[Freesurfer] Samseg Choroid Plexus Segmentation T1 and T2-FLAIR separate argument

External Email - Use Caution Hello, I am attempting to segment the choroid plexus using T1 and T2-FLAIR images as inputs to Samseg. On our T1 images, the choroid plexus is hardly visible, but it is much more visible on T2-FLAIR. Samseg seems to be failing to segment the choroid

[Freesurfer] Postdoctoral Fellow Position in Simultaneous Spinal Cord-Brain fMRI

External Email - Use Caution DESCRIPTION The Systems Neuroscience & Pain Laboratory at Stanford University (SNAPL) is actively recruiting a postdoctoral fellow who will join our research project on chronic pain. Funded by the National Institute of Health and directed by neuros

[Freesurfer] mri_glmfit 0 voxels in mask ERROR

External Email - Use Caution Dear Freesurfer Team, I have been struggling with an error using the mri_gmfit command. I have been trying to run a simple surface-based group analysis on 28 subjects testing whether a continuous variable "OMEGA3_457" relates to various RSI measures

[Freesurfer] Postdoctoral Fellow Position in Simultaneous Spinal Cord-Brain fMRI

External Email - Use Caution DESCRIPTION The Systems Neuroscience & Pain Laboratory at Stanford University (SNAPL) is actively recruiting a postdoctoral fellow who will join our research project on chronic pain. Funded by the National Institute of Health and directed by neuros

Re: [Freesurfer] Update FS version and manually edited controls

You should just make a copy of your subject, then re-run with version 7x. It should automatically see the edits and incorporate them. On 9/13/2021 3:40 PM, Funk, Quentin wrote: External Email - Use Caution Freesurfer experts, I have a collection of older controls that I have reconstr

Re: [Freesurfer] Different volume measurements Freesurfer V7.1.1

First, make sure you are not running into this problem https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes The global morphometry statistics embedded in aseg.stats and other files have an error when the input volume has a voxel resolution different than 1mm^3. See MorphometryStats

Re: [Freesurfer] Calculating GMV

On 9/13/2021 10:11 PM, Brigitte Pace wrote: External Email - Use Caution We are trying to calculate the volume of grey matter of the significant clusters within each region identified by our initial analyses. Is there a procedure already written in matlab to accomplish this calcula

Re: [Freesurfer] mri_vol2surf clarification

Sorry, I don't understand what you are trying to do. Extract ROI (eg, hippocampal) time courses? On 9/14/2021 4:29 AM, Alice Giubergia wrote: External Email - Use Caution Dear Freesurfer's experts, I am dealing with time course extraction from preprocessed (prerpoc-sess) task functio

Re: [Freesurfer] ERROR: mri_ca_register with non-zero status 1

I can't tell what the problem is. Have you looked at your images in these cases to see if there  is anything wrong with them? What resolution is your data? On 9/14/2021 1:59 PM, Xiong, Yanyu wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recond

Re: [Freesurfer] Samseg Choroid Plexus Segmentation T1 and T2-FLAIR separate argument

There is not, but you could create your own. By default, it uses this table to determine which superclass each segment goes into $FREESURFER/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/sharedGMMParameters.txt YOu can see that CP is in the CSF glass. You can try creating its own

Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR

Can't see the image. Can you just cut-and-paste the full terminal output into the email? On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote: External Email - Use Caution Dear Freesurfer Team, I have been struggling with an error using the mri_gmfit command. I have been trying to run a s

Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR

External Email - Use Caution Sorry about that! Here's the full terminal output: cwd /space/syn01/1/data/MMILDB/MCE_RBS/fsurf cmdline mri_glmfit.bin --y lh.N0s2_e4pos.10.mgh --fsgd ./fsgd_omega/e4_positive.fsgd dods --C ./mtx_omega/e4_positive.mtx --surf fsaverage lh --cortex -

Re: [Freesurfer] Freesurfer 7.1.0 VirtualBox password

External Email - Use Caution Sending the info to your local email shortly. - R. On Sep 14, 2021, at 12:58, Camila Fernandes da Silva wrote:External Email - Use CautionDear admin, I instaled Freesurfer 7.1.0 using the VirtualBox i

[Freesurfer] Migrating data from v6 to v7

External Email - Use Caution Hi fellow FreeSurfer users, I am part of a longitudinal project and have a large dataset that has been processed in v6. I have now upgraded to v7 and would like to update my processed data, retaining the existing manual masks and pial edits. I foun