Freesurfer

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30132 discussions

Error in longitudinal pipeline {Disarmed}
by vittal korann 24 Nov '20

24 Nov '20

External Email - Use Caution Hi FreeSurfer experts Recently I started working on the longitudinal data. I followed the pipeline described in the below link. Also, I attached my longitudinal table along with freesurfer data. https://secure-web.cisco.com/1DF2osKRIq2P6tkekGvGP9JanombamauC9_0TALJPJG645… I got the error while executing the following commands: CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)]; F_lhstats = lme_mass_F(lhstats,CM); And the Matlab threw an error shown below >> CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] > zeros(3,5)]; > >> F_lhstats = lme_mass_F(lhstats,CM); > Error using lme_mass_F (line 50) > The number of colums in the contrast matrix CM(1).C is different from the > corresponding number of fixed effects in stats(1).Bhat Any help would be appreciated! With regards Korann

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Re: [Freesurfer] Freesurfer Digest, Vol 201, Issue 34 {Disarmed}
by vittal korann 24 Nov '20

24 Nov '20

External Email - Use Caution Thanks, Kersten! The design matrix X has a dimension of 47x6 and the contrast matrix CM.C has a dimension of 3x17. I wish to know the steps to correct this error? Thanks again for your kind help! With regards Korann On Mon, Nov 23, 2020 at 10:31 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/1Yf2I0SaCp4AVxLwAORs81BeTMH0g33xRhY1CDT68ohUBJ… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: License error on Windows Subsystem for Linux (Shen Lunhao) > 2. smooth longitudinal analysis {Disarmed} (Agurne Sampedro Calvete) > 3. Re: Error in longitudinal pipeline {Disarmed} > (Diers, Kersten /DZNE) > 4. Smoothing GWC mgh data (Valentina Meregalli) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 Nov 2020 06:26:28 +0000 > From: Shen Lunhao <lunhao0104(a)hotmail.com> > Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > DM6PR02MB6493EB25230B280B7DCFF288DBFC0(a)DM6PR02MB6493.namprd02.prod.outlook.com > > > > Content-Type: text/plain; charset="gb2312" > > External Email - Use Caution > > Hi Andrew, > > The following is the information of four systems. System #3 and #4 are > same configuration where license error occurred. > > #1 #2 #3 #4 > Core Intel(R) Xeon(R) CPU E5-2620 Intel i7 AMD R9 5900X > AMD R9 5900X > Mem 32GB 16GB 32GB 32GB > Platform Linux version 4.15.0-112-generic (buildd@lcy01-amd64-027) > (gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)) Window subsystem for > linux(WSL2) + Ubuntu20.04 Window subsystem for linux(WSL2) + Ubuntu20.04 > Window subsystem for linux(WSL2) + Ubuntu20.04 > > Worked Worked Didn?t work Didn?t work > The freesurfer package I used is > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0which downloaded from > freesurfer website. The license file was four lines type. Hope this > information is helpful. > > Thanks, > Lunhao > > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu < > freesurfer-bounces(a)nmr.mgh.harvard.edu> ?? Hoopes, Andrew < > AHOOPES(a)mgh.harvard.edu> > Date: 2020?11?21? 1:19 > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux > > > Hi Lunhao, > > > > Interesting. Can you provide some details on the configurations where this > worked? Were you using the same linux subsystem and windows versions? > > > > thanks > > Andrew > > > > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Shen Lunhao < > lunhao0104(a)hotmail.com> > Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> > Date: Friday, November 20, 2020 at 2:44 AM > To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] License error on Windows Subsystem for Linux > > > > External Email - Use Caution > > Hello FreeSurfer Developers, > > > > I'm attempting to use freesurfer 5.3.0 on Windows Subsystem for Linux > (Ubuntu 20.04), but I got license error message as described below: > > > > -------------------------------------------------------------------------- > > ERROR: Invalid FreeSurfer license key found in license file > /space/tools/freesurfer/5.3.0/license.txt > > If you are outside the NMR-Martinos Center, > > go to > http://secure-web.cisco.com/1gwoaE20Y7b27ULq16GgvwkvDuYOzRdARFYzw1XJCoskz3-… > to > > get a valid license file (it's free). > > If you are inside the NMR-Martinos Center, > > make sure to source the standard environment. > > -------------------------------------------------------------------------- > > > > I tried with the same 5.3.0 packages and same license file on four > different computers, and two of them work well with the other two got > similar license error. Does anyone have any thoughts on how to > trouble-shoot this one? > > > > 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > 2) Platform: Windows Subsystem for Linux (Ubuntu 20.04) > > 3) uname -a: Linux DESKTOP-SJ2K1B2 4.4.0-19041-Microsoft #488-Microsoft > Mon Sep 01 13:43:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux > > > Best, > Lunhao > > >

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Files or directories required for subField calculation {Disarmed}
by Keith Harenski 24 Nov '20

24 Nov '20

External Email - Use Caution Hello, We have 3369 freesurfer 5.3 extractions stored on backup. It amounts to about 1.5TB of data. We would like to run the amygdala / hippocampal subField extraction on that data. I am hesitant to run the extraction on our backup copy so I was going to restore the data onto our servers and run from there. However 1.5TB is a lot to restore. Is there a file or directory list from the initial freesurfer extraction the subField calculation requires that could be restored in lieu of each subject's entire directory? Thank you, Keith -- Keith Harenski Mobile MRI Manager Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office (Cell): 505.504.1338 | Fax: 505.272.8002 kharenski(a)mrn.org | http://secure-web.cisco.com/1gWpd7SLX7SCx_SqHWpaZjPyzfQUb2S7o0MHqR3XnN7i4gG… | http://secure-web.cisco.com/1iYBgiu2d5mXVxDO2FVhHcsbuSoThRu0-wDpbW4j4Ai7dTg…

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mri_vol2surf
by Alberto Del Cerro Leon 24 Nov '20

24 Nov '20

External Email - Use Caution Hello, I am trying to run mri_vol2sur to obtain the AAL atlas on freesurfer. i used this command line "mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img" However i received an error saying that ncols 161783 in volume exceeds 32768. I was reading the wiki, could I avoid the error with -noreshape command?

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Re: [Freesurfer] License error on Windows Subsystem for Linux
by Hoopes, Andrew 23 Nov '20

23 Nov '20

Hi Lunhao, Interesting. Can you provide some details on the configurations where this worked? Were you using the same linux subsystem and windows versions? thanks Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Shen Lunhao <lunhao0104(a)hotmail.com> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, November 20, 2020 at 2:44 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] License error on Windows Subsystem for Linux External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use freesurfer 5.3.0 on Windows Subsystem for Linux (Ubuntu 20.04), but I got license error message as described below: -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /space/tools/freesurfer/5.3.0/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I tried with the same 5.3.0 packages and same license file on four different computers, and two of them work well with the other two got similar license error. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Windows Subsystem for Linux (Ubuntu 20.04) 3) uname -a: Linux DESKTOP-SJ2K1B2 4.4.0-19041-Microsoft #488-Microsoft Mon Sep 01 13:43:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux Best, Lunhao

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Smoothing GWC mgh data
by Valentina Meregalli 23 Nov '20

23 Nov '20

External Email - Use Caution Dear all, I computed the gray/white matter contrast using the function 'pctsurfcon' for an individual subject. The output is a .mgh file containing the GWC values for each vertex. It is possible to smooth these data using freesurfer? If it's not, there is another way in which I could do that? Thanks for the help, Valentina Meregalli

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smooth longitudinal analysis {Disarmed}
by Agurne Sampedro Calvete 23 Nov '20

23 Nov '20

External Email - Use Caution Dear Freesurfer experts, I am doing a longitudinal repeated measures analysis and I would like to know which smooth is better to use (with the mri_surf2surf command). In the repeated measures guide ( https://secure-web.cisco.com/1VH4PbpfczyEHmEvf-DmwaQIY3QzK6JXAwbehilCfVS00w…) the example includes an spatial smooth of 5mm FWHM, but in the group analysis guide ( https://secure-web.cisco.com/1oS1UIb6CdjIYlaVy9MrNL5Jmb_OznCDVVe5aIhhhjuuRF…) the example includes a smooth of 10mm. Which one would be more appropriate? And, does it depend on the kind of analysis I am doing (e.g., longitudinal analysis VS a simple group analysis)? Thank you very much in advance. Kind regards, Agurne Sampedro Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015)

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Re: [Freesurfer] eddy_correct with DTI {Disarmed}
by Antonín Škoch 21 Nov '20

21 Nov '20

External Email - Use Caution Hi, Wei, I would recommend to use dwifslpreproc script from mrtrix3 suite instead. https://secure-web.cisco.com/1EpWqxf1LAo_9zZza7TvgPO7braRXyCjrY1yjVepX0Quqt… https://secure-web.cisco.com/1x4J2O9fRBQ-_W3GZxA80BfHGRWeAweDMEk3J-4c05mkYq… https://secure-web.cisco.com/1FCDgvyDpzpGDaCElxPoPOlaMat5sHcKsF-7uMfRSQe8dp… The eddy_correct tool used in dt_recon is very old and suboptimal method for DWI preprocessing. Antonin Hi, DouglasSorry to bother you again, do you think the problem is the old version of FSL? Best, Wei On Fri, Nov 13, 2020 at 1:32 PM Wei Shao <ws...(a)research.baycrest.org> wrote: > Hi Douglas > > I think it's 5.0.11 > > [weishao@gra-login2 ~]$ module load nixpkgs/16.09 freesurfer/7.1.0 > To initialize FreeSurfer, > do (sh, ash, ksh, and bash) > source $EBROOTFREESURFER/FreeSurferEnv.sh > or (csh, tcsh) > $EBROOTFREESURFER/FreeSurferEnv.csh > > [weishao@gra-login2 ~]$ module load fsl > [weishao@gra-login2 ~]$ which fsl > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/fsl > [weishao@gra-login2 ~]$ > > Best, > Wei > > On Fri, Nov 13, 2020 at 10:11 AM Douglas N. Greve <dgr...(a)mgh.harvard.edu> > wrote: > >> What version of FSL are you using? >> >> On 11/10/2020 12:19 AM, Wei Shao wrote: >> >> External Email - Use Caution >> Hi, Freesurfer team, >> >> My name is Weishao, Here is a problem that bothers me a lot I try to run >> DTI. I have loaded the FSL module and use the most recent version of >> Freesurfer. it's appreciated if someone can help. Thanks. >> >> Here is the script. >> >> dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval >> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec >> --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> --s /home/weishao/scratch/rawdata/sub-AVP6176/ >> --o /home/weishao/scratch/rawdata/sub-AVP6176/ >> >> Here is feedback >> >> -rw-r----- 1 weishao weishao 49041968 Sep 9 11:41 >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> INFO: SUBJECTS_DIR is >> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects >> dt_recon logfile >> Tue Oct 27 16:19:28 EDT 2020 >> VERSION dt_recon 7.1.0 >> setenv SUBJECTS_DIR >> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects >> cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi >> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon >> --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval >> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i >> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s >> /home/weishao/scratch/rawdata/sub-AVP6176/ --o >> /home/weishao/scratch/rawdata/sub-AVP6176/ >> gra95 >> weishao >> /cvmfs/*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct >> <http://secure-web.cisco.com/13U2x8LxxvC3rroBw84sAsKDdxMd5ljIVys9mm4GHsZ9POU…> >> ECRefTP 0 >> #@#------------------------------- >> Converting input >> Tue Oct 27 16:19:28 EDT 2020 >> cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi >> mri_convert >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz >> mri_convert >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz >> reading from >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz... >> TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-0.999608, 0.017447, -0.021891) >> j_ras = (0.0104682, 0.958258, 0.285714) >> k_ras = (-0.0259621, -0.285373, 0.958065) >> writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz... >> >> >> #@#------------------------------- >> Eddy/Motion Correct >> Tue Oct 27 16:19:44 EDT 2020 >> cd /scratch/weishao/rawdata/sub-AVP6176/ectmp >> eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz >> /scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0 >> /cvmfs/*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct >> <http://secure-web.cisco.com/13U2x8LxxvC3rroBw84sAsKDdxMd5ljIVys9mm4GHsZ9POU…>: >> line 95: /cvmfs/*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/imglob >> <http://secure-web.cisco.com/14GGFn_nc9xX-9O7KFUQlMhTcuKP2UzYHSyRZ1KY8WmZVDH…> >> : *No such file or directory* >> >> Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value >> in seconds] >> -t : concatenate images in time >> -x : concatenate images in the x direction >> -y : concatenate images in the y direction >> -z : concatenate images in the z direction >> -a : auto-choose: single slices -> volume, volumes -> 4D (time >> series) >> -tr : concatenate images in time and set the output image tr to the >> final option value >> >> *ERROR: when running eddy_correct * >> >> >> Best, >> Wei >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1UPFJbsNdF96Nz5jI3AlTvvxeJFJTSTC6MLT1osyRwjDOD… > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1kA1YhaD_HwWmiThUjz3uRjfLXaKwWelfI_BPjIwTqDh8G…

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PETSURFER for AV1451
by Shane Schofield 20 Nov '20

20 Nov '20

External Email - Use Caution Hi PETSURFERs, A quick question to the group: Does any one have experience using PETSURFER on dynamic AV1451 scans? How can I know whether the MRTM1 or MRTM2 using midbrains (due to off target AV1451 binding) is suitable for my data? Thank you! Best Wishes,Shane

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License error on Windows Subsystem for Linux
by Shen Lunhao 20 Nov '20

20 Nov '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use freesurfer 5.3.0 on Windows Subsystem for Linux (Ubuntu 20.04), but I got license error message as described below: -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /space/tools/freesurfer/5.3.0/license.txt If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/1mRpyN1Z9v5JHXH1zmAAAeYDA0yZIV6qPhpsQo-ZvQydU0B… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I tried with the same 5.3.0 packages and same license file on four different computers, and two of them work well with the other two got similar license error. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Windows Subsystem for Linux (Ubuntu 20.04) 3) uname -a: Linux DESKTOP-SJ2K1B2 4.4.0-19041-Microsoft #488-Microsoft Mon Sep 01 13:43:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux Best, Lunhao

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