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30132 discussions

mri_glmfit with flag -pvr
by Vicky Shi 31 Jan '20

31 Jan '20

External Email - Use Caution Dear Freesurfer team, I am running the glm analysis on CBF maps. I have two class and I want to see the group difference regressing out the cortex thickness. I know that I can add the average cortical thickness as one covariable in FSDG file. However, I think it might worth trying to do this with GLM by using a per vertex regressor (thickness). My fsgd file is like below: Class Patient Class CTL INPUT subj1 Patient INPUT subj2 CTL .... My command is below: mri_glmfit --y lh.fsaverage.cbf.sm10.mgz --fsgd fsgd.txt --C contrast.mtx --glmdir lh.output.glmdir --surf fsaverage lh --pvr lh.thickness.sm10.mgz My contrast matrix is -1 1 0. I am wondering if what I do is correct or not. Does it make sense or I should use the mean thickness as regressor? Thank you for your time! Best regards, Vicky

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Question longitudinal study about treatment effect with change of scanner and head coil?
by Markus Gschwind 31 Jan '20

31 Jan '20

External Email - Use Caution Dear experts, I am reviewing a study that proposes a longitudinal study in patients across several years on the effect of medical treatment in terms of fcMRI and DTI-connectivity measures. However, in several but not all patients, the scanner was upgraded from Trio to Prisma and the head coil was changed from a 12 to a 20-channel. Every patient had the upgrade at another time point. I would like to hear your opinion on this. In my experience, the scanner upgrade and especially the head coil upgrade heavily affected the images. So I have fundamental doubts about the feasibility. What would be the conditions under which it could be acceptable? Thank you in advance! Best, Markus

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Software support
by Ricardo J Rodriguez Colon 31 Jan '20

31 Jan '20

External Email - Use Caution Hi, I was wondering if there is a version available for Windows OS or is this available for Mac and Linux only? Thank you, - Ricardo J. Rodríguez

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recon-all errors - mri_segstats and mri_relabel_hypointensities
by Laurel Quinlan 31 Jan '20

31 Jan '20

External Email - Use Caution Hi FS Support, I have two brains for which recon-all exited with errors after I edited the wm.mgz volume. It seems that the problem occurs during the mri_segstats and mri_relabel_hypointensities steps (if I'm reading the output of the command "tail scripts/recon-all.log" correctly). I attached one of the recon-all.log files as a zipped txt file. Please let me know if you have troubleshooting suggestions. Thank you for your help! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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XL defect in recon-all
by Devika K 31 Jan '20

31 Jan '20

External Email - Use Caution Hi, I am running recon-all on Freesurfer version 6. Few of my subject's have XL defect error as shown below. CORRECTING DEFECT 0 (vertices=18408, convex hull=3300, v0=0) XL defect detected... This has been running for more than a day. How can I fix this error? Please give me some commands to solve this issue. Looking forward to hearing from you Thanks and Regards Devika K

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Tuning WM threshold
by Wright, Paul 31 Jan '20

31 Jan '20

External Email - Use Caution Dear FreeSurfer experts I am a relative novice with FreeSurfer. I am reprocessing some older images with v6.0 that were previously processed with v5.3. In the newer batch, the GM-WM boundary is wider and the pial boundary is pushed out, but the newer version does a better job in the hippocampus. I am trying to figure out what parameters might differ between versions so I can get a cortical reconstruction as well as hippocampal segmentation. Both batches used plain vanilla recon-all -all. The attached figure shows v5.3 on top and v6.0 below, with aseg.mgz over T1.mgz. I used an example that as well as thin cortex in the new version, shows a hippocampal error in the older version. (The slices are aligned at the hippocampus, but the pitch is slightly different so they don't line up more superiorly.) >From the T1, it looks like the step that sets white matter to 110 is more aggressive in 6.0. I looked through recon-all.cmd and noticed both normalization steps include the -mprage flag in 6.0 not 5.3.Could this be the why the results differ? (The images are SPGR not MPRAGE.) Looking at help for mri_normalize it doesn't mention this flag or how to switch it off, so I'm stuck here. Of course, it might be something else, not the -mprage flag. I'd much appreciate any guidance from the list. Best wishes Paul Paul Wright, PhD<http://kclpure.kcl.ac.uk/portal/p.wright.html> Postdoctoral Researcher, Department of Neuroimaging King's College London Maurice Wohl Clinical Neuroscience Institute 125 Coldharbour Lane London SE5 8NU Desk: +44 20 7848 8579 Mobile: +44 7491 905754 Email: p.wright(a)kcl.ac.uk

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Re: [Freesurfer] Error Bad CPU
by fsbuild 30 Jan '20

30 Jan '20

External Email - Use Caution Hello Phillip, If you run the following command on that file - which is from the 6.0.0 freesurfer release, $ file /Applications/freesurfer/tktools/tkregister2.bin I think you will see that it reports it is a i386 binary - which is 32 bit - and cannot run on Catalina.  That is also why you get bad CPU type, % file tkregister2.bin tkregister2.bin: Mach-O executable i386 % ./tkregister2.bin ../tkregister2.bin: Bad CPU type in executable. The last version of MacOS that can run 32 bit binaries is 10.14, Mojave, but with Mac OS 10.15 (Catalina) none of the old 32 bit binaries will run.   So if you need to be compatible with running the 6.0.0 freesurfer release, then I suggest you look into reverting back to the previous version of the OS you were running before the upgrade, i.e., hopefully you made a backup before upgrading.  Or if you have 10.13 (High Sierra), 10.12 (Sierra), or older, etc., that would work as well. - R. On Jan 30, 2020, at 10:50, Philipp Barzyk <philipp.barzyk(a)uni-konstanz.de> wrote:       External Email - Use Caution        Tanks for the quick reply.what exactly do you mean by all FS executables? It happens for various commands I am using but they all work on my Imac.I am working from a 2019 macbook air using catalina, and installed it myself. The imac where it works is from 2013 and runs on Mojave.Greets,PhilippOn 30.01.20, 16:31, "Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote:   Hi Philipp   does this happen for all the FS executables? What kind of machine are you    trying it from and who installed it? Sounds like you are on a mac and    maybe trying to use a version installed for a different kind of computer   cheers   Bruce   On Thu, 30 Jan 2020, Philipp Barzyk    wrote:       External Email - Use Caution        Hello,I am new to freesurfer and currently analysing and working on fMRI Data formy master thesis. I’ve come to an issue, that I can’t seem to solve.The following error occurs and I cannot find a threat or forum entry thatsolves it. /Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type inexecutable.It would be great if you could help me figure out a solution. Thanks in advance,Philipp Barzyk_______________________________________________   Freesurfer mailing list   Freesurfer@nmr.mgh.harvard.edu   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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(no subject)
by fsbuild 30 Jan '20

30 Jan '20

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format bvalues bvectors tracula
by Renew Andrade 30 Jan '20

30 Jan '20

External Email - Use Caution Dear FreeSurfer experts:I have tried to run tracula -prep but I cannot get to no where for the moment. I keep receiving this error. I assumed numbers had to be aligned in rows and columns. But none either that or one space in between seems to work. I don't know what format means with respect to bvalues o bvectors. It is not clear enough to me in the tutorial how do I have to fix the issue. Sincerely, Andrade. root@andraderenew:/home/andraderenew# trac-all -prep -c '/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/dmrirc.IXI' Too many ('s. INFO: SUBJECTS_DIR is /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed INFO: Diffusion root is /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed Actual FREESURFER_HOME /usr/local/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /Applications/freesurfer trac-preproc -c /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/dmrirc.local -log /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.log -cmd /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections mié ene 29 17:42:22 CET 2020 mri_convert --bvec-voxel /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998725, -0.0503472, 0.00377193) j_ras = (-0.0504772, 0.994141, -0.0955763) k_ras = (-0.00106217, 0.0956448, 0.995415) writing to /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz... cp /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/bvec/gradients.txt /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.bvecs ERROR: Must specify input table of b-values Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at mié ene 29 17:42:22 CET 2020

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Error Bad CPU
by Philipp Barzyk 30 Jan '20

30 Jan '20

External Email - Use Caution Hello, I am new to freesurfer and currently analysing and working on fMRI Data for my master thesis. I’ve come to an issue, that I can’t seem to solve. The following error occurs and I cannot find a threat or forum entry that solves it. /Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable. It would be great if you could help me figure out a solution. Thanks in advance, Philipp Barzyk

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