Re: [Freesurfer] fsaverage folder

  Best,   Yujing       From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of yunus soleymani Sent: Wednesday, November 29, 2023 5:54 AM To: Freesurfer Support List Subject: [Freesurfer] fsaverage folder   External Email - Use Caution Hello Freesurfers

Re: [Freesurfer] fsaverage folder

: [Freesurfer] fsaverage folder External Email - Use Caution Hello Freesurfers, I am currently using the parallel recon-all code in Freesurfer to analyze my subjects. While reviewing the results folder, I came across a folder named 'fsaverage' which had a locked icon next to it, alon

[Freesurfer] fsaverage folder

External Email - Use Caution Hello Freesurfers, I am currently using the parallel recon-all code in Freesurfer to analyze my subjects. While reviewing the results folder, I came across a folder named 'fsaverage' which had a locked icon next to it, along with the folders for each

Re: [Freesurfer] fsaverage nifti to gifti

External Email - Use Caution Hi Tom, you could try mris_convert with the -c option. E.g.: mris_convert -c ~/data/study1/subject1/surf/rh.sulc.nii.gz ~/data/study1/subject1/surf/rh.white ~/blah.gii The command requires an existing surface file that matches the per-vertex data

[Freesurfer] fsaverage nifti to gifti

External Email - Use Caution Hello, I have a question regarding the conversion of functional fsaverage lh and rh files (created from the Yeo lab MNI to fsaverage projection software: https://secure-web.cisco.com/1nRJbdVDTJHwxxGMU9q1fmvcPt_Df0AIfr6uIaGGD96UkPwARZlPIxtczdIoGt6VZEzws

Re: [Freesurfer] fsaverage file download

most or even all of the distribution. best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Shruthi Srinivasan Date: Saturday, July 17, 2021 at 2:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] fsaverage file download External Email - Use Caution Good

[Freesurfer] fsaverage file download

External Email - Use CautionGood afternoon!I would like to ask if there is there anyway that I would be able to redownload just fsaverage to my WSL without redownloading the whole Freesurfer distribution? I was trying to understand how to find the location of the output data for rec

Re: [Freesurfer] Fsaverage stats

External Email - Use Caution Are you sure that you want to compare their thickness with fsaverage? What is your research question? It is more common to compare to a control group with matched demographics. Tim > On July 6, 2020 at 12:57 PM Alina Rojas wrote: > > > Ex

[Freesurfer] Fsaverage stats

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to compare the cortical thickness values from the stats (?h.aparc.stats) of a stack of subjects and compare them with fsaverage. With aparcstats2table I did it for my subjects without problem, but the fsave

Re: [Freesurfer] FSAVERAGE and LabelROI

On 2/12/2020 2:46 PM, Faizan Anwar wrote: External Email - Use Caution Hello, My name is Faizan Anwar. I am currently a undergraduate student at UCLA. I had two questions regarding freesurfer: * Is FSAVERAGE file a universal template that could be used with any set of subjec

[Freesurfer] FSAVERAGE and LabelROI

External Email - Use Caution Hello, My name is Faizan Anwar. I am currently a undergraduate student at UCLA. I had two questions regarding freesurfer: - Is FSAVERAGE file a universal template that could be used with any set of subject data, or is it a specific file created

Re: [Freesurfer] fsaverage for externally preprocessed subjects.

On 12/7/19 5:42 PM, Alvarado,Luis R wrote: > > External Email - Use Caution > > Hi all, > > I have a couple of questions regarding fsaverage: > > 1. Is this file updated every time a new subject is process with > recon-all? > No, fsaverage will not be changed. > > 1. If I obtain ext

[Freesurfer] fsaverage for externally preprocessed subjects.

External Email - Use Caution Hi all, I have a couple of questions regarding fsaverage: 1. Is this file updated every time a new subject is process with recon-all? 2. If I obtain externally preprocessed datasets (e.g., from the 1000 Functional Connectomes Project) should I

Re: [Freesurfer] fsaverage label into functional space

External Email - Use Caution To confirm, your label is starting on the fsaverage surface. You can open tksurfer fsaverage ?h pial and open the label and it shows up? From my experience using fcseed-sess & fcseed-config using FS v6.0.0 what you want to do is move the label from fsa

Re: [Freesurfer] fsaverage label into functional space

This appears to be a bug in mri_label2vol when you specify a surface. Instead, you can create a volume in the conformed space, and then use mri_label2vol with that volume as the --seg input. BTW, you should use mri_label2label to map from fsaverage into the individual subject space, then do the

[Freesurfer] fsaverage label into functional space

External Email - Use Caution Dear FreeSurfers! I would like to confirm something before I proceed with my analyses. I think I am just confused again. I am doing resting state analysis using fsfast. I am trying to use a label defined in the fsaverage space as a seed using the

Re: [Freesurfer] fsaverage error with recon-all

Hi Jiachen does the fsaverage dir exist? It should be symlinked from you $SUBJECTS_DIR to $FREESUFER_HOME/subjects/fsaverage. cheers Bruce On Sun, 16 Jun 2019, chen wrote: External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set, but batching ex

Re: [Freesurfer] fsaverage error with recon-all

What is the output of running: ls -ld /home/dujiachen/HCP/human_connectome/female_processed/fsaverage From: on behalf of chen <824247...@qq.com> Reply-To: FS Help Date: Thursday, April 25, 2019 at 7:46 AM To: FS Help Subject: [Freesurfer] fsaverage error with recon-all Ex

Re: [Freesurfer] fsaverage, brainstem and cerebellum

You are going about it in the right way. Not sure about a better template. You could create the surfaces on an individual and then apply a linear transform to get it into fsaverage space. Again, another hack ... On 1/22/19 1:56 PM, john Anderson wrote: > External Email - Use Caution > >

Re: [Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Hi Dr Greve, thank you for the response... It is a genius hack ;-) Results are way much better. My objective is just to improve visualization... I would like to project statistical maps from vertex wise analysis of subcortical regions. The same last f

Re: [Freesurfer] fsaverage, brainstem and cerebellum

You can try mri_binarize with both --erode and --dilate (specifying the structures with --match and and output surface with --surf). Dilating then eroding might remove some of the holes (though it is a hack) On 1/22/19 10:43 AM, Bruce Fischl wrote: > Hi John > > sorry, not really. If you constra

Re: [Freesurfer] fsaverage, brainstem and cerebellum

Hi John sorry, not really. If you constrain the topology of the cerebellum you will probably loose a lot of it since the folia are so small. You can try using Florent Segonne's old code (mri_topologycorrection), which will generate a discrete segmentation that has the correct topology (hopeful

Re: [Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Hi Dr Bruce, I applied your recommendations and I was able to create surfaces to the cerebellum and brain stem using the command mri_tesselate. I am not happy with the topology though... There are holes and some defects. Would you recommend any comma

Re: [Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Ah! great!! thank you so much for the great help!! Have a good day, John Sent with ProtonMail Secure Email. ‐‐‐ Original Message ‐‐‐ On Thursday, January 10, 2019 1:03 PM, Bruce Fischl wrote: > Hi John > > we distribute an aseg.mgs with fs

Re: [Freesurfer] fsaverage, brainstem and cerebellum

Hi John we distribute an aseg.mgs with fsaverage I believe. You can just tesselate that. cheers Bruce On Thu, 10 Jan 2019, john Anderson wrote: External Email - Use Caution Hi Dr Bruce, I highly appreciate your guidance. I would like to load the cerebellum and brain stem st

Re: [Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Hi Dr Bruce, I highly appreciate your guidance. I would like to load the cerebellum and brain stem structures as an average structure similar to "fsaverage" , I usually use the command tksurferfv fsaverage lh pial -overlay mri_tessellate or mri_mc w

Re: [Freesurfer] fsaverage, brainstem and cerebellum

Hi John you could use mri_tessellate or mri_mc to create a surface for those structures, then smooth them with mris_smooth and load them into freeview. Shouldn't be too hard. cheers Bruce On Thu, 10 Jan 2019, john Anderson wrote: External Email - Use Caution Dear FS ex

[Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Dear FS experts, For visualization purposes, is there any way to show the cerebellum and brain stem regions (similar to the attached figure), this figure was published used CONN toolbox but I am not sure how they were able to map functional data in b

Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

I'm not sure what this is referring to, but you should be very careful flipping images. If you want to compare left and right, then use the xhemi tool https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 9/4/18 10:41 AM, Martin Reuter wrote: Hi Xiaoyu, please keep the previous conversation as i

Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

Hi Xiaoyu, please keep the previous conversation as inline citation below so I know what we discussed before. What I mean is to process every subject only once and not twice (with flipped images, if that is what you did?). Then run xhemi analysis on the subject-level. Invert the sign of the

Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

External Email - Use Caution Thanks Martin, Yes, I did mean to have the right hemisphere added to the left hemisphere as a new time point. Can you explain on what you mean by run every subject only once? Do you mean to run xhemi for all of the subjects and then run a paired anal

Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal Comparison

Hi Xiaoyu, I don't think it makes sense to model the hemisphere each as a different group. Do you mean different time point? The problem is that left hemispheres are probably anatomically slightly different than right hemispheres (on average in healthy people). I would run every subject only o

[Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal Comparison

External Email - Use Caution Hello Freesurfer Experts, I am trying to compare the left and right hemisphere of a group of PD patients with Mass-Univarate LME. >From what I can see in the wiki tutorial, the mris_preproc only assembles data >from one hemisphere at a time, which i

Re: [Freesurfer] FSAVERAGE - RECON-All

Hi Savas no, the data is not resampled to fsaverage (except internally during the parcellation procedure, but that is transparent to you). All the reported stats are in subject space. cheers Bruce On Wed, 3 Jan 2018, Savaş Aker wrote: Dear all, I would like to learn the following: I r

[Freesurfer] FSAVERAGE - RECON-All

Dear all, I would like to learn the following: I ran recon-all -all command, and now want to use only parcellation results of Desikan-Killiany Atlas or Destrieux (mean curvature, cortical thickness, etc.). So I will use values under STATS folder (e.g. lh.aparc or Lh.aparc.2009 for mean curvatu

Re: [Freesurfer] fsaverage template appropriate to use with pediatric population?

Hi Avi we have found fsaverage to be fine in that age range, but if you are concerned you can use make_average_subject to build your own average. cheers Bruce On Tue, 21 Nov 2017, Avideh Gharehgazlou wrote: Hi experts, I have a few questions regarding the use of fsaverage template for my r

[Freesurfer] fsaverage template appropriate to use with pediatric population?

Hi experts, I have a few questions regarding the use of fsaverage template for my research: 1. Is the fsaverage template appropriate for use with pediatric population? (My sample is 6-16 years of age) 2. What possible errors can be expected ? What could possible alignment errors be? 3. Are ther

Re: [Freesurfer] Fsaverage

I don't know that it has really been tested. The registration is surface-based so it will be much less sensitive to different gross anatomy than volume-based methods. On 03/09/2016 11:37 AM, Kasper Jessen wrote: > Dear FreeSurfer experts, > > In regard to fsaverage, we are wondering whether it i

[Freesurfer] Fsaverage

Dear FreeSurfer experts, In regard to fsaverage, we are wondering whether it is recommended to use the default fsaverage or if a new fsaverage should be created for the individual dataset. If there are no recommendations, what are the advantages and disadvantages? Best regards, Kasper Jessen MD,

Re: [Freesurfer] fsaverage error with recon-all

Thanks Douglas Now it's ok. I checked the OSX version. My OSX version was 10.9.5. I removed the XQuartz 2.7.7 and installed 2.7.5 I run this command is below recon-all -all -i /Volumes/yang/S002_AD1118_20090116/NCKU-0003--1.dcm -s S002_20151005 ( remove -sd and -ba_labels) thank you

Re: [Freesurfer] fsaverage error with recon-all

Try removing -ba_labels (it will do that with -all anyway) On 9/29/15 9:02 PM, 葉丁瑞 wrote: Dear All, I ran the following script: recon-all -i /Volumes/yang/S002_AD1118_20090116/NCKU-0003--1.dcm -s S002_ba -sd /Volumes/yang/S002_AD1118_20090116/ -all -ba_labels and got the error below at

Re: [Freesurfer] fsaverage problem

Hi Ashkan the mapping is nonlinear so can't be represented by a matrix. Because it's (highly) nonlinear, under it most subjects look a lot like each other, so adding subjects to fsaverage doesn't usually change it. That said, try out make_average_subject and see what it produces if you want an

[Freesurfer] fsaverage problem

Hello Bruce, thank you for your reply, and sorry that i couldn't reply on your mail (i don't know how). What do you mean by mapping an image to fsaverage space? do you mean we get a matrix of transformation? and if yes do we have access to this matrix? or do mean that when a subject is added the f

Re: [Freesurfer] Fsaverage template, labeling and group analysis

Hi Silas usually the fsaverage folder is a symlink, so you may only have one. Create the label, then use mri_label2label to map it across subjects. I would certainly look at it to make sure it is ok, but frequently it won't need editing (it depends on where in the brain you draw it, and whethe

[Freesurfer] Fsaverage template, labeling and group analysis

Dear Freesurfer team, I would like to create a label using the fsaverage template (tksurfer) and then map this label to my subjects. The problem is that i currently have several fsaverage folders; one in each subject folder. How do i get one single fsaverage file? And is it possible to create a

Re: [Freesurfer] fsaverage surfaces correspondence across hemispheres

We don't have anything to do this directly. However, we do have this tool: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi See if that meets your needs. doug On 2/17/15 12:49 PM, David Moreno-Dominguez wrote: > Hello, > I am performing clustering ofer data sampled to the fsaverage5 surfaces. > I

[Freesurfer] fsaverage surfaces correspondence across hemispheres

Hello, I am performing clustering ofer data sampled to the fsaverage5 surfaces. I would now like to be able to do color matchign and other processes that require a vertex correspondence across both surfaces. I have noticed that the vertices do not correspond directly (vertex 25 of lh is not the

Re: [Freesurfer] Fsaverage for ROI analysis of children

flag. > > Best, > > Michael S. > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas > Greve > *Sent:* Monday, November 03, 2014 9:32 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Free

Re: [Freesurfer] Fsaverage for ROI analysis of children

9:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all, I have been conduct

Re: [Freesurfer] Fsaverage for ROI analysis of children

t list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, November 3, 2014 at 10:10 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Fsaverage for ROI analysis of ch

Re: [Freesurfer] Fsaverage for ROI analysis of children

2014 at 9:31 AM To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children Can you back up and tell us what it is you are trying to do? Where did the

Re: [Freesurfer] Fsaverage for ROI analysis of children

surfer@nmr.mgh.harvard.edu>> Date: Monday, November 3, 2014 at 9:31 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children Can you back up and tell

Re: [Freesurfer] Fsaverage for ROI analysis of children

Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nm

[Freesurfer] Fsaverage for ROI analysis of children

Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsavera

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

I dont know all the details regarding shared directories between the host and guest, but the bottom line is that if you can not manually create a symbolic link in the subjects dir than you will not be able to run recon-all. Another option is to use the shared directory to copy the subjects dir

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Zeke, I'm running Ubuntu 14.04 as guest on a VMware® Workstation 10 and Windows 7-64 as host. I made a shared directory between windows and Ubuntu named DBSI where then I put the /volumetric/MGZ under it. So, how can I give permission for that ? Mahmoud On Wed, Sep 17, 2014 at 10:21 AM, Z K wro

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Yeah, I was starting to wonder if he was having permissions issues as well. On Wed, Sep 17, 2014 at 10:16 AM, Mahmoud wrote: > Paul, > > I am using bash instead of tcsh. Does it make any difference ? > > Mahmoud > > On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach wrote: > >> Hmm. Well I'm stumped.

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

No it doesnt make a difference. Are you using a the virtual machine version of freesurfer with a shared folder? Or some other system where you are mounting a readonly file system? That is most likely your issue. You will have to place your subjects directory onto a location in which you have w

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Paul, I am using bash instead of tcsh. Does it make any difference ? Mahmoud On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach wrote: > Hmm. Well I'm stumped. Sorry. :-/ > > Any Freesurfer gurus have some ideas here? > > On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud wrote: > >> Paul >> >> it shows agai

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Hmm. Well I'm stumped. Sorry. :-/ Any Freesurfer gurus have some ideas here? On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud wrote: > Paul > > it shows again: > ln: failed to create symbolic link ‘./fsaverage’: Operation not supported > > !!! > > On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach wrote: >

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Paul it shows again: ln: failed to create symbolic link ‘./fsaverage’: Operation not supported !!! On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach wrote: > you have to tell the symbolic link where to put the directory > > copy this exactly into your terminal, including the period at the end > > SU

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

you have to tell the symbolic link where to put the directory copy this exactly into your terminal, including the period at the end SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage . On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud wrote: > Paul,

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Paul, I tried this: SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage and got this: ln: failed to create symbolic link ‘./fsaverage’: Operation not supported any idea ? Mahmoud On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach wrote: > Try someth

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Try something like: cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage . Confirm the linked directory is now in your $SUBJECTS_DIR, then try running your script. On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud wrote: > Paul, > > The fsaverages are in $FREESURFER_HOME/subjects. So does it mean

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Paul, The fsaverages are in $FREESURFER_HOME/subjects. So does it mean that the program couldn't make a link between my actual image places and $FREESURFER_HOME/subjects/fsaverage ? what can I do to fix it ? Thank you, Mahmoud On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach wrote: > The general fs

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

The general fsaverage (as well as it's other iterations, fsaverages 3-6) should be located in your $FREESURFER_HOME/subjects directory. You could symbolically link it over to your $SUBJECTS_DIR. On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud wrote: > Dear All, > > I ran the following script: > > #!/bi

[Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Dear All, I ran the following script: #!/bin/bash SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm -subject case022_tp2 -all and got the error below at the end. Could anybody please let me know how to fix it. Thank you, Mahmoud Repo

Re: [Freesurfer] fsaverage cortex thickness

That thickness file is already there, for what it is worth. doug On 8/12/14 4:59 AM, Bruce Fischl wrote: Hi Wilder Fsaverage doesn't really have a thickness associated with it. I guess we could comput the mean thickness of the subjects that went into it, but I'm not sure how useful that would

Re: [Freesurfer] fsaverage cortex thickness

Hi Wilder Fsaverage doesn't really have a thickness associated with it. I guess we could comput the mean thickness of the subjects that went into it, but I'm not sure how useful that would be as they are intentionally varied in terms of age and pathology Cheers Bruce > On Aug 12, 2014, at 3:5

[Freesurfer] fsaverage cortex thickness

Hi, all, How to calculate the mean cortex thickness of fsaverage? Thanks! Wilder___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for

Re: [Freesurfer] fsaverage mesh has duplicate pt

Can confirm also true for lh.white, but not lh.sphere and lh.inflated. --Thomas On Thu, Apr 10, 2014 at 1:11 PM, Xuelong Zhao wrote: > > Hi, > > I loaded the lh.orig cortex for fsaverage into Matlab. My colleague and I > found that it actually has a duplicate point. > > The index of the duplicat

Re: [Freesurfer] fsaverage mesh has duplicate pt

Hi, I loaded the lh.orig cortex for fsaverage into Matlab. My colleague and I found that it actually has a duplicate point. The index of the duplicate points are: 1 40970 I checked that both have the same vertices coordinates: -36.7233 -18.4039 64.3611 I'm not sure if this is inte

Re: [Freesurfer] fsaverage -> fsaverage3

Hi Itamar, fsaverage3/4 are just different icosahedral supersamplings. They were actually used to create fsaverage (which you can think of as fsaverage7). That is, fsaverage1 has 12 vertices, fsaverage2 42, etc..., and the first 12 of fsaverage[234567] are the ones from fsaverage1, the first

[Freesurfer] fsaverage -> fsaverage3

Greetings, We would like to downsample surfaces (e.g. using mris_decimate) but we want to duplicate the way it was done with fsaverage (namely, find out how fsaverage3/4/5 were created from the original fsaverage). Also, we wish to be able to project using mri_surf2surf but we don’t have sphere

Re: [Freesurfer] FSAverage headmodel composition.

Thanks a lot! 2014-03-25 19:34 GMT+04:00 Douglas N Greve : > > Here's the info that we have > > 39 Subjects > 14 Male, 25 Female > Ages 18-87 > Young (18-22): 10 > Mid (40-60): 10 > Old Healthy (69+): 8 > Old Alzheimer's (68+): 11 > Siemens 1.5T Vision (Wash U) > > Whole Brain Segmentation: Auto

Re: [Freesurfer] FSAverage headmodel composition.

Here's the info that we have 39 Subjects 14 Male, 25 Female Ages 18-87 Young (18-22): 10 Mid (40-60): 10 Old Healthy (69+): 8 Old Alzheimer's (68+): 11 Siemens 1.5T Vision (Wash U) Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl, B., D.H. Sa

[Freesurfer] FSAverage headmodel composition.

Hi all, Could you tell me about the gender composition of FSAverage head model? All the information about it is that it consits of 40 subjects of different ages. Best, Igor. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.h

Re: [Freesurfer] FsAverage

: Tuesday, February 25, 2014 11:28 AM To: Boadu, Osei B; free surfer Subject: Re: [Freesurfer] FsAverage but fsaverage should already exist in $FREESURFER_HOME/subjects/fsaverage does it not? On 02/25/2014 11:15 AM, Boadu, Osei B wrote: > Sorry, I thought I replied all. I'm trying to do MNE

Re: [Freesurfer] FsAverage

gt; To: Boadu, Osei B; free surfer > Subject: Re: [Freesurfer] FsAverage > > Please post questions to the list. Thanks! You need fsaverage. What are > you trying to do? Usually people point SUBJECTS_DIR to a folder in space > where they have write permission, then create a symlink fr

Re: [Freesurfer] FsAverage

ong others. From: Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, February 25, 2014 10:48 AM To: Boadu, Osei B; free surfer Subject: Re: [Freesurfer] FsAverage Please post questions to the list. Thanks! You need fsaverage. What are you trying to do? Usually pe

Re: [Freesurfer] FsAverage

ay, February 24, 2014 6:39 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FsAverage > > Do you have write permission into that folder? > > > On 02/24/2014 05:28 PM, Boadu, Osei B wrote: >> Hello, >> >> When trying to either create a

Re: [Freesurfer] FsAverage

Do you have write permission into that folder? On 02/24/2014 05:28 PM, Boadu, Osei B wrote: > Hello, > > When trying to either create a symbolic link or copy the fsaverage > folder, I am told that permission has been denied. E.g.: > ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage > ln: crea

[Freesurfer] FsAverage

Hello, When trying to either create a symbolic link or copy the fsaverage folder, I am told that permission has been denied. E.g.: ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage ln: creating symbolic link `fsaverage/fsaverage': Permission denied I'm not sure what I should do. Thanks, Osei

Re: [Freesurfer] fsaverage

Hi Franciso, I think that we made some small mods to the spherical registration in that time to make it more robust, so things probably did change cheers Bruce On Tue, 6 Aug 2013, Fco. Javier Román wrote: Hello! I want to know if there are any change in the files of the folder fsaverage in

[Freesurfer] fsaverage

Hello! I want to know if there are any change in the files of the folder *fsaverage * in the different versions of freesurfer. Specifically, I'm interested in know if the files lh.pial_avg and rh.pial_avg are the same in the versions v4.5.0 and v5.3.0 Many thanks in advance, Best, -- Francisco

Re: [Freesurfer] fsaverage vertex index to talairach

Hi Cesar, you can run mris_convert lh.white lh.white.asc to convert to ascii. Each vertex is in MNI305 space. Is that good enough? There is a matlab script by Matthew Brett that attempts to convert to Tal coords. You could easily convert to MNI152 as well. doug On 6/24/13 4:34 PM, Cesar

[Freesurfer] fsaverage vertex index to talairach

Hello, Anyone know of a fast way to get the talairach coordinates of a vertex index in fsaverage. A function or script is best since I want to do this for a large number of vertices. Thank you for any help you guys can provide. Cesar ___ Freesurfer mail

Re: [Freesurfer] Fsaverage b0

no, sorry On 05/16/2013 11:13 AM, Fotiadis, Panagiotis wrote: > Hi FreeSurfer experts, > > I was wondering whether there is an average b0 scan in the fsaverage space or > in the MNI space? > > Thank you, > Panagiotis. > ___ > Freesurfer mailing list > Fr

[Freesurfer] Fsaverage b0

Hi FreeSurfer experts, I was wondering whether there is an average b0 scan in the fsaverage space or in the MNI space? Thank you, Panagiotis. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] fsaverage mappings

Hi Satra the first 12 vertices will be from the 0th order icosahedron, the next 30 from the 2nd order, etc Bruce On Sat, 6 Apr 2013, Satrajit Ghosh wrote: > hi folks, > are there predefined mappings between the fsaverage surfaces? for example, i > have an array of numbers for all the verti

[Freesurfer] fsaverage mappings

hi folks, are there predefined mappings between the fsaverage surfaces? for example, i have an array of numbers for all the vertices in fsaverage4. is there an easy way to map those to vertices on to fsaverage/fsaverage5/... without going through surf2surf? something perhaps implemented in matlab

Re: [Freesurfer] fsaverage across versions

thanks bruce. indeed, we are not expecting identical output and in these cases that we are looking at it's all 5.x for most part. cheers, satra On Mon, Feb 4, 2013 at 9:34 AM, Bruce Fischl wrote: > Hi Satra, > > certainly fsaverage will change if we change things in spherical > registration, or

Re: [Freesurfer] fsaverage across versions

Hi Satra, certainly fsaverage will change if we change things in spherical registration, or potentially elsewhere. I don't anticipate any large changes, but I wouldn't count on them being identical Bruce On Mon, 4 Feb 2013, Satrajit Ghosh wrote: > hi bruce and others, > are there any specific

[Freesurfer] fsaverage across versions

hi bruce and others, are there any specific implications we should be worried about (e.g., with qdec or surf2surf) when using an fsaverage that's from a different version that ran the recon. cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.

Re: [Freesurfer] fsaverage

hi, that line from the wiki appears to be in tcsh syntax, you are using bash, which is the default shell of most operating systems. you can try either in bash, like this: if [ ! -e fsaverage ]; then ln -s $FREESURFER_HOME/subjects/fsaverage; fi ...or in tcsh, which you might need to install fi

[Freesurfer] fsaverage

Hello, I'm trying to run qdec on my own data and I'm trying to create fsaverage. Following the wiki tutorial, I copied the command: if (! -e fsaverage) ln -s $FREESURFER_HOME/subjects/fsaverage but I got the following error: bash: syntax error near unexpected token `ln' Can anyone help me in

[Freesurfer] fsaverage documentation

Hi All, I was looking for documentation on the fsaverage brain but I do not have permission to access the *Buckner40page for notes on building fsaverage*. http://surfer.nmr.mgh.harvard.edu/fswiki/Buckner40 Has the information on this page been re

Re: [Freesurfer] fsaverage error - too many levels of symbolic links

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 21 February 2012 18:03 To: Gibbard, Clare Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsaverage error - too many levels of symbolic links Hi Clare, try moving your SUBJECTS_DIR outside of the

Re: [Freesurfer] fsaverage error - too many levels of symbolic links

Hi Clare, try moving your SUBJECTS_DIR outside of the freesurfer tree. doug Gibbard, Clare wrote: > Hi, > > I am running recon-all on several scans, but it is exiting with an > error. I think the error is occurring because my symbolic link to > fsaverage is self-referential. However, the symbo

[Freesurfer] fsaverage error - too many levels of symbolic links

Hi, I am running recon-all on several scans, but it is exiting with an error. I think the error is occurring because my symbolic link to fsaverage is self-referential. However, the symbolic link is generated automatically during recon-all so I cannot see how to correct it. I have tried delet

  1   2   >