[Freesurfer] bbregister --init-spm with Freesurfer 6.0

Hi Freesurfer Experts, I was running bbregister and came across an issue. I have used previous versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at it worked perfectly for a specific subject. I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm option with

Re: [Freesurfer] dt_recon image inputs -i flag

Hi Bryan - It'll convert whatever input you give it to nifti, so it's fine if your input is already nifti. Best, a.y On Wed, 6 Apr 2016, Chiu, Bryan (PHTH) wrote: Hi, I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI images in par/rec. I ran dcm2nii and have

Re: [Freesurfer] mri_vol2surf after recon-all

Hi Dr. Fischl I have a mixture - some of the labels were painted in the MNI305 space (older ones) and the more recent ones are registered to the ICBM152 nonlinear symmetric VI (2006) template. Best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On

[Freesurfer] dt_recon image inputs -i flag

Hi, I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI images in par/rec. I ran dcm2nii and have retrieved the associated *bval, *bvec and *nii.gz files that come out. In the tutorial it mentions the -i flag requiring a dcm image. Is it possible to pass a *.nii.gz

Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

Almost correct! recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp/I0001.dcm T2hipp Also, this is assuming that you have defined the environment variable SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd . Cheers, /Eugenio Juan Eugenio Iglesias

Re: [Freesurfer] mri_vol2surf after recon-all

Hi Trisanna what space are your labels in? cheers Bruce On Tue, 5 Apr 2016, Trisanna Sprung-Much wrote: > Hi Freesurfer > > I have some labels (.mnc) that are painted voxels generated from a Montreal > Neurological Institute software. I am trying to project the labels onto the > surfaces

Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

Hi Eugenio, Thank you so much for the quick and helpful reply. I checked the images in Freeview and they actually line up quite nicely! Can you provide further guidance on how to run recon-all once with both the -all and the hippocampal-subfields-T1T2 flags? For example, in my rawdata

[Freesurfer] mri_vol2surf after recon-all

Hi Freesurfer I have some labels (.mnc) that are painted voxels generated from a Montreal Neurological Institute software. I am trying to project the labels onto the surfaces generated from recon-all that I applied to the corresponding MRI volumes. *I used mri_vol2surf: * mri_vol2surf --src

Re: [Freesurfer] mixed models and longitudinal streaming

Hi Martin, thank you for your help. I still have problems in running mixed models analyses. Do I need some additional toolbox in matlab? (I did not find this information in the web) I tried to run the module in two versions of matlab, but the same problem occurr. I used these commands: [M,Y,ni] =

Re: [Freesurfer] Installation issue

Try following the mac os install directions. On Tue, Apr 5, 2016 at 1:57 PM, wrote: > Hi list, > > I'm reinstalling FS on my PC (iMac end of 2012). > This error occur: > > freeview > > /Applications/freesurfer/bin/freeview.bin: Exec format error. Binary file > not

Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only

[Freesurfer] octave fast_selxavg3() failed\n

Hi listthis error occurs using octave in FS-FAST.Thanks, Stefano --- octave output LD_LIBRARY_PATH :/usr/local/octave/3.8.0/lib /usr/local/octave/3.8.0/bin: Permission denied. -- ERROR: fast_selxavg3() failed\n

[Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

Hello, I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain. My understanding

[Freesurfer] Installation issue

Hi list, I'm reinstalling FS on my PC (iMac end of 2012).This error occur: freeview /Applications/freesurfer/bin/freeview.bin: Exec format error. Binary file not executable. Please take in account:freesurfer[1] 1818 [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% FreeSurfer

[Freesurfer] Preprocessing task data with multiple B0-corrected runs

Dear Doug, I'm trying to use FSFAST to analyze task data with multiple runs. Before using the preproc-sess pipeline, I ran B0 correction on each of the runs, so I have 3 different b0dcmap files. I'm trying to figure out the best way to run preprocessing on the three runs simultaneously using

Re: [Freesurfer] longitudinal pipeline surface error

Hi Mihaela, you can use our BrainPrint tool (after running FS) to see how closely the brain shape matches: http://reuter.mit.edu/publications/pid/wachinger-brainprint15 http://reuter.mit.edu/software/brainprint/ Best, Martin On 04/05/2016 12:49 PM, Mihaela Stefan wrote: Hi Martin, Just an

Re: [Freesurfer] longitudinal pipeline surface error

Hi Martin, Just an update on this. It turned out that there was just a DICOM mismatch for this subject but now that you mentioned it, I wonder what people do to make sure that the same person returns for follow-up in a longitudinal study. Even when there is one study coordinator for the entire

[Freesurfer] White matter parcellation based on ROIs from fMRI

Hello Freesurfers, I have a dataset of T1s and DWIs, and I have cortical ROIs defined on the T1s. I want to use the ROIs for tractography, and therefore need them to include the underlying white matter. I I am aware that freesurfer can do this after running the subjects through recon-all

Re: [Freesurfer] License invalid for Development Version

Hello Ben, The license file should still work. Please send me your .license file to MY PERSONAL EMAIL ADDRESS so I can test it. Also, please send me your build-stamp.txt file as well. Thanks. -Zeke > On Apr 5, 2016, at 7:31 AM, Jeurissen Ben wrote: > > Dear

Re: [Freesurfer] Tracula problems (creating symbolic link)

Hi Efrat - You could just use cp instead of ln -s. This will duplicate the file, instead of creating a link to it. a.y On Tue, 5 Apr 2016, Efrat Kliper wrote: Dear Anastasia,   Thank you for the fast replay. I have tried both suggestions, however it still reports:  Operation not

[Freesurfer] License invalid for Development Version

Dear Freesurfer experts, I am affected by the PERL incompatibility described in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043504.html . To get around this issue, I switched to the newest development version as suggested in that post. However, my license file (which

[Freesurfer] Postdoctoral research fellows, University of Oslo, Norway

2 three-year positions as Postdoctoral Research Fellow at the Norwegian Centre for Mental Disorders Research, University of Oslo are currently available. http://uio.easycruit.com/vacancy/1599437/65775?iso=no NORMENT is a Norwegian Centre of Excellence, and coordinates a translational

[Freesurfer] Qdec DOSS

Hi Freesurfers, I posted this question a few days ago but didn't get any replies. Would you mind answering this for me? I compared 2 groups, while controlling for 1 covariate in qdec using freesurfer 5.1. There were no significant interactions with the covariate so I need to use DOSS. I read

Re: [Freesurfer] Tracula problems (creating symbolic link)

Dear Anastasia, Thank you for the fast replay. I have tried both suggestions, however it still reports: Operation not supported Also, I have used the links that you have sent me but non work. This time (after changing according to the links), I got the message: operation denied I don’t