[Freesurfer] recon-all dimensions

Hello Freesurfer, My MPRAGE dimensions are 1x1x1.33. The output of recon-all appears to be 1x1x1, judging by the fact that the aseg.stats columns for voxel number and volume in mm3 are identical. Should I conclude from this that recon-all resamples the scan into 1x1x1 voxels? Thank you, Je

Re: [Freesurfer] Variability in bedpostx output

Thank you Anastasia. Unfortunately, I posted the question to the FSL list first and after a few go-rounds with clarification and more info, they felt like it was potentially a problem of the calls to the bedposts command from within Freesurfer. Their final assessment was that there should be n

[Freesurfer] Variability in bedpostx output

Hello all, I have run bedpostx on a series of DTI scans over ~1 year, the earlier ones in stable 5.1 and later ones in 5.3. I'm seeing quite a lot of variability in intensity from the earlier to later versions - re-running bedpostx in 5.3 on an older scan and comparing with 5.1 yields up to 10%

Re: [Freesurfer] Mean diffusivity

Hello all, I have run bedpostx on a series of DTI scans over ~1 year, the earlier ones in stable 5.1 and latter. I'm seeing quite a lot of variability in intensity from the earlier to later versions - re-running bedpostx in 5.3 on an older scan and comparing with 5.1 yields up to 10% variation

[Freesurfer] Error from func2roi-sess

Hello Freesurfers, I am re-running an older analysis in stable3. I know that this version is out of date, but I'm trying to line up new data with old data. I have previously run a script that uses the func2roi-sess command with no problems. Now, when I run the same script, I'm getting a new e

[Freesurfer] Error from func2roi-sess

Hello Freesurfers, I am re-running an older analysis in stable3. I know that this version is out of date, but I'm trying to line up new data with old data. I have previously run a script that uses the func2roi-sess command with no problems. Now, when I run the same script, I'm getting a new e

[Freesurfer] How to convert from .label to nifti format?

Hi all, Is there an easy way to convert a freesurfer .label file to .nii.gz format? Thanks, Jeff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-m

Re: [Freesurfer] The v5.3 release is here

Thanks Nick, I have group of subject's for which recon-all was run in versions prior to v5.2, but subsequent steps (such as mri_cor2label, func2roi-sess, etc) were run in v5.2. Does the v5.2 bug affect steps beyond recon-all? Thanks, Jeff Freesurfers, > > The new version of Freesurfe

Re: [Freesurfer] problem with func2roi-sess

I have checked the label file directly - it is of comparable size with others, and has the same structure. I've rerun the mri_cor2label command and regenerated the labels for all subjects. Most confusing, func2roi works for some subjects in this cohort and not others. In contrast, the whole coho

[Freesurfer] problem with func2roi-sess

Hello Freesurfers, I would appreciate any advice or help you can provide. I am using the following command, run under Stable 3 (to keep the current analysis comparable to prior papers): func2roi-sess -roidef MedOrbitofrontal_LH_t6_0_sm5_0thresh -analysis newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_s

Re: [Freesurfer] Using mri_cor2label

Thanks Doug, The command line I am running is: mri_cor2label --c /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aseg.mgz --id 1029 --l /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/suppar_ctx_LH_${identif

[Freesurfer] Using mri_cor2label

Hello Freesurfers, I would like to use mri_cor2label for areas of the cortext defined in the FreeSurferColorLUT.txt. There are many ROIs whose IDs are >255, the numerical limit imposed on mri_cor2label. How can I define labels using these larger-numbered ROIs? I am specifically interested in

Re: [Freesurfer] Using the muscle ROI in the FreeSurferColorLUT

Thanks Bruce, Sorry for the naiive questions - I'm still pretty green. If I define a label for, say, the head of the left sternocleidomastoid, using tkmedit, could I then generalize that label to the rest of my patient cohort using mri_label2label? Thanks, Jeff > Hi Jeff > > our standa

[Freesurfer] Using the muscle ROI in the FreeSurferColorLUT

Hello Freesurfers, I would like to use the muscle ROI in the LUT (number 123). Can anyone tell me which muscles (all cranial? cervical too?) are included? I tried making a subject-specific label using the following command: mri_cor2label --c /cluster/ablood/1/${experimental_directory}/$

Re: [Freesurfer] Fw: Making cuts using tksurfer

Expanding this question a bit futher... It looks like the cutting planes are used for cleaving surfaces. Is there a comparable tool for cleaving a volume into distinct sub-volumes (e.g., medial and lateral)? Thanks, Jeff > > > > - Forwarded Message - > From: Anupa AV > To: Bruce

[Freesurfer] makelabels error

Hello, I am trying to adapt our ROIs used for tractography into a format that can be used in Freesurfer. I first used mri_cor2label to convert from nifti to .label format. When I run the following makelabels command: mri_label2label --srclabel /cluster/ablood/1/${experiment_directory}/${recons_di

[Freesurfer] unpacksdcmdir error

Dear Freesurfer community, I am using the unpacksdcmdir command as part of a DTI analysis in stable51: unpacksdcmdir -src /space/archive/60/siemens/Allegra-20401-20051011-143458-528000 -targ ./ -run 009 dti NII CD_cerv_ctrl2_sess2_dti.nii -unpackerr and am getting the following error: ERROR: n

[Freesurfer] Sourcing error?

Hello, I am having difficulty with an fMRI command line program that we have run successfully in the past, but which we haven't used in ~4 months. In response to the following command lines (from a csh script): "setenv FSL_DIR $FSLDIR source /usr/local/freesurfer/nmr-stable3-env source ${FSLDIR}/