anatomical to functional
by Manenti, Giorgio 31 Mar '22

31 Mar '22

External Email - Use Caution Hi Douglas, thank you for your time; I am trying to get the ribbon at functional space resolution (I need it to extract the white matter from my ROIs) Here I am copying the 2 commands (one using .reg file, the second using .lta) I am using, and the terminal terminal outputs. Attached you will also find 3 screenshots from freeview with 1) original ribbon https://secure-web.cisco.com/1jGfE_s0T0UpZC_37qNgkpXRnP-y87LEZivCMZpnxa5A-P… 2) ribbon transformed in functional space using the .reg file https://secure-web.cisco.com/1W46SeJXfyvYiIdzN0-Mgw8u9m_sVqChPLDxI9ZFbN355R… and 3) ribbon transformed using the .lta file https://secure-web.cisco.com/1D0QDP9T6GVwkO7J6BbTviZB6BzyWoBMt6z9cMQuKWuK6-… . (Please Note: I am using Matlab to integrate this analysis in the general pipeline, so the command are started by the s=system() function ) %%%%%%REG s=system(['mri_vol2vol --reg ' regpath ' --mov ' inputvol ' --targ ' funcTemp ' --o ' outputvol ]); regio_read_register: loading lta Matrix from regfile: 0.99982 -0.01069 -0.01533 -0.11505; 0.01423 -0.09676 0.99521 -0.84297; 0.01212 0.99525 0.09659 -5.72961; 0.00000 0.00000 0.00000 1.00000; movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz targvol FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1649422337 Final tkRAS-to-tkRAS Matrix is: 0.99982 -0.01069 -0.01533 -0.11505; 0.01423 -0.09676 0.99521 -0.84297; 0.01212 0.99525 0.09659 -5.72961; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 2.01888 -0.03096 0.02351 23.93213; 0.02447 0.19504 -2.18955 197.85437; -0.02873 -2.00955 -0.21287 240.49161; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done %%%%%%LTA s=system(['mri_vol2vol --lta ' ltapath ' --mov ' inputvol ' --targ ' funcTemp ' --o ' outputvol ]); Matrix from LTA: 0.99983 -0.01069 -0.01533 -0.11505; 0.01423 -0.09676 0.99521 -0.84293; 0.01212 0.99525 0.09659 -5.72960; 0.00000 0.00000 0.00000 1.00000; Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii INFO: src volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, -0.0000, -0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : (-0.0000, 1.0000, 0.0000) c_(ras) : ( 0.2540, 9.2232, 8.1562) file : Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz volume geometry: extent : (104, 104, 69) voxel : ( 2.0192, 2.0192, 2.2000) x_(ras) : (-0.9995, -0.0137, 0.0296) y_(ras) : ( 0.0126, -0.9991, -0.0397) z_(ras) : ( 0.0301, -0.0393, 0.9988) c_(ras) : ( 1.5530, 16.4346, 14.9788) file : bold/template.nii.gz INFO: dst volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (104, 104, 69) voxel : ( 2.0192, 2.0192, 2.2000) x_(ras) : (-0.9995, -0.0137, 0.0296) y_(ras) : ( 0.0126, -0.9991, -0.0397) z_(ras) : ( 0.0301, -0.0393, 0.9988) c_(ras) : ( 1.5530, 16.4345, 14.9788) file : FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, -0.0000, -0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : (-0.0000, 1.0000, 0.0000) c_(ras) : ( 0.2540, 9.2232, 8.1562) file : Anatomy_Processed/hum_15496.long.long002/mri/orig.mgz movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz targvol FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1649445621 Final tkRAS-to-tkRAS Matrix is: 0.99828 0.04446 -0.03809 2.43217; 0.03729 0.01869 0.99913 9.13850; -0.04513 0.99884 -0.01700 12.13850; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 2.01577 -0.07692 -0.09781 28.12225; -0.09113 -0.03433 -2.19744 198.19705; -0.07530 -2.01747 0.04112 244.54424; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done Many thanks again, Best Giorgio Message: 10 Date: Sun, 27 Mar 2022 17:16:25 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mri_vol2vol anatomical to functional To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <50029d97-24be-17a3-2358-3c93982dea41(a)mgh.harvard.edu> Content-Type: text/plain; charset=UTF-8; format=flowed I'm not sure I understand what you are saying or what the problem is. Can you provide the actual command line you are using, all the terminal output, and a picture that shows what the problem is? On 3/23/2022 2:46 PM, Manenti, Giorgio wrote: > External Email - Use Caution > > Dear Freesurfer experts, > > I am getting problems to transform my xh.ribbon.mgh from anatomical 256x256x256 to functional 104x104x69 space. > > When converting the ribbon via ? mri_vol2vol ?reg REGfile ?mov INPUT ?targ funcTEMPLATE ?o OUTPUT ? and checking via freeview, i am getting the right functional space dimensions but the INPUT and OUTPUT .mgz are never overlapping. Why am i getting this misplacement ? Is this problem due to the register file i provide or maybe it is just a visualisation error (perhaps freeview is not the best way to check the conversion). > > I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) register.dof6.lta (changing ??reg with ?lta?). I am getting an almost perfect merge when using the .lta file but still the two volumes are misaligned. > I tried mri_label2vol as well, but as expected i got worse results. > > To provide a minimum more detail, after recon-all i process the anatomy with the longitudinal recon. At that point i use the longitudinal anatomy to register the functional data, which i process by 1) mk-template 2) topup & applytopup. > > Many thanks in advance > Warm regards > > Giorgio > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1hfmecYxKY1NpcMzDGJ7lJmVMNisZgCocWDE73UzXQE8q4…

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FREESURFER Maintaining vertex Id during transformations
by Alison McDonnell 30 Mar '22

30 Mar '22

External Email - Use Caution Hi all, I have been able to create my flat map in freesurfer and then do calculations using it to find a point. I then want to map that point back into the 3D space maintaining the coordinates. I was wondering if anyone had done something similar before and had any ideas. I am using MATLAB for the calculations and transformations. Ali

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Re: [Freesurfer] password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z
by fsbuild 30 Mar '22

30 Mar '22

External Email - Use Caution Hello Roya, Sending the info to your email shortly. - R On Mar 30, 2022, at 09:37, Roya Afshari <roya.afshari(a)unibas.ch> wrote:        External Email - Use Caution        Hello,I hope this email finds you well.I would like to request for the password to FS_7_2_0_Ubuntu_18_04_06.ova.7z file to be able to expand it.Thank you for your time.Roya AfshariPhD studentDivision of Radiological Physics, Department of Radiology,University Hospital Basel, Basel, Switzerland_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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