Freesurfer

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30132 discussions

Freesurfer skullstripping error
by LIN, Yezhe 30 Nov '20

30 Nov '20

External Email - Use Caution Dear Freesurfer users, Hope this finds you well. I preprocessed our dataset with recon-all <subj> -s <subj> -all -qcache and found a number of our subjects had different levels of skullstrip errors. I tried fixing them by a couple of different approaches, such as -gcut and adjusted watershed threshold, but they both failed to fix the overlapping of dura mater (Fig1 and 2). I tried two methods on different subjects and received the same outcome. I wonder if you have any ideas to fix this error. At this point, for some who had less skullstripping, I can erase them manually and run -autorecon-pial or -make. But for the others with multiple locations of skullstripping (like Fig 3 and 4), do you have any ideas on how to approach to them at a systemic level? Also I found the skullstripping error in over half of our subjects, is it normal that we have a such proportion? Thank you so much! ------------------ Best regards, Yezhe Yezhe Lin, MD MMed  (she/her/hers) Postdoctoral Associate, Department of Psychiatry University of Rochester Medical Center yezhe.lin.bee(a)gmail.com Twitter: @LinYezhe | LinkedIn | Researchgate  

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Re: [Freesurfer] arguments to use after pial edits
by Darko Komnenić 30 Nov '20

30 Nov '20

External Email - Use Caution Thanks Matt! Should I also add the -autorecon3 flag, or does that get performed automatically if I put in "autorecon2"? Best, Darko > Message: 4 > Date: Mon, 30 Nov 2020 19:16:06 +0000 > From: "Glasser, Matthew" <glasserm(a)wustl.edu> > Subject: Re: [Freesurfer] arguments to use after pial edits {Disarmed} > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <274FD511-F94F-4BC1-AE0C-804F1A6A3A24(a)wustl.edu> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > I find the recon-all table to be helpful: > > > http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc… > > In this case, you probably need to run -autorecon2, as all subsequent > steps are affected by the brainmask.mgz file. > > Matt. > > >

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Freesurfer skullstripping error
by LIN, Yezhe 30 Nov '20

30 Nov '20

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arguments to use after pial edits {Disarmed}
by Darko Komnenić 30 Nov '20

30 Nov '20

External Email - Use Caution Dear Freesurfer experts, I am using Human Connectone Project pipelines to calculate cortical myelin levels. These pipelines use Freesurfer 6. Since certain subjects' brain surfaces had some chunks and spikes sticking out, I edited the brainmask.mgz file for those subjects as described in this tutorial. https://secure-web.cisco.com/134OA5xpyRuAJ4raLibeAZDGkJ8VFvtiCm69m7hXhYD442… To get the myelin maps again, I got the instruction from the HCP mailing list that I should call again the FreeSurferPipeline script, but add the --existing-subject and --extra-reconall-arg flags. If I understood correctly, after --extra-reconall-arg flag, there should be an equal sign, and then keywords that specify which recon-all stages I want to run. Could you please tell me what those stages are, i.e. what keywords I should use after the equal sign? I want to keep the brainmask.mgz file that I edited, and then repeat all the steps that happen after braimask.mgz is generated. I was referred to the FS tutorials/wiki at the HCP mailing list, but I would like to double-check with someone here. Based on the tutorial link above, it seems this should be "-autorecon-pial -subjid pial_edits_before", but I'm not sure if this would be applicable in this case. Thanks in advance and I hope my question wasn't too confusing. Best, Darko

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Sources Sought: Octave/MATLAB programmer {Disarmed}
by Anderson M. Winkler 30 Nov '20

30 Nov '20

External Email - Use Caution Dear all, The NIMH/NIH is looking for a skilled Octave/MATLAB programmer, with knowledge of multivariate statistics, to implement inference for canonical correlation analysis (CCA) using permutations, as described in the recent paper (https://secure-web.cisco.com/1OvbxEv9_JHQute8AUV1-CRpI494R210wv39uPXMnlrig7…) together with other features that have already been published and which are part of PALM, as described in the "Sources Sought" notice linked below: https://secure-web.cisco.com/1fHXlDSQEyeCMPT25xy9Gg_S11v-upDxypVxM2AtRSYwhk… Note: - The search is open to persons or businesses. - The search is not limited to US citizens or to vendors based in the US. - The prospective vendor must have a Data Universal Numbering System (DUNS) number and an NATO Commercial and Government Entity Code (NCAGE code). - The prospective vendor must have either a Social Security Number (SSN) or a Tax Identification Number (TIN). - This is not employment or scholarship, but provision of a specific service to the US government. Please, read thoroughly the Sources Sought page in the link above. If you have availability and capability to perform this potential requirement, please contact Mr. Thien Nguyen (thien.nguyen2(a)nih.gov, +1-301-827-0914). All the best, Anderson

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Multiple regression analysis
by Marina Fernández 30 Nov '20

30 Nov '20

External Email - Use Caution Dear all, I am doing a multiple regression analysis with 3 covariates of interest. I know that for testing two-way and three-way interactions I must create new variables by multiplying the covariates of interest. As Freesurfer transforms continuous variables to z score before applying statistic, is it correct to transform to z score the result of the previous multiplication? I am asking this because the result of multiplying two z transformed variables would be different. Thanks a lot in advance. Marina

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mri_surf2surf Cannot allocate memory
by 1248742467 30 Nov '20

30 Nov '20

External Email - Use Caution Hello,Fs When I used mri_surf2surf command to template the lh.thickness to fsaverage5 space, the error appeared: Command: mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval thickness --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/thickness --trg_type curv --hemi lh Error message: Reading source surface reg /home/tj/application/freesurfer/subjects/OASIS-TRT-20-1/surf/lh.sphere.reg TAGskip: tag=1601402226, failed to calloc 1931488256 bytes! Do you know how to salve it? The memory is : tj@bme01:~/application/freesurfer/subjects$ free               total        used        free      shared  buff/cache   available Mem:      131673804     1398160    79091688        2416    51183956   129212776 Swap:       8388604      169108     8219496 Looking forward to your reply.

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what command can be used to template .vtk file to fsaverage5 space?
by 1248742467 30 Nov '20

30 Nov '20

External Email - Use Caution Hello, what command can map VTK file to fsaverage5 space? I want its vertex number to be 10242. If you know, please give me an example. Looking forward to your reply

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Re: [Freesurfer] Longitudinal pipeline {Disarmed}
by vittal korann 30 Nov '20

30 Nov '20

External Email - Use Caution No problem, thanks! So I shall send an email only to freesurfer or would it fine if I put you in cc? With regards Vittal On Mon, Nov 30, 2020 at 4:25 PM Diers, Kersten /DZNE <Kersten.Diers(a)dzne.de> wrote: > Hi Vittal, > > Sorry, I can only help on the public freesurfer list, so I suggest moving > the discussion back to there. > > Best, > > Kersten > > Am 27.11.2020 um 18:21 schrieb vittal korann <vittalkorann(a)gmail.com>: > > Hi Kersten > > Thank you for kind response. > > I think we need to talk about the design matrix X first (sorry, I did not > look at your xlsx file; I think it's probably better to send simple csv > files if at all). > I attached longitudinal data in csv format. > > Besides the covariates that you mention, the matrix needs to contain an > intercept, a variable for ?time?, a variable for ?group? (assuming you have > a control group also), and a group-by-time interaction term in order to > asses differential change over time (again, if you have a control group). > I do not have a control group. Right now I have only schizophrenia > patients who underwent 2 scans: first is baseline and second one is after 3 > months of yoga therapy. Wish to know the how can I proceed with my availabe > data. > > Just to make sure: ?age? should be ?age at baseline? (i.e. constant across > time per subject), otherwise it will be confounded with time. > Yes, I used same across the study. > > Could you review (and possibly adapt) your design matrix X with respect to > which columns it contains, and write it in the reply? > I tried but couldn't get there. > > Looking forward to your response. > > Thanks, > Vittal > <longitudinal_data.csv> > > > -- > Kersten Diers > Image Analysis Group (AG Reuter) > German Center for Neurodegenerative Diseases (DZNE) > B.1.114 | Building 99 | Venusberg-Campus 1 | 53127 Bonn | Germany > https://secure-web.cisco.com/17CxNooomAxq34c9Xe027kzVg8TPcPTffQaYq5Q3lzWgiM… > Phone: +49 / 228 / 43302 - 381 > >

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lme_mass_fit_Rgw will only fit 20 % and then it quits using Matlab 2020b
by Knut J Bjuland 30 Nov '20

30 Nov '20

External Email - Use Caution Dear freesurfer experts When I run lme_mass_fit_Rgw it stop fitting after i have runed 20 % as seen below. I have listed freesurfer matlab toolbox first in the Matlab 2020b path list. I am running on Fedora 33 and the mgh files work when I am running the same script on a macbook. Are there any step I can take to debug this issues? Region 4214: Convergence at iteration 9. Initial and final likelihoods: 3004.2484, 3047.3654. Region 4227: Convergence at iteration 15. Initial and final likelihoods: 2466.513, 2550.6373. Region 4234: Convergence at iteration 16. Initial and final likelihoods: 2091.6167, 2576.1704. Region 4247: Convergence at iteration 11. Initial and final likelihoods: 1638.1748, 1830.6099. Region 4254: Convergence at iteration 11. Initial and final likelihoods: 1963.5263, 2122.7052. Region 4267: Convergence at iteration 7. Initial and final likelihoods: 1917.7245, 1924.1933. Region 4274: Convergence at iteration 15. Initial and final likelihoods: 1787.8884, 1895.3745. Region 4287: Convergence at iteration 6. Initial and final likelihoods: 1935.1202, 1950.6581. Region 4294: Convergence at iteration 5. Initial and final likelihoods: 2173.2547, 2185.9629. Region 4307: Convergence at iteration 4. Initial and final likelihoods: 1025.3896, 1058.5496. Region 4314: Convergence at iteration 13. Initial and final likelihoods: 1209.8828, 1245.91. Region 4327: Convergence at iteration 26. Initial and final likelihoods: 1132.3554, 1321.7057. Region 4334: Convergence at iteration 9. Initial and final likelihoods: 1157.4764, 1196.4451. Region 4347: Convergence at iteration 7. Initial and final likelihoods: 1432.242, 1437.6161. Region 4354: Convergence at iteration 11. Initial and final likelihoods: 1187.0457, 1282.0549. Region 4367: Convergence at iteration 8. Initial and final likelihoods: 1340.9078, 1494.0789. Region 4374: Convergence at iteration 8. Initial and final likelihoods: 1071.3221, 1095.6163. Region 4387: Convergence at iteration 11. Initial and final likelihoods: 1202.6703, 1227.2202. Region 4394: Convergence at iteration 9. Initial and final likelihoods: 1067.2966, 1100.0462. Region 4407: Convergence at iteration 12. Initial and final likelihoods: 1190.4148, 1221.8727. Region 4414: Convergence at iteration 5. Initial and final likelihoods: 1190.0332, 1193.3426. Region 4427: Convergence at iteration 10. Initial and final likelihoods: 1295.3867, 1416.8343. Region 4434: Convergence at iteration 14. Initial and final likelihoods: 1479.4723, 1498.5227. Region 4447: Convergence at iteration 4. Initial and final likelihoods: 492.8232, 495.8952. Region 4454: Convergence at iteration 4. Initial and final likelihoods: 345.9289, 350.5215. Region 4467: Convergence at iteration 4. Initial and final likelihoods: 420.0601, 420.7848. Region 4474: Convergence at iteration 5. Initial and final likelihoods: 543.539, 554.8185. Region 4487: Convergence at iteration 4. Initial and final likelihoods: 425.3509, 428.4245. Region 4494: Convergence at iteration 3. Initial and final likelihoods: 458.8256, 459.5319. Region 4507: Convergence at iteration 3. Initial and final likelihoods: 372.6527, 373.0735. Region 4514: Convergence at iteration 5. Initial and final likelihoods: 389.5679, 392.0076. Aproximate percentage of fitted locations: 100% Parallel pool using the 'local' profile is shutting down. Summary: Algorithm did not converge at 0.022139 percent of the total number of regions. Elapsed time is 3.7353 minutes. Saving output ...

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