Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

Reorientation of raw images?
by chenchunhuichina 02 Feb '10

02 Feb '10

Hello Bruce, and Freesurfers, Sorry for asking an old question, but I really need more confirmation. I am running recon-all to processing my structural data, but i am not sure do I have to reorient the data or not. The data were acquired in sagital view, and dicom data were converted into nift format using dcm2nii, the transformed nii file (called original image below) are in wrong orienation, in fslview, it's X axis is acturally from anterior to posterior, the Y, Z axises were also wrong. dcm2nii also created a o*.nii image, which is in right orientation. I run recon-all using both images, and the results (volume for each region) are a little bit different, about 0.25%, for example, volume of a brain rigion got with original image is 2000 , but got with o*.nii image is 1995. It's not a big problem, but since they are exactly the same data, why the results are not exactly the same? is it better to use original image or even dicom files or to use reoriented data? the resolution of my data is 1*1*2 mm. Another related quetion is, if data are left-right fliped, do I have to flip the raw data and run recon-all again or can I just flip left-right of results, i.e., consider volume got for a left region as that of the corresponding right region? Thank you very much! 2010-02-02 Chunhui Chen _________________ Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人： Bruce Fischl 发送时间： 2010-01-22 12:38:11 收件人： chenchunhuichina 抄送：主题： Re: Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data no, that shouldn't matter On Fri, 22 Jan 2010, chenchunhuichina wrote: > May I ask a related question? > > My structural data are acquired in sagital view, do I have to re-orient it before I run recon-all? In fslview, it's X axis is acturally from anterior to posterior. > > Thanks! > > > 2010-01-22 > > > > chenchunhuichina > > > > 发件人： Bruce Fischl > 发送时间： 2010-01-22 07:06:58 > 收件人： yzhangd(a)artsci.wustl.edu > 抄送： freesurfer(a)nmr.mgh.harvard.edu > 主题： Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data > > How do you know? It should be in the same space. > Bruce > > > > On Jan 21, 2010, at 5:01 PM, yzhangd(a)artsci.wustl.edu wrote: > > > I have run the following command to create a 001.mgz file from raw > > *.dcm > > data: > > > > recon-all -s <subjid > -i <path to *.dcm data > > > > > The output 001.mgz file is not in the same native space as the > > original > > *.dcm data. Could anyone tell me what space the 001.mgz file is in? > > Does > > the above command change the orientation (i.e does it rotate/ > > translate) > > besides simply converting from .dcm to 001.mgz > > > > thanks a lot > > > > yuning > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

Re: [Freesurfer] Reorientation of raw images?
by chenchunhuichina 02 Feb '10

02 Feb '10

in some regions like left amygdata, the difference exceed 5% 2010-02-02 Chunhui Chen _________________ Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人： Bruce Fischl 发送时间： 2010-01-22 12:38:11 收件人： chenchunhuichina 抄送：主题： Re: Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data no, that shouldn't matter On Fri, 22 Jan 2010, chenchunhuichina wrote: > May I ask a related question? > > My structural data are acquired in sagital view, do I have to re-orient it before I run recon-all? In fslview, it's X axis is acturally from anterior to posterior. > > Thanks! > > > 2010-01-22 > > > > chenchunhuichina > > > > 发件人： Bruce Fischl > 发送时间： 2010-01-22 07:06:58 > 收件人： yzhangd(a)artsci.wustl.edu > 抄送： freesurfer(a)nmr.mgh.harvard.edu > 主题： Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data > > How do you know? It should be in the same space. > Bruce > > > > On Jan 21, 2010, at 5:01 PM, yzhangd(a)artsci.wustl.edu wrote: > > > I have run the following command to create a 001.mgz file from raw > > *.dcm > > data: > > > > recon-all -s <subjid > -i <path to *.dcm data > > > > > The output 001.mgz file is not in the same native space as the > > original > > *.dcm data. Could anyone tell me what space the 001.mgz file is in? > > Does > > the above command change the orientation (i.e does it rotate/ > > translate) > > besides simply converting from .dcm to 001.mgz > > > > thanks a lot > > > > yuning > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

FreeSurfer & Matlab
by Raghav Puranmalka 01 Feb '10

01 Feb '10

Hi all, I am working on a project that aims to: (1) Use an MRI image, skullstrip and convert the brain volume to a surface (2) Import that surface onto Matlab and visualize it there. (3) On top of that surface in Matlab, add pictures of electrodes as well as 3D "heat maps" of neural activity. It seems that FreeSurfer may be an option for me. I have a few questions that I have been unable to find the answers to: (1) Can one visualize the surface created by FreeSurface in Matlab? If so, would somebody be able to point me to the documentation? (2) Can one start the freesurfer from Matlab? It seems that the matlab files that come with freesurfer are more for reading and writing data rather than using/starting the freesurfer binaries. Thanks for your help! Best, Raghav Raghav Puranmalka Candidate B.S. Engineering | Major: Bioengineering Candidate M.S. Engineering | Major: Bioengineering SEAS | University of Pennsylvania raghav.puranmalka(a)gmail.com

3 3

Re: [Freesurfer] FreeSurfer & Matlab
by Raghav Puranmalka 01 Feb '10

01 Feb '10

Thanks all. The reason to use start FreeSurfer within Matlab would be to, for example, build a kind of integrated GUI able to accomplish DICOM -> Surface Visualization. But, for my case, its not that necessary; running FreeSurfer externally is acceptable. Thanks again for your help, Raghav On 02/01/2010 03:34 PM, Thomas Yeo wrote: > To visualize surfaces, I usually use the matlab function "trisurf" > > --Thomas > > > On Feb 1, 2010, at 3:27 PM, Bruce Fischl wrote: > >> Hi Raghav, >> >> yes, people have done visualization of surfaces in matlab, maybe >> Thomas (ccd) can comment. As for 2, I'm not sure I understand what >> you mean. Why would you need to run freesurfer from within matlab? I >> guess you could use eval to run recon-all if you had to, but I >> wouldn't think you would need to. >> >> cheers >> Bruce >> >> On Mon, 1 Feb 2010, Raghav Puranmalka wrote: >> >>> Hi all, >>> >>> I am working on a project that aims to: >>> >>> (1) Use an MRI image, skullstrip and convert the brain volume to a >>> surface >>> >>> (2) Import that surface onto Matlab and visualize it there. >>> >>> (3) On top of that surface in Matlab, add pictures of electrodes as >>> well >>> as 3D "heat maps" of neural activity. >>> >>> It seems that FreeSurfer may be an option for me. I have a few >>> questions >>> that I have been unable to find the answers to: >>> >>> (1) Can one visualize the surface created by FreeSurface in Matlab? If >>> so, would somebody be able to point me to the documentation? >>> >>> (2) Can one start the freesurfer from Matlab? It seems that the matlab >>> files that come with freesurfer are more for reading and writing data >>> rather than using/starting the freesurfer binaries. >>> >>> Thanks for your help! >>> >>> Best, >>> >>> Raghav >>> Raghav Puranmalka >>> Candidate B.S. Engineering | Major: Bioengineering >>> Candidate M.S. Engineering | Major: Bioengineering >>> SEAS | University of Pennsylvania >>> raghav.puranmalka(a)gmail.com >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >

1 0

Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results
by Stefan Ehrlich 01 Feb '10

01 Feb '10

Thank you all for the very good and detailed advice. We reran our cluster-wise correction after lowering the initial p-value (the one which is applied to the T-maps) to 0.01 or 0.001. Interestingly we then get the very same blob like in the FDR controlled approach (supramarginal gyrus). However, when using an initial p of 0.001 we loose the finding in the right middle temporal lobe. So I guess there are 2 remaining questions: 1) What is an appropriate initial p values (to define the clusters before simulation)?2) Is there any way to use the proposed fancier methods like TFCE or cluster-mass method within freesurfer? Thank you so much! Stefan Message: 1 Date: Fri, 29 Jan 2010 14:57:34 -0800 From: Don Hagler <dhaglerjr(a)hotmail.com> Subject: Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results To: Doug Greve <greve(a)nmr.mgh.harvard.edu> Cc: freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <SNT129-W21E7C86C55DB35F30A018FA65B0(a)phx.gbl> Content-Type: text/plain; charset="windows-1252" In my experience, which is more in fMRI than thickness analyses, 0.05 can yield very large mega-clusters that should actually be considered a conglomeration of smaller clusters. I found that regardless of whether one does Monte Carlo or GRF. Because 0.05 for uncorrected p values is quite liberal, only the very large clusters survive the multiple comparisons correction. So you can end up losing the smaller, but still significant clusters. For very smooth data (e.g. dSPMs from MEG/EEG), you may just get one huge cluster if you use 0.05. > Date: Fri, 29 Jan 2010 14:08:04 -0500 > From: greve(a)nmr.mgh.harvard.edu > To: dhaglerjr(a)hotmail.com > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results > > Don, why do you say that .05 is too liberal? We use a simulation-based > test, not GRF, so we don't have to worry about the GRF assumptions > breaking down at higher p-values. > > doug > > Don Hagler wrote: > > Who says FDR is more conservative? It all depends on the thresholds > > you choose. > > > > Note that the FDR threshold is different from the cluster-based p > > threshold, and it isn't necessarily appropriate to use the same for both. > > > > The cluster-based p threshold controls the overall probability that > > you will get 1 or more false positives. With p<0.05, the idea is that > > if you repeated your study 20 times, 19 times out of 20, you would > > have NO false positives. > > > > With an FDR threshold of 0.05, you are guaranteed that 5% of your > > "significant" vertices are false positives. A more conservative > > threshold would be 0.01. > > > > By the way, for cluster thresholding, there are two p thresholds that > > are important. The first is the p threshold applied to the z-stats or > > t-stats before finding clusters. 0.05 would usually be too liberal. > > 0.01 or 0.001 would be better. The second is the multiple comparison > > corrected p value, for which you would usually use 0.05. > > > > ------------------------------------------------------------------------ > > Date: Fri, 29 Jan 2010 10:02:45 -0500 > > From: stefan.brauns(a)googlemail.com > > To: Freesurfer(a)nmr.mgh.harvard.edu > > Subject: [Freesurfer] thickness maps: FDR versus Monte Carlo - > > different results > > > > Hi there, > > > > we are struggling with one question and haven't yet heard back. We > > would be very grateful for any advice or recommendation. > > > > We were running an analysis (95 subjects) examining a group effect > > (two groups, controlling for the effects of a covariate and two > > cofactors, DODS model) on cortical thickness with mri_glmfit. We then > > corrected our results for multiple comparisons using two methods, FDR > > and Monte Carlo simulation with 4000 repeats. The threshold was set at > > p=0.05 respectively. Although examining the same population we got > > results in very different regions. > > > > command for the simulation: > > > > mri_glmfit-sim --glmdir xxxx.glmdir --sim mc-z 4000 1.301 mc-z > > abs.1.301 --sim-sign abs > > > > the fdr results were obtained setting the fdr-threshold at p=0.05 with > > the tksurfer script command (sclv_set current_threshold_using_fdr 0.05 0) > > > > With the fdr method we found a spot in the left supramarginal gyrus > > and with the clusterwise correction we got a cluster in the right > > middle temporal lobe (see pictures of corrected and uncorrected > > results attached). No other clusters/findings survived one of the > > correction methods. > > > > We are well aware of the fact that FDR and Monte Carlo simulation are > > very different statistical methods and that FDR is more conservative. > > Does that explain the discrepant results? Would you expect a highly > > robust FDR finding to not show up at all when using Monte Carlo? What > > additional information could be used to decide which method to use for > > the final models? > > > > Thank you, > > > > Stefan

1 0

rebuild_gca_atlas.csh question
by Guang Zeng 01 Feb '10

01 Feb '10

Hi, there, I am running rebuild_gca_atlas.csh now, and met a problem at the first mri_ca_normalize step, my rebuild_gca_atlas.log file looks like below, .................... \n\n mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/norm.mgz mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/norm.mgz mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/norm.mgz mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/norm.mgz \n\n ...................... Is this noatlas noxform valid here, should it be -noatlas -noxform? Actually, what I got from my terminal is; Log file is /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/rebuild_gca_atlas_2010-02-01.log mri_ca_normalize each subject using its seg_edited.mgz, producing norm.mgz... mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/norm.mgz Unable to read script file because of error: error opening mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/bra: No such file or directory mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/norm.mgz Unable to read script file because of error: error opening mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502: No such file or directory mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/norm.mgz Unable to read script file because of error: error opening mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523: No such file or directory mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/norm.mgz Unable to read script file because of error: error opening mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129: No such file or directory But all the files and directories are there? any suggestions? Thanks! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/

2 1

group analysis with qdec
by Manabu Kubota 01 Feb '10

01 Feb '10

Dear all, Hi, I am a new user of freesurfer, and have a questions on group analysis with qdec. I compared average thickness between two groups (a control group and a patient group). What I am trying to do next is to make a mask where the patient group showed reduction of cortical thickness (for example, p<0.05, FDR), then examine the correlation between clinical scales and cortical thickness in the masked regions, by doing group analysis in the regions (not entire brain). I searched past archives, but couldn't find one. Does anyone know how to do this with qdec ? Thanks for your help, Kind regards Manabu Kubota kubotajp(a)kuhp.kyoto-u.ac.jp Kyoto University

2 3

extracting brodmann labels
by Benjamin Groisser 01 Feb '10

01 Feb '10

Hello, I'm trying to extract freesurfer generated labels BA4a, BA4p, and BA6. Are these labels (#404, 405, and 406) generated for each subject? If so, could you please tell me which file to extract them from? I don't fully understand how freesurfer organizes these labels compared to, say, cortical structures. Thanks! -bgroisse

3 2

Problem starting
by Janani Dhinakaran 01 Feb '10

01 Feb '10

Hello, I'm operating freesurfer through a virtual box. I checked the memory space it is around 4G. It's not starting. Any idea what I can do about it? -- I am the Sun, I know no darkness.

2 1

Segment the grey matter volume
by leemon albert 01 Feb '10

01 Feb '10

Hey, all Whether the FS only segment the white matter volume (WM - mri/wm) by default . How about the GM? If I want to get GM volume, is it a right way to use brain.mgz to subtract the wm.mgz? Best Wishes, -- Meng Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

2 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer