Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

4 4

Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

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group analysis of large data sets
by Wang, Xin 22 Apr '20

22 Apr '20

Hello, FreeSurfer Group, What is the maximal matrix size for glm_fit process? How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes? Thank you. Xin

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Course in Advanced Neuroimaging (Barcelona)
by Erick Canales 20 Sep '19

20 Sep '19

Dear colleagues, I am pleased to announce our upcoming Course in Advanced Neuroimaging held annually in Barcelona. It takes a practical approach and does not require qualifications or previous experience in neuroimaging. It will be taught in Spanish. The multidisciplinary programme provides thorough training in the analysis of brain images from different MRI modalities and data modeling techniques, including voxel-based morphometry, cortical thickness, diffusion tensor imaging, fibre tracking, functional MRI and brain connectivity, as well as the statistical methods behind these techniques including elements of meta-analysis, and more. The course consists of a five-month online theoretical module (starting on November 6th) and a period of practical face-to-face training (split between two days in November and two weeks at the end of April) held in Barcelona. For further information, please visit the website: www.cursoneuroimagen.com Best regards, Erick J. Canales-Rodríguez Joaquim Radua Raymond Salvador Edith Pomarol-Clotet FIDMAG Research Foundation and Sociedad Española de Neuroimagen *www.fidmag.com <http://www.fidmag.com/>*

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T2 seq. for hippocampus ??
by Anik Dar 25 Jun '19

25 Jun '19

External Email - Use Caution Hi All, I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1 cubic mm MPRAGE. Can you please let me know whether I should use only T1 or should I use one of the additional seq. for hippocampal subfield segmentation ? cheers Nik

3 4

mri_glmfit-sim error correcting for MC for LGI analysis
by C.P.E. Rollins 18 Apr '19

18 Apr '19

External Email - Use Caution Dear Freesurfer Developers, I have a 2-part question: 1) I was advised to use permutation to control for multiple comparisons in an LGI analysis, would you mind elaborating how to do this in command line (in terms of command and parameters)? 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error (attached). I was wondering if you might have any advice? The file /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can view it in freeview. Many thanks, Colleen

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Beta extraction
by Jahan, Bushra 28 Feb '19

28 Feb '19

I am wondering how to extract beta values from the clusters of task functional data, particularly output of the multiple comparisons correction? Aava Jahan

2 3

partial FoV - registration failure
by Francesca Strappini 19 Feb '19

19 Feb '19

External Email - Use Caution Dear freesurfer experts, I am using freesurfer to analyze some fMRI data collected on two monkeys. My runs have a partial field of view, since just the posterior part of the brain was scanned. Unfortunately, no full-head EPI was collected. The registration between the processed functional data and the T1 is bad. All the values in the register.dof6.mincost file are above 0.8 and also visually I can see some mismatch. I though to run bbregister, could you suggest me which is the best procedure and which steps of the preprocessing I should re-run after? Thanks -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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updateing freesurfer.
by Aaron Tanenbaum 22 Jan '19

22 Jan '19

External Email - Use Caution I tried updating freesurfer 6.0 using the command fs_update. I get the following output. > Build is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > Running this will update some of your freesurfer binaries. > > Shall I proceed? [y/n/Abort]: y > > rsync -zbrlv --progress --suffix=.1539713469_bak rsync:// > surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Linux-cen… > /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_6_0/ > receiving incremental file list > rsync: change_dir > "/dist/freesurfer/patches/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c" > (in pub) failed: No such file or directory (2) > > sent 8 bytes received 173 bytes 362.00 bytes/sec > total size is 0 speedup is 0.00 > rsync error: some files/attrs were not transferred (see previous errors) > (code 23) at main.c(1655) [Receiver=3.1.1] >

2 1

mris_apply_reg failing for area/volume
by James Michael Roe 14 Jan '19

14 Jan '19

External Email - Use Caution ? Dear freesurfer experts I'm running the following commands to register RH area and volume files per sub to both hemispheres of a symmetrical template following Xhemi routines. The commands have already worked for many subs, but are failing to write the target file for a number of others (and all run fine without the --jac flag) #right to left mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \ --jac #right to right mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \ --jac The error is not template-specific as the output is the same using fsaverage_sym Attached is the log file. Thanks in advance! ?- James

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Freesurfer November 2018