[Freesurfer] mri_segstats for lobar intensity values

External Email - Use Caution Hi Freesurfer team, I want to calculate the average PET intensity values per lobe. I want to use the lobar annotations as outlined here in 'lobe mapping': https://secure-web.cisco.com/1Opn2TyIP5_MF5tP6PRtaju8QtoITdCtzrmIlxZvYGO1bUWJFDMXcyGSrhgGeBk9csj3

[Freesurfer] Segment the centrum semiovale

External Email - Use Caution Dear Freesurfer team, I was wondering if FS has a way to segment the centrum semiovale? The freesurfer colorLUT table mentions "Centrum semiovale is also labled with 5001 (left) and 5002 (right)." (see https://secure-web.cisco.com/16ntnqYurxLXfYvZCsM5e

[Freesurfer] --pv flag in mri_segstats

External Email - Use Caution Hello FS team, If I want to calculate the average diffusion-weighted signal from a DWI image within WM regions using mri_segstats, would it be beneficial to use the --pv flag for "partial volume correction" , or would this only have an influence on the

[Freesurfer] Longitudinal FS: does ordering of time points matter in the command

External Email - Use Caution Hi FS team, I just wanted to double check if, for the longitudinal pipeline, it matters which time point is being read first? For example, in the command below, should -tp -tp in the order of the scans being acquired? recon-all -base -tp -tp ...

Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

External Email - Use Caution Hi, I just wanted to check in with my questions below? Thanks! Julie On Thu, 10 Nov 2022 at 17:03, Julie Ottoy wrote: > Hi, > > Yes you are right! Taking out the -parallel solved the issue! Does this > mean v7 longitudinal recon-

Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

s > causing the error. > > > > The process should work if you remove ‘-parallel’ from recon-all command. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *

Re: [Freesurfer] Spatial distance between regions

of the schaefer parcels? (My final goal is to calculate the distances between each of the centroids) Thank you! Best wishes for the new year. Julie On Sun, 2 Jan 2022 at 16:11, Douglas N. Greve wrote: > Try mri_segcentroids. Run it with --help to get docs > > On 12/20/2021 3:34 AM, Ju

Re: [Freesurfer] Spatial distance between regions

External Email - Use Caution Hi Doug, Just checking in with the question below. Does Freesurfer have such an option? Thanks, Julie On Tue, 14 Dec 2021 at 18:38, Julie Ottoy wrote: > Hello FreeSurfer team, > > I was wondering if there is a way to calculate a distan

[Freesurfer] Fwd: Failed tissue type check {Disarmed}

External Email - Use Caution Hi Doug, Did you have a chance to look at this subject ? Thanks a lot, Julie -- Forwarded message - From: Julie Ottoy Date: Thu, 18 Mar 2021 at 13:08 Subject: Re: [Freesurfer] Failed tissue type check {Disarmed} To: Freesurfer

Re: [Freesurfer] Failed tissue type check {Disarmed}

External Email - Use Caution Hi Doug, Any other suggestions I could try? It seems to be only an issue with the non-pvc data. Thanks Julie On Tue, 2 Feb 2021 at 11:10, Julie Ottoy wrote: > Hi Doug, > > I tried these fixes but they still give me the error message bel

Re: [Freesurfer] Failed tissue type check {Disarmed}

External Email - Use Caution Hi Doug, I tried these fixes but they still give me the error message below. I did replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab in the aux folder ? Thanks, Julie On Tue, 12 Jan 2021 at 10:37, Julie Ottoy wrote: >

Re: [Freesurfer] almost empty mask.mgh with glmfit

gt; > On 1/14/2021 11:38 AM, Julie Ottoy wrote: > > External Email - Use Caution > Hi Doug, thank you for your reply! > When I look at my surface-projected non-pvc data per subject, initially it > seemed as there were a lot of values zero, but when I go to configure > and &g

Re: [Freesurfer] almost empty mask.mgh with glmfit

t; 0 interpretable in this case? > > On 1/11/2021 6:15 PM, Julie Ottoy wrote: > > External Email - Use Caution > Dear Doug, > > I was wondering why the flag --prune is recommended (petsurfer website) > when creating a stacked pet file and during surface-smoothing. I

Re: [Freesurfer] Non-uniform voxel size

olume of the ROIs instead of the uptake > > > On 1/6/2021 6:00 PM, Julie Ottoy wrote: > > External Email - Use Caution > Thank you Doug! > I have another question related to voxel size. > > In the GTM PVC pipeline, the gtm.stats.dat file also outputs the NVoxels.

[Freesurfer] matrix is ill-conditioned or badly scaled

External Email - Use Caution Hi freesurfer experts, I am trying to run a GLM fit between cortical thickness and some other continuous marker. My cortical thickness were stacked before using the mris_preproc and surf2surf commands. I have an FSGD file with the same subjects as used

Re: [Freesurfer] Transform rescaled non-pvc PET to surface

run mri_gtmpvc already, you can add --save-input and it will > save a file called input.rescaled.nii.gz which will be rescaled to your > reference region > > On 12/29/2020 4:19 PM, Julie Ottoy wrote: > > External Email - Use Caution > Dear Freesurfer team, > > I hav

Re: [Freesurfer] Failed tissue type check {Disarmed}

Try using --replace 29 2 > > > On 12/29/2020 12:48 PM, Julie Ottoy wrote: > > External Email - Use Caution > Hi Doug > > Thanks for your reply. I tried both your suggestions, but it seems as > though they both ran into an error. > > For your first suggestion,

[Freesurfer] almost empty mask.mgh with glmfit

External Email - Use Caution Dear Doug, I was wondering why the flag --prune is recommended (petsurfer website) when creating a stacked pet file and during surface-smoothing. If I understood correctly, this would set all vertices that are 0 in at least one subject to 0 ("set vox t

Re: [Freesurfer] Non-uniform voxel size

Julie On Wed, 23 Dec 2020 at 13:11, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > No, not a problem. > > > On 12/21/2020 12:52 PM, Julie Ottoy wrote: > > External Email - Use Caution > Dear freesurfer team, > > I am dealing with PET scans tha

[Freesurfer] Transform rescaled non-pvc PET to surface

External Email - Use Caution Dear Freesurfer team, I have a question related to petsurfer. On the website, it is stated that "If you are not using PVC, you can use the template.reg.lta to sample the PET volume onto the surface using mri_vol2surf, then apply standard surface-based

Re: [Freesurfer] Failed tissue type check {Disarmed}

l or you can add the following > line any were into the gtmseg.ctab file: > 29 Left-undetermined 135 206 235 0 3 > > > On 12/18/2020 11:06 PM, Julie Ottoy wrote: > > External Email - Use Caution > Sorry I would like to correct my previous post

[Freesurfer] No extracerebral CSF in sGTM

External Email - Use Caution Dear Petsurfer team Does the sGTM PVC correct for the uptake in extra cerebral CSF? If not, how would this affect the reliability of the cortical PVC measures, considering the spill-out of grey matter uptake to csf is being ignored? Thank you! Best re

[Freesurfer] Non-uniform voxel size

External Email - Use Caution Dear freesurfer team, I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac

Re: [Freesurfer] Failed tissue type check {Disarmed}

2020 at 00:09, Julie Ottoy wrote: > External Email - Use Caution > > Dear Doug, > > I have the same issue as the people below. I was wondering if this was > solved in the meantime. > > I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and >

[Freesurfer] Failed tissue type check {Disarmed}

External Email - Use Caution Dear Doug, I have the same issue as the people below. I was wondering if this was solved in the meantime. I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got the following error in only one of my subjects. When I ran the same

[Freesurfer] PVE correction tool Petsurfer {Disarmed}

External Email - Use Caution Dear FreeSurfer Team, I am interested in the answer to the question of Subin below. I don't think this question was answered -- at least I cannot find the reply. If the PET images are already smoothed to 8mm (which is the case with the post-processed A

Re: [Freesurfer] Fixing error with pial surface {Disarmed}

> Send an email that the file has been and the name of the file. > > > On 11/3/2020 12:38 PM, Julie Ottoy wrote: > > External Email - Use Caution > Hi Bruce, > > Thanks for your answer and cc'ing Rob. > I did use anonymous as the username. > > T

Re: [Freesurfer] Fixing error with pial surface {Disarmed}

gt; > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy > *Sent:* Tuesday, November 3, 2020 11:12 AM > *To:* Freesurfer support list > *Subject:* R

Re: [Freesurfer] Fixing error with pial surface {Disarmed}

ingle slice. Is there white matter in the > wm.mgz that doesn’t have surface (?h.white) covering it? That would > indicate a topological defect. > > > If you upload the entire gzipped and tarred subject’s directory we will > take a look > > > > Cheers > >

[Freesurfer] Skull strip t1 in recon-all

External Email - Use Caution Dear freesurfer team I'm trying to use my own skull stripped T1 when running recon-all. For this, I'm doing following steps: 1) run recon-all with -autorecon-1 -noskullstrip 2) mri_convert --in_type nii --out_type mgz -rl ./FreeSurfer/ID/mri/orig.mgz -

[Freesurfer] Fwd: using own skull stripped t1

External Email - Use Caution Hi Freesurfer team I was wondering if you’d have some time to take a look at question below. Thanks! -- Forwarded message - From: Julie Ottoy Date: Thu, 30 Jul 2020 at 13:22 Subject: using own skull stripped t1 To: Freesurfer support

[Freesurfer] using own skull stripped t1

External Email - Use Caution Dear freesurfer team I'm trying to use my own skull stripped T1 when running recon-all. For this, I'm doing following steps: 1) run recon-all with -autorecon-1 -noskullstrip 2) mri_convert --in_type nii --out_type mgz -rl ./FreeSurfer/ID/mri/orig.mgz -

[Freesurfer] Fwd: Fwd: question regarding mri_vol2label

External Email - Use Caution Hi FS team, I was wondering if you could take a look at the question below. Thanks! -- Forwarded message - From: Julie Ottoy Date: Fri, 10 Jul 2020 at 20:49 Subject: Re: [Freesurfer] Fwd: question regarding mri_vol2label To

Re: [Freesurfer] Fwd: question regarding mri_vol2label

ionvolumes.nii.gz --projfrac-max -.5 1 .1 > --hemi lh --o lh.parcellationvolumes.mgz --regheader subject > mri_cor2label --i lh.parcellationvolumes.mgz --id 20 --surf subject lh > --l lh.20.label > > > On 7/10/2020 3:46 PM, Julie Ottoy wrote: > > External Email - Use Cautio

[Freesurfer] combining left and right pial surface

External Email - Use Caution Hi Freesurfer team, I am trying to combine the left and right pial surfaces into one surface. I tried to use the following code: mris_convert --combinesurfs lh.pial rh.pial rh+lh.pial But the outcome is not correct (it has a lot of gaps in the combin

[Freesurfer] Fwd: question regarding mri_vol2label

External Email - Use Caution Hi Freesurfer team I am trying to convert parcellation (cortical) volumes that I acquired through another platform into surface labels using freesurfer. I tried following code to convert the volume with ID 20 from the parcellationvolumes.nii.gz file in

[Freesurfer] PETsurfer: --usf in gtmseg

External Email - Use Caution Hi, In PETsurfer gtmseg, there is the --usf (upsampling factor) which is by default 2, corresponding to 0.5 mm voxelsize. I was wondering if the usf is recommended to be chosen depending on your mri voxelsize (eg, usf 1 for 1mm voxelsize of the mri), o