Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

Sulcus depth
by Hanbyul Cho 28 Sep '16

28 Sep '16

Dear FreeSurfer Team, I have questions about the sulcal depth. 1) I heard that the output/surf/?h.sulc is showing the sulcal depth. Is it correct that the sulcal depth measure unit is normalized z-score, mm? And is it correct that the (-) values of sulcal depth mean gyral region (green), and (+) values mean sulcal region (red)? 2) I wonder if ?h.sulc is based on white matter surface or pial matter surface. 3) I analyzed the sulcal depth by vertex-level. if the results include the sulc (-) values region, Is it meaning that the gyral height? 4) I wonder the method/commands for extracting the sulc value by label-level. 5) Could you let me know the recommended smoothing option if it possible? (e.g. --fwhm-trg [N]) I appreciate your help. Thank you. Han Byul Cho

2 3

Co-registering different source data
by Crawford, Anna 28 Sep '16

28 Sep '16

Hello, I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface? Thanks, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall
by GAJENDRA KATUWAL (RIT Student) 28 Sep '16

28 Sep '16

Hello FreeSurfers, I am considering using Freesurfer recon-all for segmentation of T1 brain MRIs of young subjects (1-4 years). I am planning to use a Freesurfer compliant pediatric template to maximize the segmentation accuracy. In the publication titled *A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0–2 year age range (* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/) by *Katyucia de Macedo Rodrigues, Emma Ben-Avi, Danielle D. Sliva, Myong-sun Choe, Marie Drottar, Ruopeng Wang, Bruce Fischl, Patricia E. Grant,and Lilla Zöllei, * it has been mentioned that "Furthermore, we are also planning on making an atlas generated from our training data sets available to the scientific community (as part of the FreeSurfer package), which can serve as a template in structural and functional studies and as a teaching tool for trainees." Has the pediatric template been released yet? Is there anyway the pediatric template can be accessed if it has been released? Is it available in the dev version or upcoming Freesurfer 6? Regards, Gajendra Jung Katuwal PhD Candidate in Imaging Science

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optseq help
by Alexandre Obert 28 Sep '16

28 Sep '16

Dear all, I would like to optimize my design by inserting null-events between my trials (in order to better catch the HRF shape with reasonable duration of the experiment) using optseq. I'm not very familiar with this useful tool and I wonder if you could check my setup? Here my design : I've got 12 trials per run (2 runs per participants). Each of my trial is 34s long and is composed as follow : -An instruction reminder screen of 4s -A video stimulus of 12s to 20s. This screen will be my "stimulus of interest". It's followed by a fixation cross in such a way that their cumulated durations will not exceed 20s -A question about the video followed by a fixation cross in such a way that their cumulated durations will not exceed 20s. -A jitter (a fixation cross), determined by optseq It's a 2 (A1; A2) x2 (B1; B2) design and I'm interested in these following contrasts: A1 vs A2 B1 vs B2 (The interaction contrast will have an exploratory value in my analysis.) In order to determine the jitters and the order of the stimuli, I set the optseq as follow: --ntp 210\ --tr 2\ --psdwin 0 40 1\ --ev evA1B1 34 3\ --ev evA1B2 34 3\ --ev evA2B1 34 3\ --ev evA2B2 34 3\ --ecv 1 1 -1 -1\ --evc 1 -1 1 -1\ --nsearch 10000\ --nkeep 3 I'm not very confident with my setup and if it's correct? I also wonder if I correctly set the ev durations and the psdwin. The stimulus of interest is the video but I set the ev using the trial duration in order to obtain ITI jitters and psdwin to the trial duration. This results in a poor efficiency and I wonder if it's possible to better optimized this design... Any help will be appreciated... Regards, Alexandre

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monte carlo continue/ desktop restarted
by miracle ozzoude 28 Sep '16

28 Sep '16

Hello experts, I was running 10000 monte carlo simulation before my desktop automatically restarted, does anyone know a command to continue from where it stopped? The simulation for left hemisphere stopped at 9146/10000 and right hemisphere at 9125/10000. Thank you Paul

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Question about mri_glmfit
by kinson li 28 Sep '16

28 Sep '16

*Hello,* *I would like to conduct an analysis using mri_glmfit but I'm getting this error:* *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08* *I am appreciated you can help me solve this problem. * *My command was:* mri_glmfit --y age9vs8ml01.mgh --fsgd new.fsgd dods --C age9vs8mlmatrix.mtx --surf fsaverage lh --cortex --glmdir glmdir.age9vs8ml Design matrix ------------------ 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Thanks Jincheng.

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Re Re Re Re: Question regarding mri_convert
by Tamara Tavares 28 Sep '16

28 Sep '16

The differences have been found in the outputs from the aseg file. Particularly, I am interested in the ventricles and the intracranial volumes. I have loaded both anatomicals in FreeView and toggled between them and have found no differences visually. I have attached the files (Via Google Drive since they are large). They are from the same participant. Thank you again, Tamara rawavg_MriConvert.mgz <https://drive.google.com/file/d/0B2XDrkcQhdARTFdYZHpwR2doTXc/view?usp=drive…> rawavgSlicer4.mgz <https://drive.google.com/file/d/0B2XDrkcQhdARV1dtZW1PZ1Z1ODA/view?usp=drive…>

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Anatomy File Orientation Question
by Sepeta, Leigh 28 Sep '16

28 Sep '16

Hi all, Sorry to re-post: I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it (along with some ROIs from FreeSurfer) to the same subject's mprage already processed (coregistered to functional data) in SPM. To do this, I used: mri_convert brainmask.mgz brainmask.nii.gz (then used gunzip) and then looked at the brainmask and mprage in SPM and they both seem to be oriented correctly (left is left, right is right for each one--using anatomical landmarks as the guide). However, in reading up on this topic, many people advise using commands like these (often with RAS) when converting mgz to nii: mri_convert --in_type mgz --out_type nii --out_orientation RAS brainmask.mgz brainmask.nii.gz OR mri_convert --out_orientation RAS -rt nearest --reslice_like <reference.nii or reference.nii.gz> <input.mgz> <output.nii> OR mri_convert -rl rawavg.mgz -rt nearest brainmask.mgz brainmask.nii.gz Are any of the options (-rl, RAS, etc) in the last 3 commands listed necessary when going between mgz/nii for freesurfer to spm analyses if you know that the mgz and nii files are in the same orientation? Thank you, Leigh <mailto:lsepeta@childrensnational.org> ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

2 1

REPOST cluster feature extraction from qdec output
by Damien MARIE 28 Sep '16

28 Sep '16

Dear FreeSurfers, Sorry for the repost. I’m still trying to extract the residuals of cortical surface area from a qdec analysis with two factors (2 levels) and 2 covariates. I tried this command line: mri_segstats --in /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh --sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf RH_Dys-CT_CSA_AgeGenderWRCSA.dat I’ve got a text file with 9 columns (number of clusters) and 69 lines (number of subjects). Now I am not 100% sure it’s really the residuals (y.mgh) so I would be glad if somebody could tell me please. Best, Damien Original post: Dear experts, I would like to know what is the best and simplest way to extract cortical surface area and thickness from clusters obtained after a Monte Carlo correction. This is a group comparison I did with qdec including gender as discrete variable + age and mean thickness or whole hemispheric surface area as nuisance factors, so I would like to get the feature residuals after the removal of the covariate effects. I am sorry, I saw several posts about that but for me it’s not completely clear what command line I should use to get tables for this… Thank you and best, Damien Damien MARIE Post-doctoral Fellow damien.marie(a)unige.ch +41 22 379 08 49 ----------------------------------------------------------------------------------------- Brain and Language Lab Department of Clinical Neuroscience Biotech Campus 9 Chemin des Mines 1202 Genève http://www.brainandlanguagelab.org -----------------------------------------------------------------------------------------

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TRACULA results
by Kang, XJ 28 Sep '16

28 Sep '16

Hi, I downloaded FreeSurfer development version built on Sep 20. Then I ran the "trac-all" for the same set of DWI data four times. The volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, are different for each run. The maximum differences can be upto +-90% for volume, +-10% for FA_avg. Any ideas for the inconsistency? Thanks. XJ Kang

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Freesurfer September 2016