Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Need Help
by HARI GURAGAIN 25 May '16

25 May '16

Hello, I am kind of new to the neuroimaging. I was trying to reproduce the following type of figure in freesurfer (3d image with thickness). But I couldn’t do that. Is it possible for anyone to explain how to generate such figure from mri data. Just to clarify, I have the mri data in the form of *.dcm. Is there any specific command to get through it? I tried to work on similar figures using tksurfer *** but couldn’t produce. Your help is greatly appreciated. Thank you, Hari This figure is from one paper. Fig. 4. 3D models of the pial surfaces generated by FreeSurfer with a colored overlay of the local cortical thickness in mm. The top row shows the pial surfaces of the left and right hemisphere based on data with an isotropic resolution of 0.5 mm and the bottom row with an isotropic resolution of 1 mm; both data sets have been acquired at 7 T.

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White matter segmentation
by Mahmoudi, Fariborz 25 May '16

25 May '16

Dear All, I want to segment white matter into 131xx and 141xx label series. I used aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone guide me how could I do this? Regards, Fari ________________________________ CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies. Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.

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Tract length
by Alan Francis 25 May '16

25 May '16

Hi Imagers - I am looking at the Uncinate fasciculus in a Cannabis use disorder (CUD). I found that CUD subjects have significantly shorter tract length and a significant group x side interaction in comparison with controls. Have you seen this before? What is the interpretation of this finding? Thank you, Alan

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FreeSurfer 5.3 OASIS
by Gouveia, Vítor 25 May '16

25 May '16

Hello, I've been trying to process a subject from the OASIS database with FreeSurfer 5.3. FS is relative new to me. I'm trying to use recon-all with -all but the format img/hdr does not seem supported. Do you have any ideia what should I do to process these images? Thank you. Sincerely, Vitor

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DTI error
by Jasmin Alves 25 May '16

25 May '16

Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Improve normalization with own average subject
by pfannmoelj＠uni-greifswald.de 25 May '16

25 May '16

Dear Experts, I am currently working with the non-linear FreeSurfer normalization. We have a small group of subjects N = 12 and in each brain we identified a single position with a fMRI localizer. The task is a group comparison of the individual results for this position. Therefore, the coordinates of each position in FSaverage was determined using mri_label2label. The radius of the region is an important quantity in my investigations. A smaller radius would help me a lot in my data processing. I tried to decrease the radius by generating a new group space template from my 12 subjects with make_average_subject. Then I used mri_label2label to determine the coordinates in the new group space template. Unfortunately, there was no difference in the radius. The intention behind this procedure was to achieve an improved normalization of the subjects. I have read much about this topic in the mailing list, but there are many details in the processing which I am not yet aware of. So, my question is if I proceeded the best possible way or if there is a better alternative to improve the normalization. Would it help to generate a new template as outlined in the second part on this web tutorial (chapter: Creating a registration template from scratch): https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates or do I need to use mris_register with my new template and my 12 subjects instead of mri_label2label in order to benfit from my new template as generated by make_average_subject (also outlined in the web tutorial in the chapter: Creating a registration template initialized with FreeSurfer template)? Even a small decrease in the radius would help to improve my results. Thanks in advance pfannmoe

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Using customized stats code for mass-univariate approach in freesurfer for structural data
by Chung, Yoonho 24 May '16

24 May '16

Hi - If I would like to try to perform mass-univariate statistics at the vertex level (thickness, area, vol at each vertex) without using the mri_glmfit, is this order a sound step (in general) for mapping stats parameter of choice (p-val or t s or weights for example) to the surface? 1. Use mris_preproc and surf2surf to get the data to common space and smooth. 2. Load the data to matlab using fs_read_Y() or MRIread 3. Perform stats at each vertex using stats toolbox to apply modeling approach of your choice (e.g., machine learning, linear mixed model etc.) 4. Extract P-values (or other parameters) for each vertex for the variable of primary interest 5. Use MRIwrite to create mgh file 6. Perform multiple comparison using freesurfer functions (e.g., FDR or monte carlo sim) 7. view corrected maps using tksufer? Any steps I should consider adding or avoid? Thank you!

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Intensity stats file for new ROI
by Sabrina Yu 24 May '16

24 May '16

Hello, I have created my own subcortical ROI in freesurfer (saved as .label file), and am trying to generate an intensity stats file for this ROI. Reading the mailing list, I think that the best way to do this is to: 1) mri_label2vol to convert my ROI to a volume file 2) mri_label_volume to generate stats on this volume I was able to achieve the first step, but am unable to generate a stats file with intensity info for the volume. This is the command I tried to use: cd /freesurfer/subjects/<subjectname>/mri mri_label_volume -s <subjectname> stroke_area.mgz label 1 Any help would be much appreciated! Thank you in advance. Sabrina

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Post-doc opening in Neuroinformatics
by Gregory Book 24 May '16

24 May '16

The Olin Neuropsychiatry Research Center has an opening for a post-doc specializing in neuroinformatics, big-data analysis, and machine learning. The Olin Center is the neuropsychiatric research center within Hartford Hospital’s Institute of Living campus, in Hartford, CT. We house a Siemens Skyra 3T whole-body MRI, multiple EEG, TMS, and eye tracking systems, an internal historical database of nearly 13,000 MRI sessions, and a 400-core Linux compute cluster. The candidate will contribute to the development of neuroimaging databases in support of multiple NIH funded projects and with several primary investigators on large scale analyses. The candidate will contribute to the development of the Neuroinformatics Database ( http://github.com/gbook/nidb) to archive data, automate data analysis using new and existing pipelines, and publish journal articles on their own research. MS degree in engineering, science, neuroscience, or psychology is required, PhD preferred. Candidate is expected to have experience in SQL programming and at least one programming language. Proficiency in multiple programming languages such as Perl, C, C++, Javascript, PHP, Matlab, and Python is highly desirable. Contact Greg Book at gregory.book(a)hhchealth.org

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Significant clusters from mri_glmfit
by sabin khadka 24 May '16

24 May '16

Hi all, I used FDR correction method to correct for multiple comparison after mri_glmfit. And I have a cluster covering multiple regions. I want to extract the thickness, surface area, lgi values for local maxima (or, multiple regions covered by the big significant cluster). I see it is not straightforward as when monte-carlo cluster correction is applied. Can anyone suggest me if there is a work around for this apart from manually creating a ROI masks and extracting values? Thanks for help! Cheers, Sabin Khadka

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Freesurfer