[Freesurfer] Qdec Outputs - Looking For Statistical Maps To Overlay In SurfStat

e a file that qdec saves that is just thickness? Or is there a way to manipulate the files so that they are not demeaned? Thank you for your assistance Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist David Geffen School of Medicine at UCLA Developmental Cognitive Neur

[Freesurfer] Cannot Configure Segmentation Brush WHen Editing Subcortical Parcellations

Thanks for your assistance. Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist UCLA Center for Cognitive Neuroscience Developmental Cognitive Neuroimaging Suite 17-369 740 Westwood Plaza Los Angeles, CA 90095 Phone: (310)525-0865 Fax: (310)

[Freesurfer] Editing Parcellations

g to older versions, all with no success. Thanks for you your assistance. Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)52

[Freesurfer] Cannot execute any freesurfer GUI- Error of failed request:

e set (SUBJECTS_DIR, FREESURFER_HOME) and I have sourced $FREESURFER_HOME/ SetUpFreeSurfer.csh. Thnaks you in advance for your help. Jennifer Bramen -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the p

[Freesurfer] White Matter Regional Volumes

. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats... If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link? Thank you Jennifer Bramen

Re: [Freesurfer] White Matter Regional Volumes

someone please send me the link? Thank you Jennifer Bramen -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is

[Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

gards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center time.dat Description: time.dat

Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

PET volumes: 5 min (300 sec) – Amyloid Brain * (5 minx 4 beds) * 40 min uptake * 10 mCi IV injection Can I just create a mean volume from this image or some other simple metric instead of KM? Thanks for your help. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research

Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 From: on behalf of Jennifer Brame

[Freesurfer] PetSurfer: subcortical volume-based analysis

subcortical gray matter mask. How do I extract mean intensity within all of the subcortical ROI? Thank you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Founda

[Freesurfer] PetSurfer: CORTICAL volume-based analysis

/subjects/fsaverage/mri.2mm/brainmask.mgz Can someone confirm or correct these commands? I am especially concerned that I have selected the wrong mask. Thanks you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

space. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

. Is that what I am doing by using the mgx image? Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

ess of whether it is GM, WM, or CSF. They will probably give you similar answers, but the GTM will be more robust. On 2/21/2022 8:48 PM, Jennifer Bramen wrote: External Email - Use Caution Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and glmd

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 |

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

External Email - Use Caution Hi Doug I want to confirm that the signal any region flagged as cortex is restricted to gray matter. If that is the case, then I finally have what I need. Thank you. Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist

[Freesurfer] mri_convert and timeseries data

Dear Freesurfer Users I am trying to use mri_convert to reorient a nifti file. The file is a bold sequence, but for some reason, mri_convert is only outputting the first volume. I get this error as well: WARNING: niiRead(): unknown time units 0 in 2010_10_20_21_bold_gp2.nii Any idea regard