Freesurfer

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30078 discussions

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.

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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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Re: [Freesurfer] Freesurfer Digest, Vol 151, Issue 30
by KALEY E ELLIS 28 Sep '16

28 Sep '16

Hi Ruopeng, When I try to open it, this is part of the error message that appears: freeview -v 2000_2/mri/T1.mgz 2000_2/mri/brainmask.mgz:colormap=heat:opacity=0.4 libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error: BadValue (integer parameter out of range for operation) 2 Extension: 150 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: BadMatch (invalid parameter attributes) 8 Extension: 150 (Uknown extension) Minor opcode: 11 (Unknown request) Resource id: 0x6000b8 If I run glxgears, this appears: [edwards@guero ~]$ glxgears libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 28 Current serial number in output stream: 30 [edwards@guero ~]$ Thank you! Kaley Message: 6 Date: Fri, 23 Sep 2016 18:53:45 -0400 From: Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freeview display problem To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <732E27D8-179E-4B66-8762-7BF26C1DFF81(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Is there any error message on the terminal? What happens if you run ?glxgears? command? Does it run? Best, Ruopeng > On Sep 23, 2016, at 4:35 PM, KALEY E ELLIS <keedwards2(a)wisc.edu> wrote: > > Hello FreeSurfer Developers, > > I am attempting to open freeview to view the brainmask on a subject in our study. Everything looks normal, except there is no image displayed (see attachment). Could you please let me know how I can fix this? > > Thank you, > Kaley > > Associate Research Specialist > Center for Healthy Minds > Waisman Center for Brain Imaging and Behavior > University of Wisconsin-Madison > <Screen Shot 2016-09-23 at 3.34.25 PM.png>_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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TR: volume to surface for ROI already in orig space
by Alain Imaging 28 Sep '16

28 Sep '16

________________________________ De : Alain Imaging <alain_imaging(a)outlook.com> Envoyé : lundi 26 septembre 2016 17:17 À : freesurfer(a)nmr.mgh.harvard.edu Objet : volume to surface for ROI already in orig space Hi everyone, I've used a couple of ROIs that have been drawn in the mni space for connectivity analysis. Since I have my connectivity results shown on a surface, I want to show the ROIs in the same way. I have checked with freeview, and the ROIs are correctly placed in the fsaverage/orig.mgz space. I wanted to use mri_vol2surf in order to reach my aim, however this command require a transformation matrix, and in this particular case I don' really know which one to use, as I don't want to change space. I thought that maybe i could provide an identity matrix, but I don't know what would it be an acceptable format for it. Have you got any suggestion ? Alain

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