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

On 9/29/15 10:59 AM, chenhf_uestc wrote: 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

Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

Em 30/09/2015 11:30, "andrea cristina Lima" escreveu: > I got the error below. Could you help me? I've already check the dti file > and it seems Ok. Tks > > macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c >

[Freesurfer] selxavg3-sess outputs

Dear Freesurfer experts, The freesurfer command 'selxavg3-sess' outputs many files in the contrast folder in addition to the three documented on the Wiki (ces, cesvar, sig). Is there more detailed documentation on what each output is and how they're computed? In particular, I was wondering if the

Re: [Freesurfer] Sulc value of given Tal coordinates

Rudolph Could you possibly tell me or point in the direction of a tutorial on how to map tal coordinates to the vertex mesh? Many thanks Karen Karen Bunday, PhD Honorary Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

Hi Martin, Thank you for helping ! 1) What should I use for the parameter estimation: "mass univariate" or Novel mass-univariate tools (spatiotemporal models)" ? 2) I have one group of subjects with different timepoints (non equally spaced and different numbers of timepoints), and would like to

[Freesurfer] mri_vol2surf

I am trying to produce a scalar overlay from PET data to overlay onto the pial surface. I have coregistered the pet with T1.mgz and then used the transform from mri_info --scanner2tkr to co-localise with orig.mgz. I then do: mri_vol2surf --src --out --out_type paint --regheader --hemi lh

[Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

I got the error below. Could you help me? I've already check the dti file and it seems Ok. Tks macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt INFO: SUBJECTS_DIR is

Re: [Freesurfer] Freesurfer methods and reviewer queries

Hi Mahinda 1. The subvoxel accuracy has been verified experimentally in Dianas Rosas' paper: http://www.ncbi.nlm.nih.gov/pubmed/11889230 where she measured the thickness under a microscope (ex vivo) and compared it to our results and found they agreed within a couple of hundred microns.

Re: [Freesurfer] Question about the negative value of surface area

Hi Feng the area of the triangls is oriented to detected changes in the jacobian. That said, they should be positive definite (you can verify thismris_remove_intersection on the ?h.sphere.reg to make sure that this is the case. Perhaps Anderson or Doug can comment? cheers Bruce On Tue, 29

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

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 thickness, surface area and so on. If not, could I mask the

[Freesurfer] WM segmentation error longitudinal stream

Hi all, We have run longitudinal analysis on two time points. The resulting longitudinal WM surface for both time points excludes large parts of the cortex. The cross sectional surfaces and the wm.mgz are correct. The base wm.mgz also seems to be fine, however, the base white and pial surfaces

Re: [Freesurfer] warping surface label to volume space

Hi Doug, Just as a reminder: I uploaded the data yesterday. Best Heidi From: Douglas Greve > Reply-To: Freesurfer support list > Date: Tuesday 29 September 2015

Re: [Freesurfer] dt_recon

Hi Doug, Thank you very much for your answers! Kindly I have one more question: At the end of DTI analysis using the tool "dt_recon" we will have " stats" file including the FA value for every segment and parcellate in the brain. Depending on this output can we use the term " DTI morphometry"

Re: [Freesurfer] 3_group_comparison

Thank you very much for your suggestion. Now it has worked well. However, I am having trouble running the simulation via: mri_glmfit-sim --glmdir NSS_3_GR.glmdir --cache 4 abs --cwp 0.05 --2spaces ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 Where can I set up the EN language with

[Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')

Dear experts, I'm trying to calculate local gyrifcation index using CIVET's surface file ('.obj'). First, I've successfully done 'CIVET --> FreeSurfer' conversion and created a '.pial' file - below are the commands that worked for 'CIVET --> FreeSurfer' and 'FreeSurfer --> CIVET'

[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

Re: [Freesurfer] problem fast_selxavg3b

Dear freesurfer experts, I included the new function but I got another problem: First error: /opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i

Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

Ok! Thank you! I will try again! 2015-09-30 19:16 GMT-03:00 andrea cristina Lima : > Em 30/09/2015 11:30, "andrea cristina Lima" > escreveu: > >> I got the error below. Could you help me? I've already check the dti file >> and it seems Ok. Tks

Re: [Freesurfer] Sulc value of given Tal coordinates

Hi Doug Thank you. Could you point me in the direction of some tutorials that might help me do this? BW Karen Karen Bunday, PhD Honorary Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London -Original

Re: [Freesurfer] problem fast_selxavg3b

Thanks Doug! I have another question: We did the fsfast analysis some time ago before we updated freesurfer version with fast_selxavg3. Now we want to analyse additional persons. Do you think it is comparable or is it better to re-do the analysis for all persons with fast_selxavg3b instead of

[Freesurfer] Error Messages for Accessing Bin

> Hello, > When I run the command "sFSstart" on version 5.0.0, I am receiving the > messages below. Would you please explain to me what the problem is? It > seems like there is trouble accessing the bin. > Thank you > > freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 > Setting

Re: [Freesurfer] Parcellation stats

that will generate a parcellation on the individual subject surface of Thomas Yeo's 17-network clustering. It won't do anything with the thickness though. What are you trying to do? On Tue, 29 Sep 2015, Ali Radaideh wrote: mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh

Re: [Freesurfer] R: import FS-FAST results in FSL

Do you mean surface-based analysis? You'd have to put them back into the volume using mri_surf2vol, write them out as nifti and then run fslview on them On 09/29/2015 11:17 AM, std...@virgilio.it wrote: > > Hi list, > > I would like to import FS-FAST results (conjunction maps) in FSL, >

[Freesurfer] Isxconcat-sess error

Hi Freesurfer experts, I'm trying to concatenate subjects using the command isxconcat-sess -d $SUBJECTS_DIR -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/TEST -analysis SIRP_LoadRegression_Stable5_072915 -c Cond2vFix -hemis -o

Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

This is really weird. Can you please confirm that the file /Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib exists? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

Re: [Freesurfer] PVE correction tool within the V 6 beta

Dear Greve, Thank you for your answer. Steps 1 and 2 are ok but in step 3 there are some unclear options (e.g. --mgx .01) Could you please explain which method is used for the pve correction and how can I obtain the 4D-pve-corrected images? Is it possible to extract the TACS of all regions?

Re: [Freesurfer] Error Messages for Accessing Bin

can you try chmod a+x on one of them and see if it can then be executed? e.g.: chmod a+x /home/tle7/freesurfer/bin/mri_convert /home/tle7/freesurfer/bin/mri_convert and see if you get an error. If not, you probably downloaded the wrong hardware version cheers Bruce On Tue, 29 Sep 2015,

[Freesurfer] Test incoming emails -

I am sending this message as a test since my income emails from FS stopped working on the 29 of September.Regards ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] mri_convert doubles file size when changing TR header information

I noticed after running slice-time correction with SPM, the resulting Nifti files do not have TR information in the header. This breaks the Freesurfer pipeline. To get around this, I attempted to use the mir_convert function with the “tr” flag to set the TR. However, in doing so, I noticed that

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

Hi Feng they are different atlases made up of a different set of manually labeled subjects but they share the same colortable cheers Bruce On Tue, 29 Sep 2015, chenhf_uestc wrote: Dear Freesurfer experts,   In the stats folder of subject in the SUBJECTS_DIR, I found the files of

[Freesurfer] qdec errors

Dear Doug/Experts, I tried to compare the right area between 2 groups (A, PC) with Age, Gender and total right surface area as covariates using Qdec but encountered the following errors. Please kindly help? Many thanks, Lena

[Freesurfer] Error using selexavg3-sess

Hi there, I’m running into difficulty executing the “selexavg3-sess” command for a few participants. For example, when I run the command: foreach c(lh rh mni305) selxavg3-sess -analysis analysis_encoding_stimXmem.$c -s nmasa_045_130621 -d . -no-preproc end I get the following error: Error

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

Yes, they are 2 separate atlases. The references are on the FS wiki. The "ctab" files are colortable files, so I believe the "25 100 40 0" are the RGB + transparency/opacity From: freesurfer-boun...@nmr.mgh.harvard.edu

[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

Re: [Freesurfer] GRF correction in mri_glmfit-sim

On 9/29/15 11:32 AM, chenhf_uestc wrote: 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"

[Freesurfer] Error Message when Accessing Bin

Hello, When I run the command "sFSstart" on version 5.0.0, I am receiving the messages below. Would you please explain to me what the problem is? It seems like there is trouble accessing the bin. Thank you freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 Setting up environment

Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')

Hi Kie Woo, The other thing that you might want to check is that the pial-outer-smoothed surface and the pial surface match, in case the transformation from the CIVET format induced any strange translation in space and they don't line up. Just open them both on a volume using tkmedit or

Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi Eugenio the maci64 directory does not exist in /Applications/freesurfer/MCRv80/bin/ Should I reinstall freesurfer? thanks! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias

Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')

Hi Kie Woo can you run mris_euler_number on those surfaces to see if they are topologically correct? cheers Bruce On Thu, 1 Oct 2015, Nam, Kie Woo wrote: Dear experts,   I’m trying to calculate local gyrifcation index using CIVET’s surface file (‘.obj’).         First, I’ve

Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

It's trying to find a file called SUBJECTS_DIR/Enzo_recon1/dti.nii. This is a relative path, i.e., it's trying to find it under the directory where you are currently cd'd. This seems like a problem with defining paths properly for unix, rather than a tracula problem per se. On Wed, 30 Sep

Re: [Freesurfer] Error Messages for Accessing Bin

Hi, I tried the chmod command, but it did not work. How I check that I've downloaded the correct version? Thank you very much Timothy On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl wrote: > can you try chmod a+x on one of them and see if it can then be executed? >

Re: [Freesurfer] Registering set of extracted hippocampus

Hello, Rewording to clarify in case the wording was confusing. What I would like to do is to use each registered ROI for intensity based analysis. I am confused how to use Freesurfer to register and align about three axis. I understand there is variability with positioning the head within

Re: [Freesurfer] Parcellation stats

Can we get any stats from this type of parcellation? I only can see two annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay. Thanks, Ali On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl wrote: > that will generate a

Re: [Freesurfer] Registering set of extracted hippocampus

Hi Chester you can use the talairach.m3z to map to a common space (which is our nonlinear atlas space). The easiest thing is probably to do (e.g.) mri_extract_label -t transforms/talairach.m3z aseg.mgz 17 lh.hippo.mgz this will extract the lh hippo label and transform it into our common

Re: [Freesurfer] Parcellation stats

sure, you can use mri_segstats to get stats from it Bruce On Thu, 1 Oct 2015, Ali Radaideh wrote: Can we get any stats from this type of parcellation? I only can see two annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay. Thanks, Ali On

[Freesurfer] FreeSurfer Ubuntu Server

Hi, could you help me please, because a couldn't find the answer for my question in the wiki. Can FreeSurfer be installed on ubuntu server 12.04? How can I do it, if it's possible? Thank you. -- Best Regards Bruno Bragança Mendes Laboratório de Alto Desempenho LAD/PUCRS Av. Ipiranga, 6681 -

[Freesurfer] freeview and ?h.cortex.patch.flat

Hi, Can the developmental freeview display ?h.cortex.patch.flat? I can't find answers in the mail list. If not, is there any way to convert the patch.flat to a format freeview can display? Thanks,Xiaomin___

[Freesurfer] Post-doctoral Positions in Affective Neuroscience at McLean Hospital/Harvard Medical School

Two post-doctoral positions are available within the Laboratory for Affective and Translational Neuroscience at McLean Hospital/Harvard Medical School, directed by Diego A. Pizzagalli, Ph.D. The laboratory is part of the Center for Depression, Anxiety and Stress Research (CDASR), a vibrant

Re: [Freesurfer] FreeSurfer Ubuntu Server

Yes, FreeSurfer can be installed on Ubuntu without any issues. There is also no functional difference between Ubuntu server and Ubuntu Desktop. Do you have a compelling reason for wanting to use Ubuntu 12.04? It was released in 2012 and is rather ancient in Ubuntu terms. The current version of

[Freesurfer] White matter Error

​ NCP140539_2_recon.rar ​Hi Freesurfer Experts, We are on the process of troubleshooting our subjects's recon and we came across with this error that we can not determine what kind of problem this is: It seems