Freesurfer March 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
172 discussions

Talairach failed
by Alexander Greiner 21 Mar '19

21 Mar '19

External Email - Use Caution Hello Freesurfer Developers, I am new to Freesurfer and I am currently only using it to reconstruct the surface structure from MRI data in order to make 3D prints. That means that I only need the files lh.pial and rh.pial in the end. This works fine as long as I am using data from fully developed brains. But for my studies it would be more important to reconstruct the surface from brains beginning from gestational week 21. If I do so, I am running into errors with recon-all: 1. Talairach failed If I skip this test using -notal-check flag I get 2. Watershed error If I add -no-wsgcaatlas I get a 3. Segmentation fault The log files are attached to the email. The general question is: Can Freesurfer also be used for not fully developed brains or even animal brains if only the both surface files mentioned above are necessary? If yes, how can this be done? If not, do you know any other (free) software that might be suited for this task? I am grateful for any suggestions! If you need further information please ask. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS Mojave 10.14.3 Kind regards Alexander Greiner

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Extracting anatomical locations for a set of RAS coordinates
by Sparsh Jain 20 Mar '19

20 Mar '19

External Email - Use Caution Good afternoon Is there is way to automatically extract the anatomical locations corresponding to a set of RAS coordinates using Freesurfer's atlas? I have a set of 200 points and I am trying to get their anatomical labels automatically. Thank you Sparsh

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Re. TRACULA configuration file
by Yuwen Hung 20 Mar '19

20 Mar '19

External Email - Use Caution Dear TRACULA expert: I wonder if it is recommended to turn on performing of registeration-based B0-inhomogeneity compensation (set dob0 = 1) and utilise the field map magnitude and phase dicom files? The default is set to not to use these functions, but I wonder whether using them may result in better outcomes? Thank you, Yuwen

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mri_glmfit in custom ROI
by Williamson, Brady 20 Mar '19

20 Mar '19

External Email - Use Caution Hi, I have a couple of specific questions about mri_glmfit that I could not quite find the answers to in the tutorials or message boards. 1. How would I run mri_glmfit in a custom ROI (or set of ROIs) and then correct for multiple comparisons? I have found information on how to use the freesurfer predefined labels but not a custom regions. Just for some background, I have a set of 50 regions that make up our network of interest and I would like to limit the glm to these regions. 2. How do I extract and use the results from a whole-brain glm, above a specified corrected threshold, and use those in subsequent analyses? I am doing a whole-brain, between groups analysis and then trying to use the significant results from that in within-subjects analyses. Thank you very much for your time, Brady

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[how to highlight a known ROI in original MR Image]
by Yi Li 20 Mar '19

20 Mar '19

External Email - Use Caution Hi, I want to highlight one known ROI (eg left caudate) in a MR image. I understand known ROIs are already in aseg or aparc and there is a color look up table, but I want to highlight one ROI at a time. I searched the website, and found the following instructions, but it highlighted the region of lh.BA45 which has label file at $sub/label/lh.BA45.label. I couldn't find label file at $sub/label/lh.caudate.label. Is there any way to get a known ROI to be highlighted as in the fig below? Thank you so much for the help. Best Regards Yi ============================================ https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI cd $SUBJECTS_DIR mri_label2label \ --srcsubject fsaverage \ --srclabel fsaverage/label/lh.BA45.label \ --trgsubject 004 \ --trglabel 004/label/lh.BA45.label \ --hemi lh \ --regmethod surface freeview -v 004/mri/orig.mgz Then on the menu bar click File > Load ROI [loadroi.jpeg] choose lh.BA45.label and hit 'Open'. The label is visible in coronal slice 153. To jump to that slice, double click on the coordinates [127,127,128] next to where it says 'orig' in the Cursor window pane. The last number is the slice number. Change it to 153 and hit enter. [cid:image003.jpg@01D4DF30.6DED4EC0] --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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mri_convert --in_center
by Song, Da-Yea 20 Mar '19

20 Mar '19

External Email - Use Caution Hello, Is it possible to change the origin of the aseg.mgz file? I tried mri_convert --in_center -117 -219 145 aseg.mgz new_aseg.img. When I opened the new_aseg.img file the origin seems to be at 0 -127 0. Any suggestions would be greatly appreciated! Thank you, Da-Yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Error in QDEC analysis between group and individual case
by 김정식 20 Mar '19

20 Mar '19

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Re: [Freesurfer] Omitting aseg regions from segmentation
by zalewk 19 Mar '19

19 Mar '19

External Email - Use Caution Thanks for getting back to me Doug/Bruce. Sounds good, yes I definitely would want to wait until the bugs have been worked out before utilizing latest release. If your dev team needs contributors to document/write the ex-vivo processing stream I'd be happy to step in and help, I've been running various ex-vivo scan acquisitions through freesurfer for a year at this point. I also have experience in C and shell scripting if that helps, as it seems that's what much of freesurfer is written in. Not sure who I would talk to about that. Best, Kody Zalewski Message: 11 Date: Tue, 19 Mar 2019 14:53:30 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Omitting aseg regions from segmentationTo: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <235d9f13-1eda-1d76-920f-d30b9c467635(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" ... but know that the dev version is not fully tested -- there may be significant bugs that will not be uncovered until it is tested. As such, we may not be able to support any problems you run into. ________________________________ On 3/18/19 8:12 PM, Bruce Fischl wrote: Hi Kody there definitely are flags like this in the dev version. e.g.: case "-no-cerebellum": case "-nocerebellum": case "-NO-CEREBELLUM": case "-NOCEREBELLUM": set nocerebellum=( -nocerebellum) breaksw ; Maybe you should just grab the dev version? And sorry, we haven't documented the ex vivo processing stream yet as it is too much of a work-in-progress. cheers Bruce ________________________________ On Thu, 14 Mar 2019, zalewk wrote: External Email - Use Caution Hi Bruce, In response to your previous email, in v6.0 it doesn't look like recon-all has a "-no-cerebellum" flag (or any cerebellum-related flags), I did verify that the recon-all script in the bin folder had hemisphere-specific flags available however. Is there any documentation on this? It still seems as if I'm missing something here, was it maybe included in previous versions of freesurfer and removed? Best, Kody Zalewski Date: Mon, 4 Mar 2019 15:07:26 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Omitting aseg regions from segmentation To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1903041505530.3767(a)gate.nmr.mgh.harvard.edu><mailto:alpine.LRH.2.20.1903041505530.3767@gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Hi Kody yes, there are some hidden options to recon-all for this. Take a look at the script for things like -no-cerebellum, -rh-only, and see if they are sufficient for what you are trying to do cheers Bruce

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Postdoctoral Position: Neuroimaging of Self-Regulation and Mental Illness
by Jeffrey Spielberg 19 Mar '19

19 Mar '19

External Email - Use Caution Applications are being sought for a postdoctoral fellow with experience in neuroimaging methods, data collection, and analysis in the PD Lab (Personality and Dysregulation Lab) of Dr. Naomi Sadeh at the University of Delaware. The lab is currently conducting studies examining brain networks that contribute to impulsive and harmful behaviors in adults with and without mental illness. The ideal candidate will have a strong background in functional/structural MRI (e.g., FSL, FreeSurfer), programming (e.g., MATLAB), and an interest in impulsivity, self-regulation, and/or externalizing psychopathology (e.g., antisocial personality disorder, alcohol/substance use disorders). Clinical training is not required, but would be considered an asset. The position is open to individuals who have completed a Ph.D. in Psychology or related field or an M.D. Preference will be given to individuals with strong organizational skills, written and oral communication skills, experience working in research teams, and a demonstrated ability to work well with others. Applications from any area of Psychology are encouraged, especially from individuals who have an interest in externalizing disorders. In addition, the fellow will have the opportunity to learn cutting-edge network-analysis methods (e.g., graph theory). The postdoctoral researcher will be heavily involved in data analysis and the preparation of findings for manuscript publication and conference presentations. The anticipated start date is Summer 2019 (with flexibility) and would last for a two-year period with potential for renewal. If you are interested in being considered for the position, please send a current CV, a brief statement of interest that outlines your qualifications for the position, reprints of selected papers, and the names of three professional references to Dr. Naomi Sadeh at nsadeh(a)udel.edu. -- Jeffrey M. Spielberg, Ph.D. Assistant Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware Newark, DE 19716 Office: 307 McKinly Laboratory Lab: Suite 405 Wolf Hall Phone: 302.831.7078 Email: jmsp(a)udel.edu Website: http://sites.udel.edu/jmsp/

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Repairing problems with aparc
by Donovan Roediger 19 Mar '19

19 Mar '19

External Email - Use Caution Hello, We have noticed that in about 10-15% of our subjects, the banksSTS is overestimated to include tissue on the gyral surface of the superior temporal gyrus, middle temporal gyrus, or other adjacent parcels. What is the preferred method to fix this problem? I know that we *can* directly edit the offending labels in tksurfer, but is that the general method-of-choice for repairing problematic parcellations in otherwise good looking data? Thanks! Donovan Roediger Dep't of Psychiatry, Univ. of Minnesota

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Freesurfer March 2019