Re: [Freesurfer] Help: when will the next version of FreeSurfer become available?

External Email - Use Caution We have no current reports about security issues with the FS release. An address using the string fsbuild will email you directly so you can respond to only that address if you would like to report an issue. Please check you spam folder. PLEASE DO

[Freesurfer] Help: when will the next version of FreeSurfer become available?

External Email - Use Caution Hi, We have been pressured by our IT Security team to address some of the vulnerabilities (e.g., OpenSSL) they found in FreeSurfer 7.4.1. I am wondering if you could share with us when would the next version of FreeSurfer become available? Thanks,

Re: [Freesurfer] Help with Recon-all Errors

External Email - Use Caution unsubscribe From: "Perumalla, Sucika" To: "freesurfer" Sent: Wednesday, February 21, 2024 4:30:39 PM Subject: [Freesurfer] Help with Recon-all Errors Questa è la prima volta che ricevi un'email da questo mittente. Assicura

[Freesurfer] Help with Recon-all Errors

Hello FreeSurfer Support, My name is Sucika Perumalla and I hope you can please help me with troubleshooting recon-all. I’m getting multiple frames errors when trying to run recon-all with my dicoms even after extracting the multiple frames. I was wondering if you can please help resolve this

Re: [Freesurfer] Help Download FreeSurfer Windows VM

External Email - Use Caution We don’t expect things to work reliably with 8G total RAM for the machine. The host machine itself will always consume some memory when running its OS, probably up to a few Gig, leaving even less than 8G to be used for running the VM with

[Freesurfer] Help Download FreeSurfer Windows VM

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to start Ubuntu via VirtualBox 7.0 on Windows 10. But I have few problems. First, I do not have the access to the compressed VM Image file (FS_7_3_2_course_ubuntu_18_04_06.ova.7z), is it still possible

Re: [Freesurfer] Help with transform matrix for SEEG

Have you seen this page https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ? On 12/10/2023 8:55 AM, Hyunchul Lee wrote: External Email - Use Caution Hello, I've just started using Freesurfer this week and I'm quite confused about coordinate systems. Specifically, I have

Re: [Freesurfer] Help (Freeview fails to launch)

External Email - Use Caution Dear R, Thank you for the information. The deb package is useful so I agree with you. Only one point is that using deb cannot handle installing two different versions. Do you have any recommendation managing two (or more) different versions using deb

Re: [Freesurfer] Help (Freeview fails to launch)

External Email - Use Caution Depending upon the state of a machine, there is no guarantee a list of "required" packages will encompass everything that needs to be installed/updated, or that a manual install will work.So we neither recommend or support manual/piecemal installs,

Re: [Freesurfer] Help (Freeview fails to launch)

External Email - Use Caution Dear Akira, I agree with R that installing FreeSurfer using the deb is preferred, but if you want to stick to tar.gz, below is the list of the packages to be installed when you install FreeSurfer using the deb package. So if you install these

Re: [Freesurfer] Help (Freeview fails to launch)

External Email - Use Caution That message could be the result of missing system libraries which the Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify, download and install for you. You can download the package via the

[Freesurfer] Help (Freeview fails to launch)

External Email - Use Caution I have installed FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar archive freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz. Freeview fails to launch with the following error message: This application failed to start because no Qt platform plugin

[Freesurfer] Help with transform matrix for SEEG

External Email - Use Caution Hello, I've just started using Freesurfer this week and I'm quite confused about coordinate systems. Specifically, I have SEEG electrode locations that have been digitized in MRI RAS space, and I'm trying to apply a transform matrix so that these

Re: [Freesurfer] Help

External Email - Use Caution It reads like something is not right with your setup/shell environment. Once you have setup the freesurfer environment via, e.g., $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetupFreesurfer.sh

[Freesurfer] Help

External Email - Use Caution Hi, I am using freesurfer. I have gone through with the installation and diagnostics and everything works fine. FOr example, using the command recon-all --help in terminal yields a bunch of directions. Yet, when I enter something like: recon-all -s

Re: [Freesurfer] Help running freesurfer for FEAT-preprocessed functional data?

External Email - Use Caution There is no way to do this. All the fsfast commands are going to expect things to be in the fsfast directory structure. On 8/11/2023 12:19 PM, Noah Lee wrote: External Email - Use Caution Hello! I am trying to run some freesurfer commands

[Freesurfer] Help running freesurfer for FEAT-preprocessed functional data?

External Email - Use Caution Hello! I am trying to run some freesurfer commands for a pipeline. However, I am coming in with functional data preprocessed by FEAT (EPI correction and general mcflirt, etc). For reference, I'm trying to run this following script: preproc-sess -s .

Re: [Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview Display

Henry Tregidgo, PhD Research Associate Centre for Medical Image Computing (CMIC), University College London (UCL) From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 胡馨月 Sent: 18 May 2023 13:15 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer

[Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview Display

External Email - Use Caution Dear FreeSurfer Experts, I hope you are doing well. I have encountered an issue while using the Thalamic NucleiDTI module in FreeSurfer and would appreciate your guidance. I am attempting to segment the thalamus using the module, but the Pc, VM, and

[Freesurfer] Help passcode

External Email - Use Caution Hello FreeSurfer, Where can I find a passcode to unzip the VW file FS_7_2_0_ubuntu_18_04_06.ova.7z I have just downloaded? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] HELP (I don't have the password to unzip on Winrar/7zip)

External Email - Use Caution Hello In this email I request help to acquire the password that the freesurfer requests when wanting to unzip the file. I have followed the steps for the installation and this problem does not let me continue. I add that the reason why I will use the

Re: [Freesurfer] [FreeSurfer] Help on installation of Freesurfer on Ubuntu 18 on Windows 11

External Email - Use Caution Hello Krystal, Doing an "upgrade" is fine, but I don't think you want to do a "dist-upgrade". Telling the system to upgrade to the distribution likely installed something causing the conflict(s) when you tried to install the 7.3.2 release. If

Re: [Freesurfer] Help with script with 7.2 on an HPC

On Behalf Of Taylor, Lisa Sent: Monday, February 6, 2023 6:17 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Help with script with 7.2 on an HPC External Email - Use Caution Hi there, I am trying to update my scripts on our university's HPC but am running into an issue. I

[Freesurfer] Help with script with 7.2 on an HPC

External Email - Use Caution Hi there, I am trying to update my scripts on our university's HPC but am running into an issue. I am not too savvy when it comes to this, so I apologize. My guess is I will have to run my old 6.0 script but without the -hippocampal-subfields-T1

Re: [Freesurfer] Help: Aparcstats and asegstats not working

t; > > > Best, > > > > Yujing > > > > > > > > *From:* vittal korann > *Sent:* Friday, December 30, 2022 3:56 PM > *To:* Huang, Yujing > *Cc:* Freesurfer support list > *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not workin

Re: [Freesurfer] Help: Aparcstats and asegstats not working

) 2. python asegstats2table –subjects … --tablefile … Best, Yujing From: vittal korann Sent: Friday, December 30, 2022 3:56 PM To: Huang, Yujing Cc: Freesurfer support list Subject: Re: [Freesurfer] Help: Aparcstats and asegstats not working External Email - Use Caution Thanks

Re: [Freesurfer] Help: Aparcstats and asegstats not working

gt; *Sent:* Friday, December 30, 2022 12:29 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Cc:* vittalkor...@gmail.com > *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not working > > > > *External Email - Use Caution* > > > SyntaxError: Missing parenth

Re: [Freesurfer] Help: Aparcstats and asegstats not working

External Email - Use Caution Thanks, for your quick response. I installed python2 and did set the default version to python 2.7.18 via aliasing. But I am getting the same old errors again. The same terminal responses were listed below. The subjects that are used for aseg/aparc

Re: [Freesurfer] Help: Aparcstats and asegstats not working

Of fsbuild Sent: Friday, December 30, 2022 12:29 AM To: freesurfer@nmr.mgh.harvard.edu Cc: vittalkor...@gmail.com Subject: Re: [Freesurfer] Help: Aparcstats and asegstats not working External Email - Use Caution SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR

Re: [Freesurfer] Help: Aparcstats and asegstats not working

External Email - Use Caution SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')?It does not look like you are running a python 2.X. That may be because only python3 is installed by default. $ which python $ which

[Freesurfer] Help: Aparcstats and asegstats not working

External Email - Use Caution Hi Freesurfer experts, I am trying to collate all morphological parameters like thickness, area, volume, etc. When I tried executing the command " asegstats2table --subjects Met001 met002 --hemi lh --meas area --tablefile Area_aseg_stats.txt ",

[Freesurfer] HELP! PASSWORD TO UNZIP FS_7_2_0_ubuntu_18_04_06.ova

External Email - Use Caution Greetings, I am writing regarding the request to grant the password to unzip FS_7_2_0_ubuntu_18_04_06.ova file Thanks and regards, Ganeshkaran ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Help: Vertex Properties

The coords are in the surface structure, which you can get by running mris_convert lh.white lh.white.asc (asc will be an ascii file)  or by loading into matlab with read_surf.m The surface area is computed for white (?h.area) and pial (?h.pial.area). These can be converted to mgz or nifti

[Freesurfer] Help: Vertex Properties

External Email - Use Caution Hi, I’m wondering if there’s a way to get the properties of individual vertices such as: 1)Coordinates 2)Surface area 3)angles 4) Side lengths 5) distance matrix from other vertices And can you get these properties for individual surfaces/

Re: [Freesurfer] help

what Anders and Marty started doing way back when Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Sarah Lavelle Sent: Tuesday, October 25, 2022 5:30 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] help External Email - Use Caution Dear freesurfer

[Freesurfer] help

External Email - Use Caution Dear freesurfer, Are there any additional resources on how to make cuts? I have found this

Re: [Freesurfer] Help with group analysis

you should be able to generalize two groups/one covariate and/or four groups one covariate. don't use gender as a continuous covariate. Make sure to normalize your covariates On 9/26/2022 10:30 AM, fernanda rohrsetzer wrote: External Email - Use Caution Hi, TKS for helping me! I

Re: [Freesurfer] Help with group analysis

External Email - Use Caution Hi, TKS for helping me! I looked at the examples of the FSGD files, but I believe that my data doesn't fit. I've three groups/three factors at three levels (LR=1, HR=2, MDD=3) and 6 covariates (gender, age and global brain measure). I don't know if I

Re: [Freesurfer] Help with group analysis

look at the fsgd examples to see if any fit your situation. Note that the input needs to be something like Input    310211    LR 1    15,5    2,678785    645292,6651 152275,2 ie, "LR" instead of "1", etc using commas (,) instead of points (.) may cause problems On 9/25/2022 1:10 PM, fernanda

Re: [Freesurfer] Help with group analysis

External Email - Use Caution I'm sorry! attached the FSGD file. Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve < dgr...@mgh.harvard.edu> escreveu: > no fsgd file was attached. Also, have you looked at >

Re: [Freesurfer] Help with group analysis

no fsgd file was attached. Also, have you looked at https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples ? On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote: External Email - Use Caution Hi Freesufer's, I need to run a group analysis but I don't know how to do it, the error always

[Freesurfer] Help with group analysis

External Email - Use Caution Hi Freesufer's, I need to run a group analysis but I don't know how to do it, the error always appears (print below). There are 3 groups ( risk_group) that I would like to insert as a class (LR = level 1, HR = level 2 and MDD = level 3) and I would

Re: [Freesurfer] Help - segmentHA_T1_long.sh "list of time points not found"

Dear Kimi, When you process the scans longitudinally with FreeSurfer, the file base-tps should be created in the subject directory of the template. Isn’t this the case? Cheers, /Eugenio Juan Eugenio Iglesias http://www.jeiglesias.com On 19 Sep 2022, at 01:02, Raikkonen Kimi

[Freesurfer] Help - segmentHA_T1_long.sh "list of time points not found"

External Email - Use Caution Dear FreeSurfer, Hi, I was trying to run longitudinal analysis of the hippocampus and amygdala segmentation pipeline after running the main FreeSurfer longitudinal pipeline. I ran segmentHA_T1_long.sh 101_MRI1.long.101_template

[Freesurfer] HELP - pass code for Freesurfer VirtualBox

External Email - Use Caution Hello, I am a PhD candidate in neurosciences at the University of Geneva, I would like to use Freesurfer on my VirtualBox to benefit from the interface between FS and BrainVisa. I write you to ask for the pass code. Thanks a lot ! Michel

[Freesurfer] Help for pass code to open Freesurfer Virtual Machine image (.7z)

chive is successfully opened. If you do not have the pass code to open the image, then *send an email to the Freesurfer help list* to receive it." I do not have the pass code to open it and therefore I'm emailing the freesurfer help list, please advise. Thank you for your help in advance! Yuuichi Oo

[Freesurfer] Help with Pass Code to open Freesurfer on Virtual Machine

ode to open the image, then send an email to the Freesurfer help list to receive it." I do not have the passcode to open the image and therefore am emailing the freesurfer help list, please advise. Best, Ellen Tatevosyan UCLA HEALTH SCIENCES IMPORTANT WA

Re: [Freesurfer] help troubleshooting lta_convert error

External Email - Use Caution Hello Megan, The errors you list below usually result from running a version of Freesurfer that does not match the operating system you are using, i.e., it looks like you are trying to run the version built for Ubuntu linux, 7.2.0

[Freesurfer] help!, I need the pass code to open the FS_7_2_0_Ubuntu_18_04_06.ova.7z

External Email - Use Caution Hello FreeSurfer Developers, I downloaded Vbox from the official website and installed it on my Windows system, and then downloaded the FS_7_2_0_Ubuntu_18_04_06.ova.7z, but I need the password to successfully open the compressed package, as

[Freesurfer] help troubleshooting lta_convert error

External Email - Use Caution Hi all, I had a working distribution on an old system a few weeks ago, but now I'm getting an error. Can anyone offer any troubleshooting ideas? I am working on a shared server with a freesurfer distribution that I own. Here is some system info:

Re: [Freesurfer] help - unzip Ubuntu ova password

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 27, 2022, at 15:31, Dan Lerner d...@findsurgicalsciences.com wrote:External Email - Use CautionHi,Setting up the Ubuntu vm provided by FreeSurfer. I'm emailing for the password as per the

[Freesurfer] help - unzip Ubuntu ova password

External Email - Use Caution Hi, Setting up the Ubuntu vm provided by FreeSurfer. I'm emailing for the password as per the instructions. Thanks, Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Seeking beta testers for new Freesurfer help forum

Hello, FreeSurfer community, The FreeSurfer administrative team is working on transitioning the current FreeSurfer mailing list infrastructure to a new, more user-friendly platform called Discourse. We’re still finalizing the website, so we’re looking for potential beta testers for this new

Re: [Freesurfer] Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image

External Email - Use Caution Sending the info to your email shortly. - R. On Feb 16, 2022, at 10:02, Cristina Pereira Priego cristinapereira...@hotmail.com wrote:External Email - Use CautionHi,My name is Cristina and I'm a PhD Student from Clinical Neurosciences Group in IRB

[Freesurfer] Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image

External Email - Use Caution Hi, My name is Cristina and I'm a PhD Student from Clinical Neurosciences Group in IRB LLEIDA. I downloaded " Freesurfer VirtualBox Image" and I need the paswword to login as the user "developer" in the login menu. I'm waiting for your answer,

Re: [Freesurfer] [Help needed] recon-all log error

you did not point out the lines that worry you. At the end, it says "finished without error", which means that you should not visually check your results. On 2/9/2022 6:28 PM, HYE JUNG YOUN wrote: External Email - Use Caution Good day, I hope this email finds you well. I’d love

Re: [Freesurfer] Help

on how to fix these defects? Thanks, Nilab *From:* Douglas N. Greve *Sent:* 11 December 2021 00:24 *To:* Nilab Nasrullah ; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Help The data look pretty noisy

Re: [Freesurfer] Help

@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Help Can you send them in plain, unzipped format? On 11/29/2021 4:07 AM, Nilab Nasrullah wrote: External Email - Use Caution I am attaching a few screenshots of the segmented brain as zip-files. Hopefully, you can see the results

Re: [Freesurfer] Help

in a different format. Thanks, Nilab *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* 29 November 2021 04:01 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Help Can you send some

Re: [Freesurfer] Help

Can you send some pictures? On 11/23/2021 4:02 AM, Nilab Nasrullah wrote: External Email - Use Caution Hi, I am editing subjects for a research project. After reconstruction, some parts of the brain are not included in the segmentation. Often, some parts of the temporal lobe and

[Freesurfer] Help

External Email - Use Caution Hi, I am editing subjects for a research project. After reconstruction, some parts of the brain are not included in the segmentation. Often, some parts of the temporal lobe and the cortex of the occipital lobe are not included. In some cases, the

Re: [Freesurfer] Help

To: freesurfer@nmr.mgh.harvard.edu Cc: gr...@nmr.mgh.harvard.edu Subject: [Freesurfer] Help External Email - Use Caution Hi, I am editing about 120 subjects for a research project. In some reconstructions, the grey matter boundary is not recognised, thus Freesurfer classifies it as white

[Freesurfer] Help

External Email - Use Caution Hi, I am editing about 120 subjects for a research project. In some reconstructions, the grey matter boundary is not recognised, thus Freesurfer classifies it as white matter. I have tried to remove additional pial surface in the area and it gets a

Re: [Freesurfer] Help segmenting all subjects in a folder

That does not apply to the recon-all command, only to mri_segment_hypothalamus_subunits On 7/1/2021 12:23 PM, g.ton...@libero.it wrote: External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I successfully set up Freesurfer and ran a test on my

[Freesurfer] Help segmenting all subjects in a folder

External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I successfully set up Freesurfer and ran a test on my computer, and I am now attempting to run recon-all on all subjects in a folder ("/home/users/s/saccaro/Groupe_0" in the example script

Re: [Freesurfer] Help with LGI pipeline output - Freeview

First, try using tksurferfv (this is the freeview version of tksurfer; tksurfer is obsolete) Second, you'll have to tell us more than "it did not work" (eg, send the terminal output or some other description) On 6/21/2021 3:03 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism

[Freesurfer] Help with LGI pipeline output - Freeview

External Email - Use Caution Dear FreeSurfer experts, Hope that everyone is well and having a great Monday. I am having some trouble opening the outputs for the LGI pipeline via Freeview - could someone please help me with this? I tried using + editing the code available on the

Re: [Freesurfer] 'help: aparcstats2table'

ting those errors, please send your full terminal output with the command run and all error messages. Best, Jackson From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeynep Boz Sent: Saturday, May 29, 2021 3:15 PM To: freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] 'help: aparcstats2table'

output with the command run and all error messages. Best, Jackson From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeynep Boz Sent: Saturday, May 29, 2021 3:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] 'help: aparcstats2table

[Freesurfer] 'help: aparcstats2table'

External Email - Use Caution Hello, I am using Ubuntu 18.05 version and Freesurfer6 version. I've completed all the recon-all parts without any problems, but I'm having trouble with the "aparcstats2table" part. The command "aparcstats2table --subject H1_deneme --hemi lh --meas

Re: [Freesurfer] help Optseq2 study design

On 5/17/2021 10:16 AM, Ellen JOOS wrote: External Email - Use Caution Dear Freesurfer team, I am currently preparing my first fMRI study and used OptSeq2 for creating the trial sequence. Since I am not experienced with the study design in MRI (I mainly conducted EEG studies so far), I would

[Freesurfer] help Optseq2 study design

External Email - Use Caution Dear Freesurfer team, I am currently preparing my first fMRI study and used OptSeq2 for creating the trial sequence. Since I am not experienced with the study design in MRI (I mainly conducted EEG studies so far), I would like to have your

Re: [Freesurfer] help with SAMSEG

tool in freesurfer. Best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alberto Del Cerro Leon Date: Wednesday, May 5, 2021 at 11:11 AM To: Freesurfer support list Subject: [Freesurfer] help with SAMSEG External Email - Use Caution Hello Freesurfer team, my group

[Freesurfer] help with SAMSEG

External Email - Use Caution Hello Freesurfer team, my group is interested in using the SAMSEG tool to evaluate white matter lesions in MCI patients. We would like to use a personalized atlas for the measure. We suppose that we need to use the flag --atlas but we don`t know if we

Re: [Freesurfer] Help

We don't have a lobar segmentation. You can get whole cerebellum (GM and WM) from our standard analysis (recon-all) or using samseg. On 3/5/2021 3:27 PM, Murray Howerth wrote: > External Email - Use Caution > > I am new to this platform and would like some direction as how to obtain >

[Freesurfer] Help

External Email - Use Caution I am new to this platform and would like some direction as how to obtain adjusted cerebellar volumes, specifically lobular cerebellum structure. With thanks, M ___ Freesurfer mailing list

Re: [Freesurfer] help with labels

You can manully edit the annotation or you can manually edit the AAL segmentation to fill in the holes On 1/28/2021 6:09 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution I found the vertex for the holes but how can i modify them or how can I solve them? El mié, 27

Re: [Freesurfer] help with labels

External Email - Use Caution I found the vertex for the holes but how can i modify them or how can I solve them? El mié, 27 ene 2021 a las 16:36, Douglas N. Greve () escribió: > Look at the surface superimposed on the volume along with the AAL > segmentation to make sure that it

Re: [Freesurfer] help with labels

Look at the surface superimposed on the volume along with the AAL segmentation to make sure that it intersects the segmentation at all vertices. You can find the vertex numbers for the holes, and then go specifically to that vertex On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:

[Freesurfer] help with labels

External Email - Use Caution Hello Freesurfer team, I did an AAL atlas on the surface using mri_vol2surf, however when I look at this overlay there are many holes in the labels with vertices that don't belong to any label. Could u help me with this problem?

Re: [Freesurfer] Help with mergecontrasts-sess function

They way you have specified your contrast is a conjunction of individual contrasts, ie, cA>cAc AND cB>cBc. If that what you want? Originally, you were just asking about  the interaction On 1/26/2021 5:17 AM, Paula Maldonado wrote: > External Email - Use Caution > > Thanks for your

Re: [Freesurfer] Help with mergecontrasts-sess function

External Email - Use Caution Thanks for your reply, However I have now a doubt regarding one aspect that I had not noticed before. What I wanted to do is to perform the contrast (condA>condAcontrol)>(condB>condBcontrol) with the order of my condition being condA, condAcontrol,

Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

If you want a cluster table, then you will have to run mri_surfcluster on the output of the conjunction. Run it with --help and write back if you need more info On 11/21/2020 10:03 AM, Paula Maldonado wrote: External Email - Use Caution Dear Douglas, Could you please tell me where

Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

External Email - Use Caution Dear Douglas, Could you please tell me where can I find the cluster table? Thank you, Best regards, Paula > Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve > ha scritto: > > There is not a summary table, it is just a map. Do you want

Re: [Freesurfer] Help with MRI labels {Disarmed}

External Email - Use Caution I want to obtain gray matter, withe matter volume, thickness and curvature based on AAL segmentation. El jue., 12 nov. 2020 15:27, Douglas N. Greve escribió: > So you want the AAL atlas on the surface? If so, then run recon-all on the > AAL

Re: [Freesurfer] Help with MRI labels

So you want the AAL atlas on the surface? If so, then run recon-all on the AAL anatomical T1w volume template, then use mri_vol2surf to sample the labels on the surface, then use this surface segmentation or extract labels (mri_cor2label with --surf option) or convert to an annotation

Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

External Email - Use Caution Yes, please, Best regards, Paula > Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve > ha scritto: > > There is not a summary table, it is just a map. Do you want a cluster table? > > On 11/10/2020 11:26 AM, Paula Maldonado wrote: >>

Re: [Freesurfer] Help with mergecontrasts-sess function

There is not a summary table, it is just a map. Do you want a cluster table? On 11/10/2020 11:26 AM, Paula Maldonado wrote: External Email - Use Caution Thanks for your reply, that worked. Can you please tell me where I can find a summary table of the activated regions resulting from

[Freesurfer] Help with MRI labels

External Email - Use Caution Good afternoon, my name is Alberto del Cerro and I am a PhD student in the cognitive and computational neuroscience laboratory (LNCyC) at the biomedical technology center (CTB) of the Polytechnic University of Madrid (UPM). I am currently extracting

Re: [Freesurfer] Help with mergecontrasts-sess function

External Email - Use Caution Thanks for your reply, that worked. Can you please tell me where I can find a summary table of the activated regions resulting from the conjunction analysis? Best regards, Paula > Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve > ha

Re: [Freesurfer] Help with mergecontrasts-sess function

You would just run mkcontrast-sess, eg, if your four conditions are ordered condA, condAcontrol, condB, condBcont, then mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 -a 4 If you want it reversed, then just reverse the a's and c's On 10/23/2020 4:39 AM, Paula Maldonado

Re: [Freesurfer] Help to create flattened images of a whole hemisphere

Hi Ornaith, Regarding your freeview question - you can use shift + Ctrl + left button to select vertex for filling uncut area. But I just found out there is a glitch on macOS that prevent that from working. A workaround is to uncheck the Cut button, which will quit Cut mode and return to

[Freesurfer] Help with mergecontrasts-sess function

External Email - Use Caution Dear experts, I am running an fMRI experiment in which I have four conditions: two main conditions (condition A and condition B) and two respective control conditions (condition Acontrol and condition Bcontrol). I would like to create a map showing

Re: [Freesurfer] Help with creating contrast matrix - 6 classes and 3 variables

With 6 classes and 3 variables, you will have 24 regression coefficients and so 24 items in your contrast matrix (so good, so far). The order will be 1. MaleMaxT-Offset 2. MaleKahn-Offset 3. 4. 5. 6. 7. MaleMaxT-AgeSlope 8 9 10 11 12 13 MaleMaxT-HRSD_Reduction-Slope 14

Re: [Freesurfer] Help!

Fouda Sent: Friday, October 16, 2020 6:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Help! External Email - Use Caution Hi Anastasia, Thank you so much for responding, please find the log attached! On Fri, Oct 16, 2020 at 3:24 PM Yendiki, Anastasia mailto:ayend

Re: [Freesurfer] Help!

ehalf of Samar Fouda < > samarsfo...@gmail.com> > *Sent:* Friday, October 16, 2020 10:00 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Help! > > > External Email - Use Caution > > Hi! I am trying to run tracula- TRAC-All and I get this er

Re: [Freesurfer] Help!

...@nmr.mgh.harvard.edu on behalf of Samar Fouda Sent: Friday, October 16, 2020 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Help! External Email - Use Caution Hi! I am trying to run tracula- TRAC-All and I get this error message, i assumed it is because that bvals and bvecs

[Freesurfer] Help!

External Email - Use Caution Hi! I am trying to run tracula- TRAC-All and I get this error message, i assumed it is because that bvals and bvecs needed to be predetermined but it seems like that is not the case and i am still getting the same error: Transform file should be

[Freesurfer] Help with creating contrast matrix - 6 classes and 3 variables

External Email - Use Caution Dear Freesurfer community, I am having trouble with my contrast matrix, and would greatly appreciate any help with this. I have 2 categorical variables, sex (2 levels) and training type (3 levels). I also have three (continuous) variables: Age,

Re: [Freesurfer] Help with LGI

External Email - Use Caution Dear Tim, 1) Here is the output after I type matlab: - Matlab does open, and the following appears on terminal: shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory pwd: error retrieving

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