[Freesurfer] Freeview coordinates

External Email - Use Caution Hi Freesurfer team, Sorry to ask a new question about FreeSurfer coordinates (I know it has been debated multiple times reading old messages) but I am still confused with all these spaces. I have a very simple use case in Freeview, when I load the T1

[Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

External Email - Use Caution Dear Freesurfer experts, I am currently attempting to include an additional T2 MRI scan in the segmentation of our T1 scan. The freesurfer version that I'm using is the freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).

Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

External Email - Use Caution It seems like a problem with mri_robust_register. Martin, any ideas? -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com From

Re: [Freesurfer] Freeview coordinates

Hi Florent if you run mris_info on the surface of interest it will print out the vox2ras-tkr matrix that you can use for this conversion. cheers Bruce On Fri, 26 Oct 2018, k3...@free.fr wrote: >External Email - Use Caution > > Hi Freesurfer team, > > Sorry to ask a new question about F

[Freesurfer] First level modelling in task-based fMRI data

External Email - Use Caution Hi FreeSurfer Experts, Now I am trying FS-FAST in analyzing task-based fMRI data. We have two runs for each participant. However, there were not enough events in some runs of some participants. Hence we'd like to concatenate the preprocessed images of

Re: [Freesurfer] Freeview coordinates

External Email - Use CautionHi Bruce,Thanks for the tip.When I run the command on 'lh.white' surface for example, I don't get an affine transform but a simpler one:vox2ras-tk:-1  0 0  128 0  0 1 -128 0 -1 0  128 0  0 0  1So when I apply this transform to a pixel position (152, 66, 7

[Freesurfer] Error in segmentHA_T1.sh

External Email - Use Caution Dear Freesurfer Developers I’ve run recon-all -all on a batch of 20 subjects on a linux based high performance computing setup and am now trying to run the segmentHA_T1 on them as well. It sets up the environment and then complains about myMRIread a

Re: [Freesurfer] Error in segmentHA_T1.sh

External Email - Use Caution Sorry, scratch that. Apparently it just didn’t realise that my subjects were in a subdirectory in the subjects directory. Running now. Note to self: “Think before you click send” Kind regards, FREDA SCHEFFLER Research Assistant / PhD Candidate

[Freesurfer] Segmentation fault

External Email - Use Caution Hey Freesurfer team, I'm working on running Tracula, and have been running into segmentation fault issues. We have consistently been running into segmentation fault issues. * The data we are working with comes from children*, and I'm concerned that

Re: [Freesurfer] Error in segmentHA_T1.sh

External Email - Use Caution No worries! Your LD_LIBRARY_PATH configuration made my day 😃 -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com From: on b

Re: [Freesurfer] Freeview coordinates

Hi Florent, I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 73, 1), you should get -24, -55, 62 Which matches what is shown in freeview. Best, Ruopeng On 10/26/2018 12:06 PM, k3...@free.fr wrote: External Email - Use Caution Hi Bruce, Thanks for the

[Freesurfer] cluster failing on HCP freesurfer script

External Email - Use Caution Dear community, My group is using the latest version of condor clustering to process our data on OS X. We have a bash script that calls freesurfer to run our HCP pipelines. I can run the script to completion when running it locally on each of the cl

Re: [Freesurfer] cluster failing on HCP freesurfer script

External Email - Use Caution What version of FreeSurfer are you using? Is the FreeSurfer environment set up correctly? Matt. From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Sanchez, Juan (NYSPI)" mailto:juan.sanc...@nyspi.columbia.edu>> Reply-To: Freesurf

[Freesurfer] Cerebellum Segmentation

External Email - Use Caution HI， Freesufer Team I want to try to segment the Cerebellum from the Brain MRI, does the freesurfer support the cerebellum segmentation? and how to process it? Many Thanks! Best Min ___ Freesurfer mailing lis

Re: [Freesurfer] cluster failing on HCP freesurfer script

External Email - Use Caution Thanks for the reply Matt freesurfer-i386-apple-darwin11.4.2-stable5-20130514 The scripts run fine outside of condor. So it must be how condor is selecting the freesurfer The Environment is set up correclty From

[Freesurfer] subfield normalization vs. covarying for whole hippocampal volume

External Email - Use Caution Hello, I’m working on a multi-site hippocampal subfields project (FSv. 6) and am wondering if it is “better” to normalize subfield volumes by dividing each subfield by whole hippocampal volume, or covary for hippocampal volume as an independent pred

Re: [Freesurfer] cluster failing on HCP freesurfer script

External Email - Use Caution That seems like an old version to me. Matt. From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Sanchez, Juan (NYSPI)" mailto:juan.sanc...@nyspi.columbia.edu>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu