Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

correlation analysis
by TMS lab 11 Apr '19

11 Apr '19

External Email - Use Caution You are right. I want simply to correlate myelin and nhpt regressing out age. I did it with the following matrix: 0 0 1 And it seems to work. Is it ok this matrix? Thanks a lot Rafael Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. < DGREVE(a)mgh.harvard.edu> ha scritto: > That will compute the average of the Age slope and the NHPT slope. > Probably not what you want to do > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer team, > > > > I'm running a correlation analysis where I'd like to corelate > > myelination and a clinical parameter (NHPT) regressing out the effect > > of age. > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > This is my FSGD FILE: > > GroupDescriptorFile 1 > > Title Myelin > > Class Main > > Variables Age NHPT > > Inputfs_CGaMain 19 18.2 > > ....... > > > > Is the matrix ok? > > > > Thanks > > Rafael > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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library to show freesurfer data embedded in a web page (mesh and axial, coronal, sagital slices)
by Gonzalo Rojas Costa 11 Apr '19

11 Apr '19

External Email - Use Caution Hi: Do you know any library that allows to show freesurfer generated data (mesh and axial, coronal, sagittal slices) embedded in a web page? We were working using "BrainBrowser Volume Viewer" (brainbrowser.cbrain.mcgill.ca) and "AMI Medical Imaging (AMI) JS Toolkit" (https://fnndsc.github.io/ami) but I have some problems... Sincerely, Gonzalo Rojas Costa

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1.5T Infant Brain Analysis
by Crawford, Anna 11 Apr '19

11 Apr '19

External Email - Use Caution Hello, I was looking to use the Freesurfer infant brains pipeline. I have found it used with 3T data, but I was wondering if it can be used with 1.5T data as well. Thanks, Anna Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). 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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Re: [Freesurfer] freesurfer longitudinal issue
by Martin Reuter 11 Apr '19

11 Apr '19

Hi Maxime, please keep previous conversation in the email (so that it is easier to check the original question). Also let’s keep this on the list. I do not understand what you mean with “there is not strict alignment”. If you open the norm.mgz from base, tp1.long.base and tp2.long.base they should all be perfectly aligned. If that is not the case something went wrong with your processing - maybe the way you called recon-all or maybe the editing/re-reunning process. I would recommend to - rename base and the 2 long directories - re-run the base and inspect surface - re-run both the long (with recon-all -long …) and inspect if everything is aligned. Best, Martin > On 11. Apr 2019, at 11:43, maxime GUILLAUME <maxime.guillaume(a)live.fr> wrote: > > Hi Martin, > > Thank you for your answer, but (un)fortunatelly, I double checked, I didn't made these mistakes. > The overlay of the surfaces (opened from each tp.long.base directories) is still wrong. > I noticed that there is not a strict alignment between the norm volume from base and the one from the tp1, whereas the alignment is correct between base and tp2.. > > Have you ever faced this situation ? And if so, is there anything else to try ? > > Hope a made myself clear, if you need more captures/informations just ask me. > > Best, > > Maxime > <Capture_PDO_surflongV01V02.xcf>

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correlation analysis
by TMS lab 10 Apr '19

10 Apr '19

External Email - Use Caution Dear Freesurfer team, I'm running a correlation analysis where I'd like to corelate myelination and a clinical parameter (NHPT) regressing out the effect of age. My contrast.mtx: 0 0 0.5 0.5 This is my FSGD FILE: GroupDescriptorFile 1 Title Myelin Class Main Variables Age NHPT Input fs_CGa Main 19 18.2 ....... Is the matrix ok? Thanks Rafael

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The mystery of the missing mcprextreg file
by Mcnorgan, Christopher 10 Apr '19

10 Apr '19

External Email - Use Caution Hello, I’ve been trying to get to the bottom of why selxavg3-sess is failing for lack of a mcprextreg motion correction parameters file for one or more of the functional runs. I have 6 runs of BOLD data, and following the last failed attempt, we cleared out the run folders to start again from scratch with preprocess on the f.nii volumes. We are running preproc-sess on a per-run basis: preproc-sess -s SUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd bold -fwhm 4 -sliceorder up After doing this, we find that the folders for runs 1,2,3,4 and 6 contain the file mcprextreg, but run 5 does not. Consequently, selxavg3-sess throws an error and aborts when it fails to find this file for run 5. Prior to our do-over, we had the same issue, so it appears that this file is reliably not being generated only for run 5. To further the mystery, a second dataset (different participant) was recently preprocessed and also is missing this file for runs 1 and 5. I notice that the runs with the missing motion correction parameter each contain a tmpdir.mcdat2extreg.##### folder, which suggests that the process might have not completed, though it’s odd that it would have completed for runs 1-4 and 6, but not 5. I was hoping someone might have some suggestions for debugging why this file might not be getting generated, as well as what steps might be taken to force its creation. I’m going to start by deleting the tmpdir folders. Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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web page library to show freesurfer data (mesh and axial, coronal, sagital slices)
by Gonzalo Rojas Costa 10 Apr '19

10 Apr '19

External Email - Use Caution Hi: Do you know any library to show freesurfer data (mesh and axial, coronal, sagittal slices) embedded a web page? Sincerely, Gonzalo Rojas Costa

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regions of Yeo 17 networks in fast
by stdp82＠virgilio.it 10 Apr '19

10 Apr '19

External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc…) in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano

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Image Analyst Position at the Yale Alzheimer's Disease Research Unit
by Adam Mecca 10 Apr '19

10 Apr '19

External Email - Use Caution The Yale University Alzheimer’s Disease Research Unit at Yale University School of Medicine has an opening for a highly qualified and motivated individual to work on research involving the development of analysis techniques integrating human imaging data including PET and fMRI for NIH-funded studies and clinical trials in Alzheimer’s disease. Applicants must have obtained a Master’s Degree or a Bachelor’s Degree with significant experience in neuroimaging analysis. Qualifications: Strong analytical, and programming skills are essential. Experience in fMRI, image analysis, algorithm development, and biological applications is highly desirable. The selected candidate will work under the direction of Drs. Christopher van Dyck and Adam Mecca. The successful candidate should have a Master’s Degree or a Bachelor’s Degree with at least three years of experience in fMRI and/or PET imaging. Application Instructions: Interested individuals should email a CV to adam.mecca(a)yale.edu. Adam Mecca, M.D. Ph.D. Yale School of Medicine, Department of Psychiatry Geriatric Psychiatry and the Alzheimer's Disease Research Unit Tel: (203) 764-8100 Fax: (203) 764-8111

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freesurfer longitudinal issue
by maxime GUILLAUME 10 Apr '19

10 Apr '19

External Email - Use Caution Dear freesurfer experts, I am performing a longitudinal study (2 time points, 1 year apart) in patients with Multiple Sclerosis using freesurfer 6.0. After following the tutorial for the CROSS, the BASE (where I only performed few manual edits of the surfaces) and the LONG steps, I am facing a problem with the results of the longitudinal pipeline: If I overlay the final surfaces of the different time points (the white and pial surfaces of the LONG step) on the BASE template, there are major differences between the two time points (see figure attached). This happened only on a subset of my subjects. One of our collaborators in this study suggested that this might be because the patient was positioned differently in the two time points, in particular with respect to the z axis (and indeed the major differences between the two surfaces are in the topmost area of the brain). Does anybody have experienced the same problem? And how can I correct for it? Thank you in advance for your help. (*in the capture surfaces of the first visit are in yellow and in green for the second visit)

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