[Freesurfer] freesurfer problem report

Dear freesurfer experts, I came across a problem when I run freesurfer. I just download the freesurfer software ( VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G ). I install the software and configuration, and I changed subjects_dir

Re: [Freesurfer] freesurfer problem report

Hi Zeke, When I enter the commands $> cd /media/sf_E_DRIVE/output/nv001/mri $> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz The output is in the attached file 1.txt. However, if I keep the subjects_dir (/usr/local/freesurfer/subjects) as

[Freesurfer] Question about the outputs of recon-all

Dear Freesurfer experts, I am a new user of freesurfer and I just performed recon-all analyses. I have some questions about the pipeline (may be very simple ^_^). In the fMRI, I used SPM8 toolkit to perform preprocessing. After normalization, the images were transform to the MNI space. In the f

Re: [Freesurfer] Question about the outputs of recon-all

ou can run mris_preproc to get a stack of data in fsaverage space prior to running group analysis with mri_glmfit. See the on-line tutorials on the wiki. On 08/11/2015 09:46 PM, chenhf_uestc wrote: > Dear Freesurfer experts, > I am a new user of freesurfer and I just performed recon-all

[Freesurfer] Is the fsaverage in the MNI space?

Dear freesurfer experts, The freesurfer online manual stated that before group analysis, we should resample data onto the common space (fsaverage). I have three questions here. First, Is the fsaverage file in the MNI space? In some previous studies, they report significant clusters with MNI co

[Freesurfer] Query about transformations in the recon-all

Dear Freesurfer experts, I have some questions in the recon-all. After reading online manual and discussing with the experts in the maillist, I have known all the recon-all procedures performed in the individual native space. However, I very confuse that there are many transformations in the re

Re: [Freesurfer] Query about transformations in the recon-all

asons. The em reg is computed once in the image with skull to help with skull stripping, then again to the GCA atlas to initialize the nonlinear transform for computing the aseg segmentation. cheers Bruce On Tue, 18 Aug 2015, chenhf_uestc wrote: > Dear Freesurfer experts, >

[Freesurfer] Questions about the correction methods in Surfstat

Dear Surfstat Users, I have a question about the RFT correction method in the Surfstat(http://www.math.mcgill.ca/keith/surfstat/). In the online manual, the command to perform RFT correction is as follows: [ pval, peak, clus ] = SurfStatP( slm, mask ); pval.P contains P-values for peaks, and p

[Freesurfer] Question about the raw thickness range

Dear Freesurfer experts, I have two question about my freesurfer results. 1. I performed recon-all analyses on my data and found all the data's maximal value of cortical thickness is 5. Is there any standardization procedure in the recon-all that normalize the maximum value to 5? In addition,

[Freesurfer] Can MRIread function read .mgz file

If this function cannot read the .mgz file, how can I read it? Best, Feng 2015-09-17 chenhf_uestc ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is i

Re: [Freesurfer] Can MRIread function read .mgz file

er] Can MRIread function read .mgz file 收件人："Freesurfer support list" 抄送： Hi Feng can you load that file into tksurfer/freeview? It sounds like something is wrong with it. You should also just run ls -l on it and see if it looks reasonable in terms of size and permissions cheers Bruc

[Freesurfer] Question about the multiple comparison correction in FreeSurfer

Dear Freesurfer experts, I have some questions about the multiple comparison correction method for group analysis in Freesurfer. The manual stated that we could use the commands as follows: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces This is t

[Freesurfer] How could I display the tksurfer correctly

Dear Freesurfer experts, I use Oracle VM VirtualBox to run Freesurfer software and I want to perform FDR correction in TKSurfer. However, I cannot get the whole window size (attached 1.png), and thus I cannot find the FDR option. Actually, there are lots of options (2.png) cannot be displayed i

Re: [Freesurfer] Question about the multiple comparison correction in FreeSurfer

dr.mgh') It is also possible with mri_surfcluster On 09/20/2015 12:47 PM, chenhf_uestc wrote: > Dear Freesurfer experts, > I have some questions about the multiple comparison correction method > for group analysis in Freesurfer. The manual stated that we could use > the

[Freesurfer] Question about the volume conversion in freesurfer

Dear freesurfer experts, I want to compute functional connectivity based on the region with significantly different cortical thickness of two groups. The fMRI data have been preprocessed by using SPM software and normalized to the MNI space. However, I do not how to use the function mri_surf2vo

[Freesurfer] Query about the fsgd file and glm model in freesurfer

Dear freesurfer experts, I have some questions about the statistical model in freesurfer. In my experiments, I would like to compare the cortical thickness of two groups (schizophrenia patients and healthy controls) with age and sex as covariates. I want to know that the variable in fsgd file

Re: [Freesurfer] .mgh file not load into surfstats

Hi, Myriam Actually, you do not need to convert a .mgh file to a .obj file, just use the SurfStatReadData function rather than SurfStatReadSurf. In addition, you can use load_mgh or MRIread function (Matlab function) in Freesurfer to read the mgh file. For the error "using + Matrix dimensions

[Freesurfer] The range of value of the area file

Dear Freesurfer experts, I read the raw area file and the area resampled to the fsaverage space and found several interesting things. raw58l = read_curv('E:\fs_result\NC058\surf\lh.area'); % the range of the area value is [-0.0471 6.2118] raw58r = read_curv('E:\fs_result\NC058\surf\rh.area'); %

Re: [Freesurfer] Question about the volume conversion in freesurfer

is not an easy thing to do. First of all, did you apply a nonlinear registration to get the fMRI to the normalized MNI space? If so, then you can not do what you want with the data you have pre-processed. On 9/24/15 2:26 AM, chenhf_uestc wrote: Dear freesurfer experts, I want to compute

[Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats

Dear Freesurfer experts, In the stats folder of subject in the SUBJECTS_DIR, I found the files of lh.aparc.DKTatlas40.stats and lh.aparc.stats. Are there statistical results belong to two different atlas? Because the values and brain regions are different in these two files. In these two file

[Freesurfer] Question about the negative value of surface area

Dear Freesurfer experts, I read the raw area file and the area resampled to the fsaverage space and found several interesting things. raw58l = read_curv('E:\fs_result\NC058\surf\lh.area'); % the range of the area value is [-0.0471 6.2118] raw58r = read_curv('E:\fs_result\NC058\surf\rh.area'); %

Re: [Freesurfer] GRF correction in mri_glmfit-sim

I am also very interested in these questions, but I do not find the response. Could anyone provide the answers? Thanks, Feng 发件人："Meiling Li" 发送时间：2015-09-22 22:09 主题：[Freesurfer] GRF correction in mri_glmfit-sim 收件人："freesurfer-help" 抄送： Dear FS experts I do GRF correction using mri_glmfit

[Freesurfer] Calculate the cortical thickness in patients with brain tumor

Hi, freesurfer experts, If my data came from the patients with brain tumors, could I perform recon-all analyses to calculate cortical thickness, surface area and so on. If not, could I mask the brain region with tumor and then conduct such analyses? I think the tumor might lead to the inaccurac

[Freesurfer] Calculate the cortical thickness in patients with brain tumor

Hi, freesurfer experts, If my data came from the patients with brain tumors, could I perform recon-all analyses to calculate cortical thickness, surface area and so on. If not, could I mask the brain region with tumor and then conduct such analyses? I think the tumor might lead to the inaccurac

Re: [Freesurfer] Question about the volume conversion in freesurfer

is not an easy thing to do. First of all, did you apply a nonlinear registration to get the fMRI to the normalized MNI space? If so, then you can not do what you want with the data you have pre-processed. On 9/24/15 2:26 AM, chenhf_uestc wrote: Dear freesurfer experts, I want to compute

Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor

urfer support list" 抄送： Hi Feng it depends on where the tumor is cheers Bruce On Wed, 30 Sep 2015, chenhf_uestc wrote: > Hi, freesurfer experts, > > If my data came from the patients with brain tumors, could I perform > recon-all analyses to calculate cortical thicknes

[Freesurfer] Query about the calculation of surface area

Dear Freesurfer experts, I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what about the surface area? Calculation based on pial or white matter? Or average the area of both of them. Is the area of each ver

Re: [Freesurfer] Query about the calculation of surface area

l cheers Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote: > Dear Freesurfer experts, > > I have a question about the calculation of surface area. The cortical > thickness is the distance between the pial and white matter. But, what about > the surface area? Calculation base

Re: [Freesurfer] Query about the calculation of surface area

On Tue, 6 Oct 2015, chenhf_uestc wrote: > Thanks, Bruce So, in the stats folder of each subject, the > lh.aparc.a2009s.stats file provides surfarea of each region. This value > is the area for the white surface, right? > Is the area of each vertex obtained by the average th

Re: [Freesurfer] Questions about the correction methods in Surfstat

luster threshould of e.g., p<0.05, right? What is the detailed correction procedure in the Surfstat software? Exactly the same, p=0.001 for defining supra-threshold clusters and p=0.05 for RFT correction. Regards, Felix. Best Regards, Donald McLaren, PhD On Sun, Sep 13, 2015 at 9:36 AM

Re: [Freesurfer] Query about the calculation of surface area

ruce On Wed, 7 Oct 2015, chenhf_uestc wrote: > Thanks a lot, Bruce > > If I want to compare the surface area between the patients and healthy > control groups, which area file should I use? The area or the area.pial? Or > I should compare both of them? If I should use both, is ther

[Freesurfer] error in qdec

Dear Freesurfer experts, I used qdec for group comparison, but there is error (acctached error.png). I check all the files but do not find where is the erros. Could anyone give me some suggestions? Best, Feng fsid.levels Description: Binary data gender.levels Description: Binary data group

[Freesurfer] A potential problem in qdec

Dear Freesurfer users, Is there anyone that use virtual box freesurfer version for group comparison via qdec? I use the freesurfer version below: VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G I used qdec for group comparison, but

[Freesurfer] A potential problem in qdec

Dear Freesurfer users, Is there anyone that use virtual box freesurfer version for group comparison via qdec? I use the freesurfer version below: VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G I used qdec for group comparison, but

Re: [Freesurfer] Problem with fsgd file

hi, Bronwyn You should change the position of parameter "dods" like this: mri_glmfit --fsgd long-2stage_ConAR.fsgd dods --glmdir long-2stage_ConAR.area.lh.spc.glmdir --y long-ConAR.lh.area-spc.stack.fwhm10.mgh Hope this helps. Best, Feng 发件人：Bronwyn Overs 发送时间：2015-10-14 08:11 主题：[Freesur

Re: [Freesurfer] extract pial surface

The area.pial file. Best, Feng 发件人：Sandy Schramm 发送时间：2015-11-06 15:24 主题：[Freesurfer] extract pial surface 收件人："freesurfer" 抄送： Dear experts, how can I extract pial surface (in mm2) of all our participants? Performing aparcstats2table -meas area extracts white area. Thanks, Sandy _