[Freesurfer] error in atlas creation

Hello, I have been stumped by this error I keep getting using the rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, so I am wondering if the problem is with the brains we parcellated, or with my installation etc. The brains consist of manually segmented cerebellums from th

Re: [Freesurfer] error in atlas creation

Hello, I just wanted to give this message a bump. Thanks! Anthony On 5/15/15 9:49 AM, Anthony Dick wrote: > Hello, > > I have been stumped by this error I keep getting using the > rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, > so I am wondering if the

[Freesurfer] error in atlas creation

Hello, I have been stumped by this error I keep getting using the rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, so I am wondering if the problem is with the brains we parcellated, or with my installation etc. The brains consist of manually segmented cerebellums from the o

Re: [Freesurfer] error in atlas creation

> cheers > Bruce > > > On Tue, 26 > May 2015, Anthony Dick wrote: > >> Hello, >> >> I have been stumped by this error I keep getting using the >> rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, >> so I am wondering if the

Re: [Freesurfer] Approximately how many brains do I need to manually edit?

This is really a question about whether you care about the data you are reporting. The reality of neuroimaging is that it is messy. Artifacts occur in acquisition and in data reconstruction. If you don't check the data, those errors will propagate as error in the analysis. It is not uncommon to

Re: [Freesurfer] error in atlas creation

Hello, I was wondering if these got uploaded correctly. Please let me know if I made a mistake and thanks, Anthony On 7/9/15 1:41 PM, Bruce Fischl wrote: > sure > On Thu, 9 Jul 2015, Anthony Dick wrote: > >> Hello Bruce, >> >> I am still getting this error after r

Re: [Freesurfer] Atlas conversion to NIFTI

AFNI's @SUMA_Make_Spec_FS command will convert the aparc+aseg file for a particular subject to BRIK/HEAD format, which can easily go to nifti. This might get you what you want in a couple of easy steps. Anthony On 7/31/15 2:26 PM, Bruce Fischl wrote: HI Pantea our atlases contain a lot more

Re: [Freesurfer] Cerebellar volumes?

Hello, This paper is very relevant to this issue: Sanfilipo MP, Benedict RH, Zivadinov R, Bakshi R (2004) Correction for intracranial volume in analysis of whole brain atrophy in multiple sclerosis: the proportion vs. residual method. Neuroimage 22:1732–1743. Anthony On 6/10/16 9:34 AM, Bru

Re: [Freesurfer] DTI of frontostriatal tracts

Hello, See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832 Anthony > On 8/2/16 12:26 PM, Ritobrato Datta wrote: >> Hello All, >> >> We are studying adolescents with HIV and are interested in >> frontostriatal tracts (anything from frontal cortex to >> caudate/putamen/nucleu

[Freesurfer] two postdoctoral positions at Florida International University, Miami, open immediately

candidates should send application materials (curriculum vitae, sample publications, three references, and a letter describing research interests) directly to Dr. Paulo Graziano (pgraz...@fiu.edu) or Dr. Anthony Dick (ad...@fiu.edu). Reviews of applications will begin immediately. -- Anthony

[Freesurfer] two postdoctoral fellowships; Florida International University, Miami, FL

Please distribute! http://myweb.fiu.edu/adick/post-doctoral-fellow-positions/ -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidi

Re: [Freesurfer] clinical pysch programs?

Hello Bruce, Our Psychology program allows a double major in Clinical Science and Cognitive Neuroscience. Please have her contact me if she is interested. There are excellent faculty in both programs and it is highly collaborative across the two programs, so lots of opportunity for training in

Re: [Freesurfer] Anatomical ROI parcellation

https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit On 1/17/17 4:47 PM, Aya Kabbara wrote: Dear Freesurfer team, I am wondering is there a way using tksurfer to edit a given atlas (for example: destrieux atlas). I would like to parcellate the superior temporal region into three

Re: [Freesurfer] Roi parcellation

Hello, Two options I can think of--develop your own atlas (time consuming), or apply the Lausanne atlas parcellation, and combine the smaller ROIs to get the ones you want. See this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043869.html https://github.com/m

Re: [Freesurfer] Attrition in longitudinal analysis

A recommendation: talk to a statistician about implementing an analysis for missing data. There are a number of options that may be available to you to allow a more straightforward and scientifically sound approach. Anthony On 1/19/17 10:15 AM, Greenberg, Jonathan wrote: Dear FreeSurfer use

Re: [Freesurfer] error in atlas creation

brains with a file called seg_edited.mgz. If you don't get the error, then maybe it is a problem with our local settings (although we get this error on multiple different computers). Thanks for any help! Anthony On 7/20/15 2:30 PM, Anthony Dick wrote: > Hello, > > I was wonderi

Re: [Freesurfer] error in atlas creation

entical. Anthony On 10/13/15 11:54 AM, Bruce Fischl wrote: HI Anthony what is the full command line? Does it happen if you only train on a single subject instead of 23? Bruce On Tue, 13 Oct 2015, Anthony Dick wrote: Hello Bruce, We have tried running the atlas creation on newly freesurfed b

Re: [Freesurfer] error in atlas creation

you create the gca? On Tue, 13 Oct 2015, Anthony Dick wrote: Hello Bruce, I will try a single subject. When I run the following command line (i.e., right out of recon-all) it works: mri_em_register -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2014-08-21.gca transforms

Re: [Freesurfer] grossly abormal brain

Don, if that doesn't work, try the procedure outlined in this paper, although it is rather involved: http://www.architalbiol.org/index.php/aib/article/viewArticle/1221 Anthony On 11/17/15 8:27 AM, Bruce Fischl wrote: Hi Don it's impossible to say. Certainly 6.0 will be your best bet as it h

[Freesurfer] ABCD postdoctoral position at Florida International University

Dear Colleagues, Please find below an advertisement for our Postdoctoral position at Florida International University, Miami, FL. Details are also provided in the attached pdf. Thank you! Anthony >>> The Cognitive Neuroscience and Imaging Center at Florida International University (FIU) in

Re: [Freesurfer] P files

Another option is to open the files in OsiriX, and export to DICOM from there. This does not, to my knowledge, have a batch option though. Anthony On 1/6/16 9:35 PM, Bruce Fischl wrote: Hi John Luca Marinelli (ccd) might be able to help you. cheers Bruce On Thu, 7 Jan 2016, John Anderson wr

Re: [Freesurfer] freesurfer with infants MRI

Hello Chiara, I believe there is some precedent for using Freesurfer for group analysis without warping: http://onlinelibrary.wiley.com/doi/10.1002/hbm.20158/abstract Anthony On 2/15/16 1:08 PM, Chiara Bulgarelli wrote: Dear All, I would like to ask you for some advice about segmenting MRI

Re: [Freesurfer] Tract length

Hello, I wouldn't mind jumping on this issue more broadly. Diffusion indices like FA, ADC, RD, and AD have more clear physiologic correlates. But what does the length of a tract, the volume of a tract, or the number of streamlines say about physiology? Tract length seems to be very dependent

Re: [Freesurfer] FreeSurfer with pediatric brain tumors?

You may want to take a look at this paper for how to deal with large lesions: http://www.ncbi.nlm.nih.gov/pubmed/21175010 On 8/2/12 5:55 PM, Jesse Bledsoe wrote: Hello FS experts, I am wondering if anyone has experience using FreeSurfer or other program to analyze cortical thickness and subc

Re: [Freesurfer] kvl binaries missing from ppc 5.1 stable release

Hello--was just thinking about upgrading to Mountain Lion. Am I to assume freesurfer will not work if I do this? Anthony On 9/10/12 11:58 AM, Nick Schmansky wrote: > Fidel, > > Sorry, but the GEMS tools are not built for our mac powerpc distribution. > we no longer support that platform (or at l

Re: [Freesurfer] terrible movement; salvagable?

gt; just the window levels of the visualization though. Usually when the > normalization fails you'll see regions of gray matter that have been > set to 110, not just reduced contrast. > > cheers > Bruce > > > On Tue, 11 Sep 2012, Anthony Dick wrote: > >&g

Re: [Freesurfer] extracting hand drawn ROIs to Afni space

Not sure if you've done this, but if you run AFNI's @SUMA_Make_Spec_FS command it will convert all .mgz files to .nii. These can then be loaded as an overlay in AFNI. If you open the @SUMA_Make_Spec_FS command in a text editor, there is a line (387 in my editor) to edit which files to convert,

[Freesurfer] license file not working

Hello, I have been using Freesurfer for a number of years, and just installed v6.0. I run into this problem: -- ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/.license If you are out

Re: [Freesurfer] license file not working

cense.txt? On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick mailto:ad...@fiu.edu>> wrote: Hello, I have been using Freesurfer for a number of years, and just installed v6.0. I run in

Re: [Freesurfer] license file not working

nd stopped accepting the old format with FS 6.0. I have used FreeSurfer for a long time too and found that I had to get a new license file with this version. Peace, Matt. From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Anthony Dick mailto:ad...@fiu.edu>> Rep

Re: [Freesurfer] license file not working

; Is this still an issue for you? So long as there is a license file (name > .license or license.txt) in the FREESURFER_HOME directory, you should be > all set. > > -Zeke > > On 02/02/2017 06:46 PM, Anthony Dick wrote: >> Thanks Matt. I already tried it with a new registration,

[Freesurfer] running hippocampal segmentation on PING

Hello, Our group is interested in running the hippocampal segmentation on the PING dataset. That dataset was already Freesurfed, v4.5. When we try to just run the –hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) it dies looking for a number of files that were not

Re: [Freesurfer] running hippocampal segmentation on PING

, so i can play with it and see if there's anything we can do? Cheers E Sent from my phone, please excuse brevity and typos From: Anthony Dick Sent: Thursday, June 1, 16:40 Subject: [Freesurfer] running hippocampal segmentation on PING To: Freesurfer support list Hello, Our group is inter

Re: [Freesurfer] (no subject)

Hello Emily, The easiest free way (that I know of) is using Osirix (http://www.osirix-viewer.com/). In that program, there are a number of export functions. You may want to view in that and export to DICOM. You can then use dicom2nii (http://people.cas.sc.edu/rorden/mricron/dcm2nii.html) to con

[Freesurfer] postdoctoral fellowship in developmental cognitive neuroscience

$50K plus benefits postdoc in Miami, FL, two years. Please take a look! http://myweb.fiu.edu/adick/post-doctoral-fellow-positions/ -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Florida International U

Re: [Freesurfer] options for a poor T1

Hello Jason, The freesurfer folks may have some suggestions for adjusting certain parameters, but you can also try some denoising approaches before going into the freesurfer pipeline. There are a number of flavors. The link below is a good place to start I think. https://www.sciencedirect.com/

[Freesurfer] FW: Memorandum: Call for CASE Distinguished Postdoctoral Scholar {Disarmed}

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[Freesurfer] software for registering two flatmaps

Hello, Can the Freesurfer software register two flatmaps that are not created in Freesurfer? Would they just need to be converted? And which program is appropriate? Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in C

Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

Hello all, I believe Ziad Saad and friends have written AFNI/SUMA to make this easy. If you run @SUMA_Make_Spec_FS on your freesurfer files, it will convert all the volume-space segmentation and parcellation files to be readable in AFNI. Takes only a couple of minutes. Run @SUMA_Make_Spec_FS

Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

Hello all, I believe Ziad Saad and friends have written AFNI/SUMA to make this easy. If you run @SUMA_Make_Spec_FS on your freesurfer files, it will convert all the volume-space segmentation and parcellation files to be readable in AFNI. Takes only a couple of minutes. Run @SUMA_Make_Spec_FS

Re: [Freesurfer] problems with Surface-based Interhemispheric Registration

Hello Angela, Have you tried just running the specific commands to get the output file you need? https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable Anthony On 7/7/14, 10:52 AM, angela.fav...@unipd.it wrote: > Dear Freesurfer team > I am sorry to bore you again with my problems, but I n

Re: [Freesurfer] Spatial smoothing in Matlab

Hello, This shell script may do close to what you want it to do, so you could modify it. It does it within AFNI using converted freesurfer surfaces. http://faculty.fiu.edu/~adick/links/alphasurface.tcsh If you see any errors please let me know. Anthony On 7/18/14, 12:39 PM, Douglas Greve wrot

Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)

?Hello, I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped. Anthony From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Matthew Riddle Sent: Thursday, October 23, 2014 7:48 AM To: f

Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)

place where you have write permissions (as User). Best, Martin On 11/05/2014 12:56 PM, Anthony Dick wrote: Hello, I am encountering the exact same problem on Yosemite (10.10). The log file is attached. Any ideas? I am pretty stumped. Anthony

Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)

the bert folder but rather with > the permissions of the bert folder itself (and the permissions within). > > To run the bert case please 'cd' into the directory containing the bert > folder and type the following: > > sudo chmod -R a+wr bert > > -Zeke >

Re: [Freesurfer] surface template N

Hi Jason, I saw this last week. I *think* the original template was on 40 brains, so 40 seems like a good number. In my opinion the bigger issue is the 8 year age range. A 3-year-old's head is much smaller than an 11-year-old's. I'm not sure I would mix them, and if there are enough subjects

Re: [Freesurfer] Hyperintense WM & WM Deletions

We have the same problem using the same coil (GE 750; mainly occipital pole), so any suggestions for how to correct this would be very helpful. Thanks! Anthony On 1/5/15, 7:05 PM, Douglas Merkitch wrote: Hello Freesurfer experts, We have T1 data from a 3T GE 32-channel head coil that exhibit

Re: [Freesurfer] the Subcortical Segmentation and the Cortical Parcellation

The subcortical segmentation identifies subcortical structures such as thalamus, basal ganglia structures, hippocampus, amygdala, and cerebellum. The cortical parcellation delineates different areas of the cortex, such as the superior temporal sulcus, the central sulcus, the pars triangularis,

[Freesurfer] overlay alignment in tkmedit

Hello, I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignme

Re: [Freesurfer] overlay alignment in tkmedit

AFNI. Anthony On 1/13/12 2:11 PM, Douglas N Greve wrote: > Hi Anthony, how are you creating the parcellation? Are you generating > it off the orig.mgz? > doug > > Anthony Dick wrote: >> Hello, >> >> I am trying to train a cerebellar atlas based on 20 manually >

Re: [Freesurfer] overlay alignment in tkmedit

rom? > > Anthony Dick wrote: >> Here is the command, in case I didn't run it right. >> >> adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz >> chuman_1_do_shft_new.nii >> mri_convert chuman_1_do_shft.nii --in_like orig.mgz >> chuman_1_do_sh

Re: [Freesurfer] overlay alignment in tkmedit

That did the trick! Thanks very much! Anthony On 1/26/12 12:31 PM, Douglas N Greve wrote: > OK, try running > mri_label2vol --seg chuman_1_do.mgz --temp orig.mgz --regheader > chuman_1_do.mgz --o chuman_1_do.conf.mgz > Then load chuman_1_do.conf.mgz as a segmentation. > doug &

Re: [Freesurfer] how can I view and process Freesurfer files using AFNI

Hello Rashmi, This is an AFNI issue. You'll have to read the SUMA manual and convert your Freesurfer files to AFNI-readable surfaces using @SUMA_Make_Spec_FS and other commands. There are too many steps to list here, but it is not too difficult once you get the hang of it. Anthony On 1/27/1

[Freesurfer] mri_label2vol cannot allocate memory

Hello, I have run the following successfully, but when I have moved on to other brains I get: mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader > chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory I am running a Mac Pro with 8GB R

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On 2/15/12 1:43 PM, Anthony Dick wrote: > Hello, > > I have run the following successfully, but when I have moved on to other > brains I get: > > mri_label2vol --seg c

Re: [Freesurfer] mri_label2vol cannot allocate memory

n 3/7/12 9:17 AM, Bruce Fischl wrote: > Hi Anthony > > sounds like there is something wrong with one of your volumes. Can you > ru mri_info on them? > > Bruce > On Wed, 7 Mar 2012, Anthony Dick wrote: > >> Hello--I am giving this message a bump. Please let me know i

Re: [Freesurfer] mri_label2vol cannot allocate memory

t; > On 04/04/2012 12:29 PM, Anthony Dick wrote: >> Hello Bruce, >> >> Sorry--just getting back to this project. The basic problem is that I am >> trying to align a cerebellar parcellation with the underlay in tkmedit. >> I was working on this with Doug, and his su

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hello--was wondering if you guys have any ideas. I am a bit stumped. Thanks for the help! Anthony On 4/4/12 4:50 PM, Anthony Dick wrote: > No, but the conversion from the original .nii works... > > [miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh > mri_convert chuman_1.mgz ju

[Freesurfer] changing data structure

Hello, I am running the rebuild_gca_atlas.csh program and got the following error for seg_edited.mgz, which is the manually defined file imported from a different program outside of freesurfer. mri_ca_train: segmentation file /seg_edited.mgz is not type UCHAR or FLOAT Is there a way to redefi

[Freesurfer] created a new subcortical atlas; what's next?

Hello, I successfully created a new subcortical atlas for the cerebellum (at least I think I did--not sure how to check it without running a new segmentation). If I want to apply this to many brains, I think I want to run: recon-all -subcortseg -subjid How do I tell it to call, e.g., RB_a

Re: [Freesurfer] improving automated cerebellar parcellation

can do this by pasting your manual labels into our aseg of > the subjects in question. > > cheers > Bruce > > > > On Fri, 20 Apr 2012, Anthony Dick wrote: > >> >> Hello, >> >> I developed a new atlas for parcellating the cerebellum, based on 20 &g

Re: [Freesurfer] improving automated cerebellar parcellation

probably in matlab > On Fri, 20 Apr 2012, Anthony Dick wrote: > >> Thanks Bruce. What's the easiest way to "paste" those labels. >> Manually through tkmedit, or through the command line? >> >> Anthony >> >> On 4/20/12 3:53 PM, Bruce Fis

Re: [Freesurfer] merging rh and lh surfaces

Hi Seok- Is there a compelling reason to combine the two hemispheres? Are you trying to identify similar vertices in both hemispheres? Anthony p...@netfilter.com.br wrote: I think Bruce or Douglas can explain better. However, the reason for both hemispheres being separated is that you need

[Freesurfer] citation for appropriateness of using freesurfer with children

Hello- I am using Freesurfer to obtain cortical parcellations for both children (aged 8-11 years) and adults. A reviewer asked for evidence that the parcellation works equally well in children and adults. Has this been tested empirically and published anywhere? I found a post saying not too

Re: [Freesurfer] (no subject)

So the segmentation and the cortical parcellation are completely independent? Or does the cortical parcellation still use information from the segmentation? Bruce Fischl wrote: > Hi Miyoung", > > it's based on the white (yellow line) and pial surfaces. > > cheers, > Bruce > > On Fri, 4 Sep 2009,

[Freesurfer] postdoctoral position at The University of Chicago (on behalf of Dr. Steven Small)

A 2-3 year post-doctoral position is available at the Human Neuroscience Laboratory of The University of Chicago (www.humanneuroscience.org). The ideal candidate should be interested in the study of the neural basis of language and/or neural plasticity characterized by changes in brain networks

Re: [Freesurfer] Viewing AFNI data on FreeSurfer surface: The Basics

One way to do it is to convert the Freesurfer brains to AFNI readable surfaces using AFNI's SUMA add-on (http://afni.nimh.nih.gov/afni/suma). The steps are detailed in the documentation. Anthony Dickinson, Annelise (NIH/NIMH) [F] wrote: > Hi all, > > Sorry if this is a REALLY dumb question, I'm

[Freesurfer] question about clustering simulation

Hello all, I am interested in using the mri_glmfit simulation to control for multiple comparisons in data I have run on the surface in AFNI. Before doing this, I have a few questions: 1. What does the simulation with the mc-z flag do, exactly? It claims to be comparable to AFNI's AlphaSim, but

[Freesurfer] error make_average_subject

Hi all- In attempting to use make_average_subject I encountered a problem. The process died during >mris_curvature >averaging curvature patterns 10 times. >total integrated curvature = 106.607*4pi (1339.664) --> -106 handles >ICI = 265.0, FI = 2956.1, variation=44197.937 >writing Gaussian curv

Re: [Freesurfer] Zen of label editing in tksurfer

Hi Graham- The link below has a step-by-step method of editing labels in Freesurfer. It may be of some use. http://www.ci.uchicago.edu/wiki/bin/view/HNL/EditROI Please let me know if it makes things any easier. Anthony Bruce Fischl wrote: Hi Graham, is this on an individual subject or on

Re: [Freesurfer] using freesurfer register program to register afni data

Hi Garrett- Ziad wrote a program for AFNI (@SUMA_Make_Spec_FS) which converts all .mgz files to nifti format using Freesurfer's mri_convert. I believe there is also an AFNI program @SUMA_FSvolToBRIK which may do what you want? The AFNI message board has some information on this, although mri_

[Freesurfer] cerebellum

Hello- Are there any plans to implement the cerebellum segmentation of Makris et al. (2005; Neuroimage, 25) as an automated segmentation into part of the freesurfer workflow? Anthony -- Anthony Steven Dick, Ph.D. Post-Doctoral Fellow Human Neuroscience Laboratory Department of Neurology The

Re: [Freesurfer] major lobes of cerebellum

Nikos Makris and friends have two papers on this: Journal of Cognitive Neuroscience (2003) 15:4, 584-599 Neuroimage (2005) 25, 1146-1160 Juranek, Jenifer wrote: Is there any interest in parcellation of the cerebellum into its major regions: corpus medullare, anterior, superior-posterior, in

Re: [Freesurfer] AFNI /freesurfer aseg files problem

Hi Liat- If you converted directly using mri_convert, you may run into some problems. If so, I suggest using the program Ziad wrote (@SUMA_Make_Spec_FS) which takes care of some of the freesurfer/AFNI conversion problems automatically. See the AFNI posts on this issue. Anthony Doug Greve wr

Re: [Freesurfer] downloadable manual

If you are just getting started, this is the best place. http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction Once you have the basics the wiki is much more manageable. I think manual is at the bottom of the list because functionality is at the top. Anthony Eliezer Kanal wrote:

Re: [Freesurfer] Description of frontal labels Destrieux 2009

It is my understanding that these are defined based on the Duvernoy atlas. If this is not the case, please let me know. Lena Palaniyappan wrote: > Dear Christophe and team > > I am writing up something on frontal measures derived from 2009 > Destrieux atlas – I need to know the anatomical bounda

[Freesurfer] Lab Coordinator Position Available

Pruden) and the Developmental Cognitive Neuroscience Laboratory (directed by Dr. Anthony Dick) at Florida International University needs a highly capable, organized, and well-spoken individual to serve as a full-time laboratory coordinator for both labs. We seek a recent college graduate who has

Re: [Freesurfer] ICV differs systematically in repeated measurements

This is just a thought, but is this issue mitigated to some degree if you can show that the regions in which you are interested meet a certain minimum signal to noise ratio? Or maybe a more stringent requirement would be necessary, such that the SNR of the ROIs don't differ significantly? Alwa

Re: [Freesurfer] ICV differs systematically in repeated measurements

cheers > Bruce > On Mon, 20 Dec 2010, Anthony Dick wrote: > >> This is just a thought, but is this issue mitigated to some degree if >> you can show that the regions in which you are interested meet a certain >> minimum signal to noise ratio? Or maybe a more stringent re

[Freesurfer] cerebellum atlas template

Hello all, We are looking to develop a cerebellum atlas training set based on the Schmahmann et al (2000) parcellation so we can automatically segment the cerebellum based on this atlas. Does this exist already? I know Makris and colleagues had done something similar to this, but I am not sure

[Freesurfer] cerebellum atlas template

I didn't get a response the last post, so I'm going to try one more time! Hello all, We are looking to develop a cerebellum atlas training set based on the Schmahmann et al (2000) parcellation so we can automatically segment the cerebellum based on this atlas. Does this exist already? I know Makr

Re: [Freesurfer] Creating DLPFC label

AFNI program FSread_annot is exactly what you are looking for. On 6/6/11 2:27 PM, Allison R. Kaup wrote: > Hi all, > > I have created a DLPFC label in Freesurfer, and am now trying to > figure out how to visualize that ROI in SUMA.We have already > successfully converted the aparc+aseg to SUMA

Re: [Freesurfer] Adding tracts to Tracula!

Hello all, Is there any atlas to which these tracs are referenced? For cortical anatomical boundaries there is broad consensus and a published referenced atlas, which makes Freesurfer's automatic parcellation of cortical regions an excellent tool. But there is not (as is often assumed) as bro

Re: [Freesurfer] Adding tracts to Tracula!

al 2007. We did > not include the IFOF exactly b/c of the controversy surrounding it. > > a.y > > On Wed, 15 Jun 2011, Anthony Dick wrote: > >> Hello all, >> >> Is there any atlas to which these tracs are referenced? For cortical >> anatomical boundaries there

Re: [Freesurfer] Adding tracts to Tracula!

ed on visual inspection of > folding patterns and presumed homology with the macaque. It's a useful > tool, but like all tools you can overintepret the results if you are > not cautious. > > cheers > Bruce > > > > > On Wed, 15 Jun 2011, Anthony Dick wrote: >

Re: [Freesurfer] literature about multiple comparison correction

That paper is great. Lazar also has a nice review of a number of approaches in her book: Lazar, N. The statistical analysis of functional MRI data. On 7/21/11 11:39 AM, Douglas N Greve wrote: > Check out hayasaka and nichols 2003. pdf below > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fl