Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

spatial scale bar question
by Nasiriavanaki, Zahra 16 Aug '19

16 Aug '19

Dear Freesurfers Hi I am trying to add a spatial scale bar to my cortical maps in tksurfer. However, as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks when you zoom in the brain. I couldn't find a scale bar option in Freeview neither. I appreciate if you could let me know how to get a scale bar. Thanks Mona

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multimodal analysis (pet and cortical thickness relationship) using --pvr
by miracle ozzoude 14 Aug '19

14 Aug '19

External Email - Use Caution Hello Experts, I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education). However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions. Thank you. Best, Paul The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14 Input YY1 g2 62 20 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvrgroup1= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvrgroup2= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education?

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Re: [Freesurfer] need for help
by Greve, Douglas N.,Ph.D. 07 Aug '19

07 Aug '19

The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > I got the mri_vol2surf output with .mgz: > > > my tksurfer command: > > tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of > mri_vol2surf was lh.inflated_MWI.mgz) > > > and the error i got: > > *freadFloat: fread failed** > No such file or directory* > > To me, opening the surfer in tksurfer is only a way to get sure my > vol2surf worked well. the main problem is i got this error for all > mris_smooth, mris_inflate, mris_sphere ... > > > Do you think that means the output of mri_vol2surf is not correct, or > otherwise i could proceed with that , even when tksurfer could not > open it, for GLM in Qdec? > > > Thanks, > > Reza > > ------------------------------------------------------------------------ > *From:* Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> > *Sent:* Tuesday, July 16, 2019 6:01:15 PM > *To:* Reza Rahmanzadeh > *Subject:* Re: need for help > what is your tksurfer command line? Also, the .w file is somewhat > obsolete (it should still work); instead you can use .mgz file (and > don't spec --paint) > > On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> Thanks Doug, >> >> >> I used the one without --inflated also, again the tksurfer could not >> open it and i got the same error. Where is the problem with my cmd.? >> >> >> In addition, i wanted to make the output of mri_vol2surf inflated >> using mris_inflate but i got the same error: >> >> *freadFloat: fread failed >> No such file or directory* >> * >> * >> *could you let me know what is the problem in registering my mwi >> volumes to surface that i getonly such errors.* >> * >> * >> *Thanks,* >> *reza >> * >> >> ------------------------------------------------------------------------ >> *From:* Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> >> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >> *To:* Reza Rahmanzadeh; Freesurfer(a)nmr.mgh.harvard.edu >> *Cc:* greve(a)nmr.mgh.harvard.edu >> *Subject:* Re: need for help >> Don't use --inflated. The inflated surface is not a biological >> surface. The default is the white surface, which is the one you want >> (--projfrac 0.5 will project it to the middle between the white and pial) >> >> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Dear Freesurfer, >>> >>> I have a batch of myelin water image (MWI) from patients and >>> controls, and trying to have inflated cortex registered on standard >>> surface for GLM (Qdec). >>> >>> With the commandlines below i get my inflated surface of MWI map of >>> my patients and controls. >>> >>> 1-using bbregister to put MWI into FS space and to calculate >>> register.dat: >>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat >>> --o mwf_FS --t1 >>> >>> 2-using mri_vol2surf to extract inflated surface of MWI: >>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>> paint--inflated (*or*--surf sphere) >>> >>> However the tksurfer could not open the inflated surface and the >>> error message is: >>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>> Probably trying to use a scalar data file as a surface!* >>> >>> I used the commandline below for #2: >>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>> mwf-lh.w --out_type paint >>> and i got the error: >>> >>> *ERROR: MRISread: file >>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many >>> more faces than vertices!** >>> Probably trying to use a scalar data file as a surface!* >>> * >>> * >>> As tksurfer could not open my surfaces with errors above, i think >>> perhaps the vol2surf procedure is not done properly. Where is the >>> problem? i need to get the inflated cortex and then putting ob >>> sphere (using mris_sphere) and the registering to standard surface >>> using mris_register for GLM in Qdec, right? >>> >>> >>> It is two weeks i am struggling with these commands, any helps >>> highly appreciated. * >>> * >>> * >>> * >>> * >>> * >>> Best, >>> Reza >>> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >

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WM surface including too much gray matter
by Brian Biekman 05 Aug '19

05 Aug '19

External Email - Use Caution To whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output. -- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman(a)uh.edu Brian.Biekman(a)times.uh.edu

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Re: [Freesurfer] Recon-all Error in output - ERROR: nu_correct
by Gregory Mierzwinski 05 Aug '19

05 Aug '19

External Email - Use Caution Hello, Even though this is an old post, the entire solution to this has not been posted and I couldn’t find it anywhere. I hit this error, and I had to (1) make sure the SUBJECT_DIR environment variable was pointing to a directory that is not on the shared Neurodebian folder, and (2) that the data given as input through `-i` was not on the shared folder. Greg

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Re: [Freesurfer] Running FSL randomise on FS cortical thickness data
by Antonin Skoch 01 Aug '19

01 Aug '19

External Email - Use Caution Dear Mark, I would suggest to use PALM instead: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed. Antonin Skoch Dear Freesurfer experts,Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple comparisons with permutation testing. We have already run about 2000 permutations, and would like to use TFCE available in randomise rather than empirical methods to set parameters such as the cluster forming threshold. So, the simple question is, how do we convert our FS format data (these are F statistics at each vertex) into a format which can be read into randomise? Thanks for any advice you can provide. Best, Mark

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UC San Diego - Postdoctoral Research Fellow Position
by Roberson, Mary 31 Jul '19

31 Jul '19

External Email - Use Caution Hello Freesurfer Community, University of California, San Diego Research Fellow Position Postdoctoral research fellow position in genomic studies of neuropsychiatric disorders at University of California, San Diego Dr. Chi-Hua Chen's laboratory is looking for highly motivated individuals to join our team for imaging genomics research in neuropsychiatric disorders and Alzheimer's disease at the Center for Multimodal Imaging and Genetics at UC San Diego. Our research projects include 1) genotype-phenotype mapping to identify genetic variants associated with brain structure in human population samples, all with MRI and genotype data; 2) translational research for genomic-guided drug target identification for brain disorders. For qualified candidates, there are excellent opportunities to pursue research interests in neuroimaging genomics, statistical modeling, bioinformatics, and brain disorders in a multi-disciplinary research setting. Salary and benefits are commensurate with research experience and accomplishments, and determined by NIH guidelines. The position is available to start immediately. The successful applicant should have: * PhD in biostatistics, bioinformatics, statistical genetics, computer science, neuroimaging or a related field. An MS or BS is acceptable if there is an exceptional record of past experience. * Knowledge of programing in Linux shell scripts, R, python or Matlab * Knowledge in biostatistics, bioinformatics or machine learning * Experience to manipulate genomic or neuroimaging datasets * Excellent analytical and problem-solving skills * Good skills in written and spoken English If interested, please email a cover letter, a current CV, and contact information for three references to Mary Roberson at: mmroberson(a)ucsd.edu. Position will be open until filled. Thank you, Mary Roberson Mary M Roberson | Executive Assistant Center for Multimodal Imaging and Genetics (CMIG), Department of Radiology UC San Diego | 9452 Medical Center Drive | MC-0841| La Jolla, CA 92037 Office: 858.534.8259 | Email: mmroberson(a)ucsd.edu<mailto:mmroberson@ucsd.edu> Drs. Ahrens | Bae | Brewer | Chang | Chen | Dale | Du | McEvoy | White [cid:image001.png@01D547AC.D4B7CCE0] The information transmitted in this e-mail is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination, or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this e-mail in error, please contact the sender and delete the material from any computer.

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How to change intensity bounds parameters in recon-all
by Caroline Chwiesko 31 Jul '19

31 Jul '19

External Email - Use Caution Dear Freesurfer experts, I have a similar problem as what was mentioned previously on this support list. I ran recon-all on all of my subjects and I am currently in the manual editing process. I noticed that for a lot of my subjects there are spots in the images where the white matter extends into the gray matter. So its looks like a systematic error with my data. I attached images of two different subjects as an example. I found the advice to change the intensity bounds parameters for mri_segment and mris_make_surfaces, but I don t know exactly how to do this. I am very new to freesurfer and I could not find the proper information on the freesurfer_wiki websites for recon-all, mri_segment and mris_make_surfaces. 1) What is exactly the parameter that I would need to change in mri_segment and mris_make_surfaces? 2) What is the recon-all command that I would need to run to change those default parameters after I made already manual changes to the brain mask (removing voxels) and added control points? Thank you very much in advance Our Freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c we run it on Linux, kernel version 4.15.0-46-generic, Ubuntu 18.04.1 LTS [image: Screen Shot 2019-07-30 at 12.09.01 PM.png] [image: Screen Shot 2019-07-30 at 12.18.32 PM.png]

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Re: [Freesurfer] Failure of mri_robust_template in fmriprep
by Frederick, Blaise B. 31 Jul '19

31 Jul '19

Ø Hi Blaise Ø * I can't even find an exit(-9) in the code. If you can track down and send us the inputs to mri_robust_template I can try to replicate it locally. Or wait for Martin to comment :) Ø Ø Bruce * Well that’s a bit disturbing… Could this be a signed vs. unsigned integer weirdness? Is there a return code of 247? If I did the math right, -9 is the two’s complement of an unsigned 247. Is there a place I could put the files so you can replicate it? I can get all the inputs. Blaise ------------------------------------------------------- Blaise Frederick Associate Professor of Psychiatry/Biophysicist Harvard Medical School/McLean Hospital bbfrederick(a)mclean.harvard.edu http://www.nirs-fmri.net

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FSL questions
by Yang, Weiqi 31 Jul '19

31 Jul '19

Dear FreeSurfers, I would like to use fsleyes for imaging. Does anybody know how to source it? And what fsl command I should use if I want to extract all ROIs in aparc+aseg file and get their uptake value from PET image? I know how to do it for a single ROI. I am just wondering if there is an easy way to extract data for all ROIs. Thanks, Weiqi

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Freesurfer July 2019