Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Re: [Freesurfer] Recon-all log
by Bohorquez Montoya, Luisa 25 Jan '21

25 Jan '21

External Email - Use Caution Hello, no it wasn’t a T1. I am trying to process a super old data with a bad T1 (the contrast is not the best). I think the recon-all is failing in the skullstrip part. Do you have any advices on how to deal with this? I already tried changing the watershed and I don’t have success. If I change this I got same T1.mgz error. I am also trying to skull strip before the recon all. “you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz” what does it means to make a link from brainmask.auto.mgz to brainmask.mgz?? just a copy? Thanks for your help!! Luisa Bohorquez, PhD. Department of Psychiatry, Medical College of Wisconsin. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Mora, Jocelyn S." <JSMORA(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, January 19, 2021 at 12:06 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all log ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Hi Luisa, There seems to be an error opening the T1.mgz file. Is there a T1.mgz file in your mri folder? Best, Jocelyn ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Bohorquez Montoya, Luisa <lbohorquez(a)mcw.edu> Sent: Monday, January 18, 2021 10:58 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all log External Email - Use Caution Good morning freesurfer, I am new using recon all. Would you mind to help me with this error I am getting? What should I do? Attached is the log and here is my command. recon-all \ -subject ${ANATDIR} \ -i ${ANATDIR}/${subject}/*Ax_FSPGR_3D_GR.nii.gz \ -T2 ${ANATDIR}/${subject}/*Ax_T2_FLAIR_SE_IR.nii.gz \ -T2pial \ -parallel -openmp 12 \ Thank you so much for your time Luisa Bohorquez, PhD. Department of Psychiatry, Medical College of Wisconsin.

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Principle of registration to fsaverage5 space
by 1248742467 25 Jan '21

25 Jan '21

External Email - Use Caution Hello, everyone I have downloaded a folder, there's manual.annot file, but no lh.area file.  So, I created a bert from this subject use recon -all command, but there's no manual.annot file.  Can I use the manual.annot file in download folder template to fsaverage5 space as my create manual.annot? I am not sure about the principle of registration to fsaverage5 space. Note: The number of vertexs in bert and download folder are different.

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Contrast and cache for one group correlation analysis
by Sara Romanella 25 Jan '21

25 Jan '21

External Email - Use Caution To Freesurfer team, Hi everyone, sorry for bothering. I am looking for correlation analysis in a cohort of subject between cortical thickness and an external score (and corrected for age). Because I am only working on one group (with 2 covariates), I think there should be no difference between DODS and DOSS. My choice for the contrast then was (DODS by default): 0 (main class) 0 (correct for age) 1 (correlate with this score). Could you please tell me if this is right? Or because it is only one group some parameters in the cache or in the contrasts should be different? Thanking you in advance. Best, Sara Romanella

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Recon-all with Tumor lesion
by Stephan Wunderlich 25 Jan '21

25 Jan '21

External Email - Use Caution Dear all, I want to process brains with tumor lesions with the recon-all -all command. Recon-all (freesurfer version 6) gets always stucked when calling the function mris_fix_topology. It used to work with freesurfer version 4.5, but I still want to use the version 6. It does work when I first run recon-all -all until it gets stucked and calculates for several days mris_fix_topology, then cancel the command and rerun with recon-all -all -nofix. Is there a more smooth way to run recon-all for tumor lesion brains? (When I add -nofix to the recon-all command from the beginning, recon-all exits with errors, since it cannot find rh/lh.orig). Best, Steph

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Job posting for OpenNeuroPET scientific software developer position
by mganz 25 Jan '21

25 Jan '21

External Email - Use Caution The Neurobiology Research Unit at the Copenhagen University Hospital (http://secure-web.cisco.com/1uBaVtOmQFxIPXxVsxcMKYnx3ZhyCqt_iroR9g_OH777278… [1]) in Copenhagen, Denmark, is seeking an experienced and motivated scientific software developer. The applicant would work within a dynamic team of researchers with expertise in brain imaging, specifically molecular brain imaging, and will be part of the OpenNeuroPET project, which will establish a data-sharing platform for molecular imaging data. Desired skills and experience: You should have a strong knowledge in scientific software engineering and possess a PhD degree in neuroscience, computer science, statistics, mathematics, bioinformatics or a similar degree. Additionally, you should ideally have: * Experience in the use of data standardization formats, specifically BIDS * Experience in scientific management of databases * Knowledge and experience working on ethics and GDPR * Track record of working ʻopenlyʼ * Extensive programming experience including in at least one of Python, MatLab, or R as well as basic knowledge of JavaScript Hiring conditions: * Salary is competitive and will correspond to qualification * Four year position starting in spring/summer 2021 Interested? Visit https://secure-web.cisco.com/194KZSHv0mjWNYc-2Df5ReoJQ72HJ680M7fjEtdD6xIYPe… or contact me directly under mganz AT nru.dk -- Yours sincerely Melanie Ganz-Benjaminsen Asst. Prof., Researcher Direct: + 45 35 45 67 18 Mail: melanie.ganz(a)nru.dk Neurobiology Research Unit Rigshospitalet, building 6931 Juliane Maries Vej 28, 3rd floor DK-2100 Copenhagen, Denmark Phone: +45 3545 6712 Fax: +45 3545 6713 URL:http://secure-web.cisco.com/1dPj_FnvYQHJBovGl1pVSXq2nuj4ZkZ2OhkBuOPRL36… This e-mail and any attachment may contain confidential and privileged material intended for the addressee only. If you are not the addressee, you are notified that no part of the e-mail or any attachment may be disclosed, copied or distributed, and that any other action related to this e-mail or attachment is strictly prohibited, and may be unlawful. If you have received this e-mail by error, please notify the sender immediately by return e-mail, and delete this message. Links: ------ [1] http://secure-web.cisco.com/1uBaVtOmQFxIPXxVsxcMKYnx3ZhyCqt_iroR9g_OH777278…

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Thickness vs surface area
by Stephanie K 25 Jan '21

25 Jan '21

External Email - Use Caution Hello, I am performing analyses looking at brain measures for a neurodegenerative disorder. I wanted to ask whether the accuracy for surface area is as high as is for thickness? I would appreciate your advice or any references. Thanks <http://secure-web.cisco.com/1s2WxUEm6XSL6Os4QbhWGVNh9SslHbUxbpObZbT9zlKw4O9…> Virus-free. http://secure-web.cisco.com/1bMTKfkeHqBmt5B7Whj8ClEmtAkQLnLLsXYt4JTx1GtIZMK… <http://secure-web.cisco.com/1s2WxUEm6XSL6Os4QbhWGVNh9SslHbUxbpObZbT9zlKw4O9…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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beta coefficient of the fixed effects
by Marina Fernández 25 Jan '21

25 Jan '21

External Email - Use Caution Dear Doug, In addition to t and p-value, I would like to report the beta coefficient of the fixed effects in the following regression equation for the vertex showing the max statistic within the cluster that survived multiple comparison correction: y = β0 + β1*sex + β2*age + β3*(sex+age) + e I know that beta.mgh contains the beta estimates corresponding to the intercepts of male and female and the slopes of age for each sex. However, what I need is the beta corresponding to the intercept (β0), and the beta for the slope of sex (β1), age (β2) and sex*age interaction (β3). I also need the residual variance of the model (e), but rvar.mgh contains 4 values, 2 for the intercepts and another two for the slopes. I would really appreciate if you could help me to obtain this information. Thanks a lot in advance Marina

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aseg stats on 001.mgz
by dg wakeman 25 Jan '21

25 Jan '21

External Email - Use Caution Hi, I can't seem to figure out the best way to load the aseg and the raw mgz file in the same space. Is there a registration file somewhere that I can use for that. I can see that FreeView can see this, but I am having trouble figuring out the right way to do this. What I need for this one instance is just to pull the mean intensity of a label from the aseg? For future reference it would be great to know how to do this generically. e.g. if I read in the data in matlab/python, how do I line them up. Thanks Dan

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Re: [Freesurfer] Missing transformation files in
by Nederpelt, D. van (David) 25 Jan '21

25 Jan '21

External Email - Use Caution Hi Douglas, I'm sorry I did not see the reply. However, according to this FSwiki page (https://secure-web.cisco.com/1ewSiiCxfbK4xZi1tAuiwuw5w7OeKME66LJV0CpSAaOHVv… , see the information I found below) the transform file should be in the longitudinal directory, if I'm not mistaken. I ran FS 6.0.1 for a previous project and the transform files were present there. Now with FS 7.1.1 they are not present. I ran the recon-all -all -3T pipeline on two different OS and didn't get the needed .lta files. The transform files are missing for each subject I ran (448) To be sure I've attached the recon-all.log file for the cross, base and longitudinal run for one subject. Thank you for your help! Kind regards, David cd $SUBJECTS_DIR/<tpid>.long.<baseid>/mri mri_convert -ait transforms/<tpid>_to_<tpid>.long.<baseid>.lta \ -rl $SUBJCECTS_DIR/<tpid>/mri/rawavg.mgz \ -rt nearest -odt uchar \ aseg.mgz aseg-in-rawavg.mgz Message: 1 Date: Fri, 15 Jan 2021 09:24:33 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FW: Missing transformation files in longitudinal pipeline To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <821a58f9-2fa0-4db1-56fc-75e63c997019(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Are you looking in the base/mri/transforms folder? If it is not there, can you send the recon-all.log file for the base run On 1/14/2021 11:12 AM, Nederpelt, D. van (David) wrote: > > ????????External Email - Use Caution > > Hi FS-team, > > I ran a longitudinal recon-all stream(FS version 7.1.1) ?and trying to > convert the aseg.mgz back to native space. However, in the transform > file the <tpid>_to_<tpid>.long.<baseid>.lta is missing. > > This is the case for every subject I ran, while the recon-all.log > showed freesurfer finished without errors. I?ve attached the .log > file. The base dir does have the needed transform files. > > How can I resolve this and transform ROI to native space? > > Thank you in advance, > > Kind regards, > > David ******************************************* ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/1LR8PaInq9faioBV4wOz8RSwnKDDD3kmimYFmZTyHAZ63Ee… AMC disclaimer : http://secure-web.cisco.com/17sYewASoS_ayfu7I7ZppvxN_xtGM_aIVV2MP-PJ1Ab-Gxu…

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Error Using samseg
by Jesper Folsted Kallehauge 23 Jan '21

23 Jan '21

External Email - Use Caution Dear All, I have encounter an error when running samseg for a fraction of my subjects. I am very new to FreeSurfer so there is a good chance it is a rookie mistake. The error message I get is the following: Traceback (most recent call last): File "/home/frog/freesurfer/python/scripts/run_samseg", line 166, in <module> reg_only=args.reg_only File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 132, in segment return self.postProcess() File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 239, in postProcess posteriors, biasFields, nodePositions, _, _ = self.computeFinalSegmentation() File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 778, in computeFinalSegmentation posteriors = self.gmm.getPosteriors(data, priors, self.classFractions) File "/home/frog/freesurfer/python/packages/freesurfer/samseg/GMM.py", line 183, in getPosteriors posteriors = posteriors / np.expand_dims(normalizer, 1) MemoryError: Unable to allocate 7.15 GiB for an array with shape (21800066, 44) and data type float64 The it finishes without a segmentation. Does anyone know the solution to this issue ? King regards Jesper Kallehauge

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