Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Flywheel is Hiring
by Andy Worth 11 Nov '20

11 Nov '20

External Email - Use Caution Hello Freesurfer and Neuroinformatics Experts, At Flywheel <https://secure-web.cisco.com/11jOUe69pAmrkatJBPAWf3tKPRB9iRsFQ1T1VU_vkte1Jm…>, we are developing a data sharing and distributed computing platform serving biomedical imaging and life sciences research. We are hiring <https://secure-web.cisco.com/1fl-xuQEhMmhR5ixf6wZmLmzBbB3uWIuQ-GPTt40NoYIdz…> to grow our Scientific Solutions Engineering team of PhDs and Engineers. Specifically, we are looking for coders with mad skills in reproducible scientific cloud computing (python, Docker), workflow / pipeline implementation (NiPype, CWL, Toil, Cromwell, Snakemake, Nextflow, Galaxy, SevenBridges, Arvados, COINSTAC, etc.), Machine Learning workflows (Kubeflow, Airflow, SKLearn, MLflow, etc.), and a research background in medical imaging or bioinformatics. Knowledge of the Brain Imaging Data Structure (BIDS) standard is a huge plus. Compensation is competitive, company is inclusive, and we are open to hire remotely (half of us are). If you are interested, please have a look at our job ad here <https://secure-web.cisco.com/1fl-xuQEhMmhR5ixf6wZmLmzBbB3uWIuQ-GPTt40NoYIdz…>. If you know someone who might be interested, please pass along the link. We really do cool things. Cheers, Andy Worth Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1p9cujki7p3fAOSgSS0m9jUN6Ox0zw7VzFNuhwyeKuHQM59…>

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mris_anatomical_stats error: stating file
by Chan, Shi Yu 11 Nov '20

11 Nov '20

Hi FreeSurfer Developers, I'm trying to calculate cortical thickness statistics from the Yeo 17 Network cortical parcellation and have used mri_surf2surf to get the .annot files for each subject. However, when I run mris_anatomical_stats, I get an error: ERROR: stating file subjects_dir/sub-001/label/sub-001/label/rh.Yeo2011_17Networks_N1000.annot It seems like the "sub-001/label" portion is repeated. The command I use for mris_anatomical_stats is: mris_anatomical_stats -th3 -mgz -cortex sub-001/label/lh.cortex.label -f sub-001/stats/lh.Yeo_17Networks.stats -b -a sub-001/label/lh.Yeo2011_17Networks_N1000.annot sub-001 lh white The command still runs despite the error, and outputs the stats files accordingly, so I'm not sure how important this error is, but I can't figure out how to fix it. This is a similar issue to: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67595.html but I've checked $SUBJECTS_DIR, and it is correct. If I run ls $SUBJECTS_DIR/sub-001 I'll see all the different sub-folders in sub-001 (mri stats labels etc) Any help would be much appreciated! Thank you!

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Canon MRI morphometry protocols
by 南修司郎 11 Nov '20

11 Nov '20

External Email - Use Caution Dear experts We are trying to take MRI with Canon magnetic resonance for FreeSurfer analysis. I'd appreciate If you could give me the recommended T1 structural protocol for Canon scanners. Thank you in advance. Shujiro Shujiro Minami M.D., Ph.D. Dpt. of Otolaryngology National Tokyo Medical Center 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan E-mail shujirominami(a)me.com

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Re: [Freesurfer] Editing Issues
by Harriet Cornwell 11 Nov '20

11 Nov '20

External Email - Use Caution Hi Jocelyn, Many thanks for your response. I just wanted to confirm a couple of things: 1. Could you advise what specific edits need to be made to the brainmask.mgz volume to fix the hole in the WM, i.e., do we need to add GM, delete GM? We are used to only editing the brainmask.mgz volume when there is an issue with the GM so just want to make sure that we are fixing this hole in the WM correctly. 2. If we are only interested in cortical thickness, surface area, volume and gyrification, can you confirm that we do not need to spend time editing issues around the ventricles? Thank you in advance. Harriet PhD Student | University of Bath -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: 10 November 2020 17:00 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 201, Issue 15 CAUTION: This email came from outside of the University. To keep your account safe, only click on links and open attachments if you know the person who sent the email, or you expected to receive this communication. 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/13lQ7nDnK-H3JJGsgcPOLKvh6e3uFroou_3nPyQucZyx16… 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. BIDS-ASL request for comments - closes THIS Friday (11/13) {Disarmed} (Franklin Feingold) 2. Re: Editing Issues (Mora, Jocelyn S.) 3. Create new .mgz from .annot (Hyon, Justin J.) 4. eddy_correct with DTI {Disarmed} (Wei Shao) 5. Correlation between thickness and csf_measures: vector (Steve Petersen) 6. color and sign of sig.mgh data (Rovai Antonin) 7. Postdoctoral Fellowship in advanced multi-parametric imaging in Parkinson?s disease, Alzheimer?s disease, and healthy aging (Maurizio Bergamino) 8. Re: Freesurfer 7.1.0 on CentOS 8.1 {Disarmed} (Snedden, Ali) 9. Re: trac-all -bedp error after successful -prep (Michele Valotti) 10. Re: Help with mergecontrasts-sess function (Paula Maldonado) ---------------------------------------------------------------------- Message: 1 Date: Mon, 9 Nov 2020 18:28:16 +0000 From: Franklin Feingold <ffein(a)stanford.edu> Subject: [Freesurfer] BIDS-ASL request for comments - closes THIS Friday (11/13) {Disarmed} To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <FA8577FC-D779-46BC-927D-79E95EE1BFEE(a)stanford.edu> Content-Type: text/plain; charset="utf-8" External Email - Use Caution The BIDS community is preparing to merge the ASL (Arterial Spin Labeling) extension. The updated draft is available for review at: https://secure-web.cisco.com/1ITF4bOtJJcQiVKXDz67qOkjGMsukmz9eyHDd76OIYTeEM…, and comments and suggestions may be submitted on GitHub at: https://secure-web.cisco.com/1VL_oxffggPudlMHXkbtyOToPXYFpi9_8kZMHoiuC326Ky…. The community review will close on Friday (Nov 13) at 11:5 9pm PT (pacific time) This BIDS extension seeks to establish how ASL data and additional metadata are organized within the BIDS structure. This encompasses the ASL sequences provided in the consensus paper [Alsop 2014], including single- and multi-time point pulsed and (pseudo)-continuous ASL. The final review entails a two week period for public commenting, with a possibility of extension for unresolved discussion. Once public comments are concluded, there will be a one week freeze, during which only critical issues will be considered. (For more details on the release protocol, see https://secure-web.cisco.com/1A8qnp7KY-M8xxjfEiWTabhYuW0g9mTh5DrlGyQ6pc4EAy…) We look forward to hearing your feedback! The BIDS Team

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question about ventricular volume calculation
by Jiao Qing 11 Nov '20

11 Nov '20

External Email - Use Caution Dear FreeSurfer Developers: I want to calculate ventricular volume using the 'recon-all' procedure. Would you like to let me know in how the ventricular volumes were calculated? Thank you! FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform:Ubuntu 14.04. Best wishes Qing Jiao, Ph.D Department of Radiology Shandong First Medical University, China

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Recon1 command
by Kelli Ann Nini 11 Nov '20

11 Nov '20

External Email - Use Caution Greetings, esteemed Surfers! I have a .nii file that I am trying to run through recon1 and I'm not sure I have my commands correct. At first I typed this command line and received this error: recon-all -subjid 1234 -i 1234.nii -autorecon1 ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. However, if I omit the -i flag, I receive this message: recon-all -subjid 1234 -autorecon1 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /home/scanlab1/Desktop/FSTraining_2020 Actual FREESURFER_HOME /usr/local/freesurfer Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Tue Nov 3 17:46:26 CST 2020 ERROR: no run data found in /home/blah/blah/blah/1234/mri. Make sure to have a volume called 001.mgz in /home/blah/blah/blah/1234/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://secure-web.cisco.com/1UQYixkLhTyJq63goY7Pg_eCT-9bgdiZTokEQSMnHq7lBQt… Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2556 exited with ERRORS at Tue Nov 3 17:46:26 CST 2020 For more details, see the log file /home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.log To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1jEiXRrElXVtXwKhwmcYmBf1ASyXbJIhbTjDDo8znrKWXGe… It's also been approx 1 year since FS was run on our machines. Perhaps an update is needed? Thank you so much! NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!

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color and sign of sig.mgh data
by Rovai Antonin 11 Nov '20

11 Nov '20

External Email - Use Caution Hello, I am creating sig.mgh overlays in a group analysis. On this map, I can see some blue and red vertices, corresponding to negative and positive values (respectively) on the map. On the other hand, I read in the documentation that sig.mgh is a map created by computing -log(p) (base 10, whatever). That cannot be true, since 0<p<1, hence -log(p)>0. After some exploration I came up with the following guess: sig.mgh is actually -sign(z)*log(p). (That is of course very useful to quickly interpret the maps.) Question 1: is this guess correct? Question 2: where is the piece of documentation I missed where this is explained? (I am asking this because I feel like I am missing a lot on the details on the machinery behind FS commands...) Cheers Antonin Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S http://secure-web.cisco.com/10VoDNoTPVxzoJ9Ip0Jm8M6aDnd42uu8rcy8brYy_9Fx9lB… Disclaimer : http://secure-web.cisco.com/130lPkFzkXUa0jrMTavOQz200HGNhc8bjmwk_Mgl3tHuW0Q…

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Correlation between thickness and csf_measures: vector
by Steve Petersen 11 Nov '20

11 Nov '20

External Email - Use Caution Dear Freesurfer experts, I am conducting a cortical thickness study in three groups. After performing the between-group analyses, I would like to evaluate the possible correlation between cortical thickness and the levels of some csf measures. To do this I included one column in the FSGD file GroupDescriptorFile 1 Title OSGM Class N Class AD_PREC Class AD_PLUS Variables CSF_A_measure Input 4048 N 1730.00 Input 4102 N 2217.00 Input 4122 PREC 652.00 Input 4146 PREC 695.00 Input 4198 PREC 938.00 Input 5049 AD_PLUS 909.00 Input 5080 AD_PLUS 987.00 Input 5096 AD_PLUS 942.00 Input 5101 AD_PLUS 881.00 Input 5232 AD_PLUS 715.00 And so on.... In order to test the possible positive relation between the CSF_A_measure and the cortical thickness, that is, *does the correlation between thickness and csf_A_measure differ from zero?, *I would use the following vector and commands for the left hemisphere. *Question 1.* Please, can you verify if this vector and commands are correct. correlation_vector.mtx -----> 0 0 0 1 1 1 mris_preproc --fsgd J3.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage \ --hemi lh \ --out lh_J3G_thickness.10.mgh \ mri_glmfit \ --y lh_J3G_thickness.10.mgh \ --fsgd J3.fsgd \ --C correlation_vector.mtx \ --surf fsaverage lh \ --cortex \ --glmdir 01_lh_thickness_results\ mri_glmfit-sim \ --glmdir 01_lh_thickness_results \ --sim mc-z 10000 2.3 mc-z.pos \ --sim-sign pos --cwpvalthresh 0.05\ --2spaces --overwrite \ *Question 2:* I tried to run these commands with the permutation method but the terminal gave to me a warning message saying that the matrix is not orthogonal and if I really want to run the analysis I should add the --perm-force argument, in this case should I use other method or can I use the --perm-force safetely?. Thank you very much for your help in advance. Best regards, Steve,

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Create new .mgz from .annot
by Hyon, Justin J. 11 Nov '20

11 Nov '20

External Email - Use Caution Hello, I’m new to Freesurfer and am trying to learn the steps to manually label some brain regions for use in source localization in MNE. So far my understanding is that I have to create label files which contain the list of coordinates for the vertices in each region, and a color lookup table which has a list of these labels and their corresponding RGB values for display. However, there are a few pieces missing in my understanding. How would I create the label files for each brain region? For example, if I wish to combine several regions found in the Desikan-Killiany atlas, how would I get from the label files generated via ?h.aparc.annot to new label files combining several labels? Also, in order to create a source space in MNE I need a single segmented .mgz output such as aparc.a2009s+aseg.mgz. If I create a new .annot based on my new label files and lookup table, how would I obtain this volume? Thank You!

2 1

Fixed factor vs nuisance factor
by Sunil Khokhar 11 Nov '20

11 Nov '20

External Email - Use Caution Dear Experts, In QDEC, to which box should the categorical variables like gender should go to, given that gender is a variable of no interest? Should it be fixed factors box or the nuisance factors box? Thanks in advance!

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