Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

Re: [Freesurfer] Hippocampal subfield version
by Iglesias Gonzalez, Eugenio 12 Apr '19

12 Apr '19

External Email - Use Caution Hi Emily, You need to download the dev version, but run the subfield/amygdala volume on cases reconned with FS6.0. Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Emily Schwartz <emily.schwartz(a)einstein.yu.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 3 April 2019 at 15:44 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal subfield version External Email - Use Caution Hello FS experts, I was planning to use the hippocampal subfield segmentation module in FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei of the amygdala segmentation, but realized I need to download the development version in order to do that. Is there any reason why I shouldn't use the development version over the 6.0 release? Thank you in advance. Best, Emily

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Fwd: Fw: mriglmfit error
by Amrita Bedi 12 Apr '19

12 Apr '19

External Email - Use Caution ---------- Forwarded message ---------- From: *abedi000(a)citymail.cuny.edu <abedi000(a)citymail.cuny.edu>* < abedi000(a)citymail.cuny.edu> Date: Thursday, April 11, 2019 Subject: Fw: mriglmfit error To: Amrita Bedi <amibedi273(a)gmail.com> Amrita Bedi *Biomedical Engineering - Class of 2018* *The City College of New York - CUNY* ------------------------------ *From:* abedi000(a)citymail.cuny.edu *Sent:* Thursday, April 11, 2019 8:38 AM *To:* Freesurfer(a)nmr.mgh.harvard.edu *Subject:* mriglmfit error Good morning Freesurfer developers, While using the mri-glmfit command on 20 subjects. I got the following error- -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf fsaverage lh --cortex --glmdir test.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 6), Max=228.790298 (col 3) The scale is much different between columns 6 and 3, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 6, all values are 0. 1. My command line used was- mri_glmfit --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf fsaverage lh --cortex --glmdir test.glmdir 2. My fsgd file and design matrix file are attached. Thank you for your help. Amrita Bedi

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Labels in nii files
by Vidal Maxime 12 Apr '19

12 Apr '19

External Email - Use Caution Hello, I have a t1w.nii file and a segmentation.nii file. For the latter, I was wondering how I could join labels together and create new labels. Best, Maxime

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Aparc stats files aren’t being generated
by Romella Durrani 12 Apr '19

12 Apr '19

External Email - Use Caution Hello, I am having problems generating the aparc stats files for all my scans. I have checked the surfaces for all scans and they were all generated correctly. However, when I go to generate the stats files, I am able to get all the aseg stats for all scans, but many of them are missing aparc stats, despite passing visual review of the surfaces. Is there a way to generate these files without having to reprocess all of them again? Thanks, Romella

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Using Custom Atlas for Segmentation of Brain Surfaces
by Mina Shire 12 Apr '19

12 Apr '19

External Email - Use Caution Dear All, I would like to extract cortical envelop from my subjects T1 images to use later on for a source reconstruction in on their EEG data. I would like to use Power et al (2011)'s atlas with 264 regions. I am pretty new to Freesurfer and my search through the mailing list and tutorials confused me very much. So I would really appreciate if anyone could explain using a custom atlas to me or direct me to the sources that I can follow please. So I have 2 questions regarding that. 1. Is there any chance that you could direct me step by step how to do this with Freesurfer. 2. While I am running extraction with Freesurfer, should I be using ROI nifti files in MNI coordinate or should I be using ROI nifti files that were inverse normalised to subject's native space? I would really appreciate if you could help me with this please. Thank you very much in advance Kind regards Mina

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Quantify recon-all results from different scan protocols
by Weber, Wade A 11 Apr '19

11 Apr '19

External Email - Use Caution Hi all you Freesurfer users! I have scans on a person that are slightly different protocols (like 1mm voxels vs. 0.8mm voxels amongst other setting differences), and I ran them through recon-all. Is there a way to quantify which one came through with fewer errors to manually correct? I searched the archives as well as I could, but I really wasn't sure what to look for. Thanks! ---- Wade A. Weber, MS Psychiatry Research Program Coordinator Dell Medical School | The University of Texas at Austin o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu

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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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Freesurfer April 2019