[Freesurfer] bring volumes to fsaverage space

Dear freesurfers, I would like to know what will be the best way to bring volumes in the individual subject's space to the fsaverage space. Thanks, Shani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

[Freesurfer] error vcsf.config

Hi list, During fcseed-sess -s subj -cfg vcsf.config a subject produces the follow error.I have rerun recon-all, cheched aparc+aseg with tkmedit. They seem to be ok.Why this error is produced? Thanks Stefano Creating output directory /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcse

[Freesurfer] free surfer 6 beta freeview crash on mac os x 10.11.1

Hi When I start freeview form command line on Mac OS X 11.10 it crash with this error message. Do I miss a file? freeview -f fsaverage/surf/lh.inflated fsaverage/surf/rh.inflated dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesur

[Freesurfer] average z-score of each subject from a common cluster

Hi list,I have two queries, please. I'd like to have the z-score from my rsfMRI data (seed-analyis). 1) I have extract the z-score from the Vtx Max In details, after groups comparison analysis, I have opened the cache.th13.pos.sig.cluster.summary contained in group.diff folder and I have read the

[Freesurfer] Tracula stats COR-.info does not exist

Dear Tracula developers, I posted a problem with tracula when I ran trac-all -stat -c dmrirc_ind_mni_cvs_all_stats.all I receive this error message Loading output reference volume from /home/spj24/app/freesurfer/subjects/cvs_avg35 corRead(): can't open file /home/spj24/app/frees

Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

what is the laus250 parcellation? The lookup tables are in text so you should be able to open one in an editor and see what the format is. It's pretty straightforward. # lines are comments, then it is cheers Bruce On Fri, 30 Oct 2015, Peled, Noam wrote: > Hey all, > I used mri_aparc2as

Re: [Freesurfer] bring volumes to fsaverage space

Hi Shani you can use mri_vol2vol with the talairach.m3z. Alternatively, you can run CVS which will give you more accurate cortical matching and use the transform that it produces. cheers Bruce On Fri, 30 Oct 2015, Shani Ben Amitay wrote: Dear freesurfers, I would like to know what will be t

Re: [Freesurfer] free surfer 6 beta freeview crash on mac os x 10.11.1

There are significant changes in the most recent OSX release El Capitan and this is one consequence of them (https://en.wikipedia.org/wiki/OS_X_El_Capitan#System_Integrity_Protection). We are currently exploring solutions but as of right now, freesurfer is not fully functional on OS X 10.11

[Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

Hi Freesurfer experts, I hope you’re all enjoying your day! Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms obtained at Martinos Center. The dicoms have the following format: MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919 MR1.3.12.2.1107.5.2.32.35006.201005261355

Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

Hi Emad, The only problems, which I have run into is major weaknesses in dcm2nii: 1. You must have write permissions on the directory the files are located in. 2. dcm2nii cannot work on symbolically linked files. Therefore, first copy the files to your own analysis workspace: e.g. /cluster// th

[Freesurfer] Voxel based vs surface based

Hi Doug and Bruce, Kindly, I have question regarding the difference between voxel based ( VBM/ FSL pipeline) and surface based analysis ( Freesurfer ).   I have two groups of subjects Group A and Group B I ran morphometric analysis in Freesurfer ( recon-all then manual edits) to check the differenc

Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

you can also try mri_convert from the dev env. It should recognize the diffusion scan and write out the bval/bvecs On 10/30/15 10:43 AM, dgw wrote: > Hi Emad, > > The only problems, which I have run into is major weaknesses in dcm2nii: > 1. You must have write permissions on the directory the fi

Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

Hi, Thank you for your quick response! I have already copied the dicoms to my cluster space: /cluster/guptagp/Emad/Epilepsy/temp/slices and the permissions of this folder seem right to me: drwxrwsr-x 2 emad guptagp 32768 Oct 30 10:30 slices The permissions on the dicom files are the same: -b

Re: [Freesurfer] error vcsf.config

That means it could not find any CSF voxels. Try checking the registration. It could also be that this is a subject with really small ventricles. On 10/30/15 3:57 AM, std...@virgilio.it wrote: Hi list, During fcseed-sess -s subj -cfg vcsf.config a subject produces the follow error. I hav

Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

You can also load the new segmentation into freeview and see the segmentation number that each gets. If you can get the color table out of the annotation, then the segmentation number will be 1000+ that number (left hemi) and 2000+that number for the right On 10/30/15 8:30 AM, Bruce Fischl w

Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

Hey Bruce, I meant for the Lausanne250 parcellation (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048121) The problem is with the #index column. To create a custom lookup table, I need to know what is the #index each label gets in the output file of mri_aparc2aseg. I want to

Re: [Freesurfer] average z-score of each subject from a common cluster

On 10/30/15 7:16 AM, std...@virgilio.it wrote: Hi list, I have two queries, please. I'd like to have the z-score from my rsfMRI data (seed-analyis). 1) I have extract the z-score from the Vtx Max In details, after groups comparison analysis, I have opened the cache.th13.pos.sig.cluster.summ

Re: [Freesurfer] free surfer 6 beta freeview crash on mac os x 10.11.1

Hi I have disable System_Integrity_Protection to get free surfer working on El Capitan Knut Jorgen On 30 Oct 2015, at 15:16, Z K wrote: > > There are significant changes in the most recent OSX release El Capitan > and this is one consequence of them > (https://en.wikipedia.org/wiki/OS_X_E

Re: [Freesurfer] unit in 'search area' in the glmfit log

That number is in voxels or vertices. If you want surface area, then use mri_segstats something like mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh --seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat doug On 10/29/15 5:10 PM, Jeni Chen wrote: > Hello, > > When running

Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

Hi Noam we should just preserve whatever index they use cheers Bruce On Fri, 30 Oct 2015, Peled, Noam wrote: > > Hey Bruce, > I meant for the Lausanne250 parcellation (http://journals.plos.org/plosone/a > rticle?id=10.1371/journal.pone.0048121) > The problem is with the #index column. To creat

Re: [Freesurfer] wrong segmentation

what version are you using? I think this won't happen in V6,but if you upload the subject dir I can check for you. To fix it check and correct the wm.mgz and the aseg.mgz in that region cheers Bruce On Thu, 29 Oct 2015, Thục Trinh wrote: Hi Freesurfer experts, I ran recon-all for our subjec

Re: [Freesurfer] Voxel based vs surface based

Hi John yes, they are different methods that measure somewhat different things so there is no reason they would show the same maps. If you look at volume change in FS it might be closer, but even that won't match VBM necessarily cheers Bruce On Fri, 30 Oct 2015, John Anderson wrote: Hi Dou

[Freesurfer] Free surfer dev env doesn't extract bvals/bvecs

Hi Freesurfers,I’m using the dev env on Launchpad to analyze DTI dicoms using TRACULA.It cannot extract the bvecs from the dicom header since it gives me the following error:ERROR: Must specify input table of gradient vectorsI’ve attached the TRACULA configuration file (dmrirc3.txt) and the log fil

Re: [Freesurfer] Voxel based vs surface based

Hello John, I would highly recommend you take a look at this paper http://cds.ismrm.org/protected/11MProceedings/files/ISMRM2011-8410.pdf (Greve, 2011. An Absolute Beginner's Guide to Surface- and Voxel- based Morphometric Analysis). I have found it to be very helpful for my understanding. -Andr

[Freesurfer] changing the index of labels

Hi, Is there a way to change the index of the segmentation of the hippocampal subfields, so that when I combine left and right, FreeSurfer treats them as different regions? Thanks! Best Heidi > >>I just checked again in freeview and indeed they have the same index >>(e.g. >>CA1 has value 206 fo

Re: [Freesurfer] changing the index of labels

Hi Heidi I guess you could do it yourself in matlab using the aseg to figure out which hemisphere you are in cheers Bruce On Fri, 30 Oct 2015, Jacobs H (NP) wrote: Hi, Is there a way to change the index of the segmentation of the hippocampal subfields, so that when I combine left and righ

[Freesurfer] cortical thickness - comparing two groups within a ROI

Dear FS experts, I have a question about extracting average cortical thickness from a manually created ROI. I am comparing 2 groups, namely PostFort and PreFort and my fsgd file appears as the following: GroupDescriptorFile 1 Title PostPreFortification Class PostFort Class PreFort InputSub

[Freesurfer] R: Re: error vcsf.config

Yes, the ventricle is very small. The segmentation in aparc and aseg is nice.How can I do to analyze this subject? I need to include it in the analysis.Many thanks, Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 30-ott-2015 16.03 A: Ogg: Re: [Freesurfer] error vc

[Freesurfer] TRACULA question- pathstats not loading

Hi, I am currently analyzing DTI data and I am having issues with one file in particular. When I run the tracheal -path -c step, all of the files are generated except the pathstats text files. Any thoughts? Thanks! Noa ___ Freesurfer mailing list Fr

Re: [Freesurfer] bring volumes to fsaverage space

Hello Can you please direct me to more information about the CVS. Thanks! Shani בתאריך 30 באוק' 2015 14:39,‏ "Bruce Fischl" כתב: > Hi Shani > > you can use mri_vol2vol with the talairach.m3z. Alternatively, you can run > CVS which will give you more accurate cortical matching and use the > transf

[Freesurfer] R: Re: average z-score of each subject from a common cluster

Thanks.I have obtained: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc --i z.nii.gz --sum summaryfile sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano UseRobust 0 Loading z.nii.g

[Freesurfer] Fwd: 2015 Call for Communications Committee Members

Forwarded Message Subject:2015 Call for Communications Committee Members Date: Fri, 30 Oct 2015 11:34:52 -0500 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu Dear OHBM Members: The Organization for H

Re: [Freesurfer] bring volumes to fsaverage space

Hi Shani, Sure. You can do mri_cvs_register --help and that should give you lots of information. Alternatively you can also go to https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register and read through the presentation that we give at the FS course: http://surfer.nmr.mgh.harvard.edu/pu

Re: [Freesurfer] changing the index of labels

Are there different files for the lh and rh? Sorry, never done the subfields analysis. On 10/30/2015 01:25 PM, Bruce Fischl wrote: > Hi Heidi > > I guess you could do it yourself in matlab using the aseg to figure > out which hemisphere you are in > > cheers > Bruce > > On Fri, 30 Oct 2015, Ja

Re: [Freesurfer] changing the index of labels

Yes, there are different mgz files for left and right (but they have the same index numbers and colors). On 10/30/15, 11:16 PM, "Douglas N Greve" wrote: > >Are there different files for the lh and rh? Sorry, never done the >subfields analysis. > > >On 10/30/2015 01:25 PM, Bruce Fischl wrote: >>

[Freesurfer] Questions about beta.nii.gz

Hi, I have two questions: 1) In an fMRI experiment, we have 64 stimulus conditions and a baseline condition. All conditions are presented in each run. After running the analysis: mkanalysis-sess -a category.rh -surface self rh -fsd bold -fwhm 3 -event-related -paradigm paradigm_category.par -nco