[Freesurfer] extract time series from surface vertices

Hi All, If I use mri_vol2surf to sample the functional volume onto surface, how can I extract the time series from surface vertices corresponding to certain ROI or Label which were created by freesurfer. Thanks! Yun ___ Freesurfer mailing list

Re: [Freesurfer] Problem with recon-all

Hi and thanks for the fast reply. Pardon my ignorance, but I am not sure that the PD images are? thanks, mads On 5 October 2015 at 21:59, Bruce Fischl wrote: > Hi Mads > > my guess is that this is a problem with the MP2RAGE. We don't see this in > the mprage or

Re: [Freesurfer] Problem with recon-all

Hi Mads my guess is that this is a problem with the MP2RAGE. We don't see this in the mprage or memprage. Can you look at the PD images in that region? Is the PD close to 0? Maybe you can threshold it out? That region is usually very dark on an mprage cheers Bruce On Mon, 5 Oct 2015, Mads

[Freesurfer] problem fast_selxavg3b

Dear freesurfer experts, I included the new function fast_selxavg3b 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

[Freesurfer] Custom parcellation for HCP data

Hi all, We want to create a custom parcellation for use with the connectome project data. However, we have not been able to achieve accurate spatial alignment between the random parcellation volume and the T1w volume. Specifically, there appears to be an "offset," possibly due to a mismatch

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

Yes, my data have been normalized to the MNI space. So, in my case, what should I do if I want to use the mri_surf2vol function? Best, Feng 发件人：Douglas Greve 发送时间：2015-09-29 00:00 主题：Re: [Freesurfer] Question about the volume conversion in freesurfer

Re: [Freesurfer] Problem with recon-all

I think the standard MP2RAGE only generates the T1 image on the scanner. With the Bloch simulation you can also figure out PD but the online image analysis doesn't do it. On 10/05/2015 04:21 PM, Bruce Fischl wrote: > I thought mp2rage lets you derive a proton-density (PD) weighted image, > but

Re: [Freesurfer] 3_group_comparison

Hi Dusan, setenv is used when you are using tcsh. since you are using bash, you can run this command to set your language: export LANG=en_US.UTF-8 Hope this helps. Best, Lee On Tue, 29 Sep 2015, Dusan Hirjak wrote: Thank you very much for your suggestion. Now it has worked well. 

Re: [Freesurfer] Error Messages for Accessing Bin

Hi, From the following output, how should I proceed? Thank you very much Timothy Le > On Oct 2, 2015, at 11:55 AM, Timothy Quang-Tin Le wrote: > > Hi, > Thank you very much for your response. The output of that command was: > > tle7@sni-vcs-gotlib:~$ ls -l

Re: [Freesurfer] Longitudinal_analysis_results

Hi Dusan, On the RepeatedMeasuresAnova page you sent, the last command doesn't include the --surface flag. You can try running your command without that part: mri_glmfit --glmdir lh.rmanova --y lh.thickness.sm15.mgh --fsgd long.table.fsgd doss --C contrast.mtx --C contrast2.mtx --C mean.mtx

Re: [Freesurfer] selxavg3-sess outputs

Yes, they do. There is also a pcc.nii.gz which is the partial correlation coefficient. On 9/30/15 1:14 PM, Jiahe Zhang wrote: 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,

Re: [Freesurfer] problem fast_selxavg3b

It is never good to mix versions, so I would re-do it. On 9/29/15 1:45 PM, Desiree Thielemann wrote: > 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

Re: [Freesurfer] mri_vol2surf

On 9/29/15 3:36 PM, Martin Tisdall wrote: > 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. What does that mean? You'll

[Freesurfer] Problem with recon-all

Hi, I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon

Re: [Freesurfer] Problem with recon-all

I thought mp2rage lets you derive a proton-density (PD) weighted image, but I could be wrong. I'll cc Andre van der Kouwe who will know On Mon, 5 Oct 2015, Mads Jensen wrote: > Hi and thanks for the fast reply. > > Pardon my ignorance, but I am not sure that the PD images are? > > thanks, >

Re: [Freesurfer] Error using selexavg3-sess

Not sure what it is. Can you send the Xtmp.mat file from the output folder? On 10/2/15 5:47 PM, Morenikeji Adebayo wrote: Just following up on this - thanks! On Sep 29, 2015, at 1:29 PM, Morenikeji Adebayo > wrote: Hi there, I’m

Re: [Freesurfer] problem fast_selxavg3b

I don't think it is a matlab problem. We call some binaries from inside matlab, and the problem is with those. It looks like the version of FS does not match your operating system or that you are missing a library. Maybe Zeke can help sort it out. doug On 10/5/15 2:31 AM, Desiree Thielemann

Re: [Freesurfer] mris_surf2vol

here you go ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol.mac64 On 10/5/15 11:24 AM, Kevin Aquino wrote: Hi Doug, Thanks for the file, do you happen to have one that is compiled for a 64bit mac installation of freesurfer? Cheers! Cheers, *Dr Kevin Aquino*

Re: [Freesurfer] extract time series from surface vertices

mri_segstats with the label option. Specify --id 1 and use the --avgwf output option to get the full time course On 10/5/15 1:34 PM, Yun Wang wrote: > Hi All, > > If I use mri_vol2surf to sample the functional volume onto surface, how can I > extract the time series from surface vertices

Re: [Freesurfer] error using mri_glmfit

Hi Andrea, can you send the files in their original format (not rtf)? On 10/5/15 12:58 PM, Gold, Andrea (NIH/NIMH) [F] wrote: Hi, I got the following error during my first time running the mri_glmfit command: mri_glmfit --y Model1_Maltx_ParentEd_Sex_Age_n58-lh-thickness.mgh --fsgd

[Freesurfer] Postdoctoral Fellow in Machine Learning in Neuroimaging

Dear All, I am looking to hire a postdoc to develop machine learning algorithms for fMRI. Topics are flexible. Example topics include dynamic functional connectivity, meta-analysis, neural mass modeling, monkey-human homologies, mental disorder subtypes, etc. Other details below. Regards,

[Freesurfer] FSGD for A mixed effect model approach in within subject dataset

Hello JorgeTrying to set up for running Linear Mixed Effects. My design has 3 groups (HC, PT relatives and PT) and therefore I am not using QDEC as suggested in the tutorial. My first question: Are there any changes from the matlab commands you suggest in the tutorial if using fsgd rather than

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] Custom parcellation for HCP data

Hi Simon,  Since you are using the HCP data, this may be more appropriate for the HCP-Users list. If you look at the current HCP pipeline code, you'll see that after converting FS surfaces to .surf.gii (using 'mris_convert'), an affine transform is then applied based on the c_ras contents

Re: [Freesurfer] White matter Error

Hi Bruce, I did check the output recon by using mris_euler_number, all the results of ?h.pial, ?.white and also ?h.inflated returned with: 0 holes. But the result from lh.inflated.nofix was: 28 holes. When I load the 3D images of ?h.inflated.nofix in freeview, it appears alot of holes and also

Re: [Freesurfer] Lost toolbar in freeview

Dear Ruopeng, I have the same problem with missing toolbars in freeView, however I am not successful with command defaults delete edu.harvard.mgh.nmr.FreeView The command shows: defaults delete: couldn't remove non-existent domain edu.harvard.mgh.nmr.FreeView My command defaults

[Freesurfer] Fwd: OHBM 2016 Call For Council Nominations

Forwarded Message Subject:OHBM 2016 Call For Council Nominations Date: Mon, 05 Oct 2015 09:59:50 -0500 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu Dear OHBM Member: Why is strong leadership so

Re: [Freesurfer] mris_surf2vol

Hi Doug, Thanks for the file, do you happen to have one that is compiled for a 64bit mac installation of freesurfer? Cheers! Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics,

[Freesurfer] wm.mgz ventricle white matter problem

Dear freesurfer experts, I have an issue with -autorecon2-wm stage results (freesurfer v.5.3.0). Sometimes the ventricles are not fully filled and the white matter is localized within the remaining gaps. After manually filling the gaps in the wm.mgz (following the wiki - Fixing Common

[Freesurfer] error using mri_glmfit

Hi, I got the following error during my first time running the mri_glmfit command: mri_glmfit --y Model1_Maltx_ParentEd_Sex_Age_n58-lh-thickness.mgh --fsgd Model1_Maltx_ParentEd_Sex_Age_n58.fsgd --C Model1_Maltx.mtx --C Model1_ParentEd.mtx --surf fsaverage lh --glmdir

Re: [Freesurfer] Exporting ROIs as .nii

Hi Eli sure, you can use mri_extract_label and specify the output volume as .nii (or .nii.gz) cheers Bruce On Mon, 5 Oct 2015, Rockers, Elijah D. wrote: Hello, We are interested in finding a way to use particular parcellations from Freesurfer in a separate program. For instance, we are

Re: [Freesurfer] White matter Error

Hi Trinh the inflated.nofix files are the ones before the topology fixer so they will always have defects in them cheers Bruce On Mon, 5 Oct 2015, Thục Trinh wrote: Hi Bruce, I did check the output recon by using mris_euler_number, all the results of ?h.pial, ?.white and also ?h.inflated

Re: [Freesurfer] Lost toolbar in freeview

What system are your running it on? I found it strange "defaults domains" only shows one item. On 10/05/2015 11:23 AM, Antonin Skoch wrote: Dear Ruopeng, I have the same problem with missing toolbars in freeView, however I am not successful with command defaults delete

Re: [Freesurfer] Lost toolbar in freeview

Can you also try delete ~/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plist Try that and "defaults delete..." together. On 10/05/2015 12:16 PM, Ruopeng Wang wrote: What system are your running it on? I found it strange "defaults domains" only shows one item. On 10/05/2015 11:23 AM,

[Freesurfer] Exporting ROIs as .nii

Hello, We are interested in finding a way to use particular parcellations from Freesurfer in a separate program. For instance, we are very happy with the way Freesurfer parcellates the Choroid Plexus and separates the Cerebellum into white and gray matter regions, and would like to import

Re: [Freesurfer] wm.mgz ventricle white matter problem

Hi Ana you might need to fix the labeling in the aseg. If you can't get this to work feel free to upload and we will take a look cheers Bruce On Mon, 5 Oct 2015, Anastasia Klimovich-Smith wrote: > Dear freesurfer experts, > > I have an issue with -autorecon2-wm stage results (freesurfer