[Freesurfer] How to make surfaces below the GM-WM boundary?

External Email - Use Caution Dear FreeSurfers, I am interested in sampling values in the superficial white matter (SWM) region, which is an area of about 0.5mm below the GM/WM boundary. To extract values of each vertex in that region, I have successfully used the mri_vol2surf

[Freesurfer] Difference between V1_exvivo.label and v1.predict.label?

External Email - Use Caution Dear FreeSurfers, I am wondering what is the difference between V1 labels obtained from V1_exvivo.label and v1.predict.label, and what is more exact? When visualizing resutls from both labels, V1_exvivo.label occupies a larger portion than

Re: [Freesurfer] recon-all for 0.85 isotropic images error (bump) {Disarmed}

: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; Lee Subin Kristine<mailto:subin9...@hotmail.com> 제목: AW: recon-all for 0.85 isotropic images error (bump) Dear Kristine, I haven't had any issues processing high resolution data with version 6 or 7 using either the -cm

Re: [Freesurfer] recon-all for 0.85 isotropic images error (bump)

986>에서 보냄 보낸 사람: Lee Subin Kristine<mailto:subin9...@hotmail.com> 보낸 날짜: Friday, October 30, 2020 9:40 PM 받는 사람: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 제목: recon-all for 0.85 isotropic images error Hello FreeSurfer Developers, I'm trying to run recon-al

[Freesurfer] recon-all for 0.85 isotropic images error

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to run recon-all (v.6) on T1- and T2-weighted images that have 0.85mm^3 isotropic voxels I have entered the command as below, with the T2, T2pial, cm, cw256 flags. recon-all -i $T1_DIR/"oT1_"$subj.nii -T2

[Freesurfer] Volume are different in asegstats vs matlab

Hi, I have a question about volume info from freesurfer vs matlab. I am looking at, say, the left hippocampus volume from asegstats, which was 3778.2 mm^3. When I try to get the same volume by loading aseg.nii on matlab, however, I get a different number, 3945. For matlab, I used the

[Freesurfer] ACPC alignment before or after running on Freesurfer?

Dear Freesurfer team, This may sound like a bit of a small question, but I could not find any exact answer elsewhere. Does the exact orientation of the input image have much effect on the accuracy of the segmentation in Freesurfer? It seems that some people apply ACPC alignment to the output

[Freesurfer] Does recon-all conduct cortical parcellation on the nu.mgz?

Dear FreeSurfer, Hello, I have been using the preprocessed images (which have already undergone N3 correction) from the Alzheimer's Disease Neuroimaging Initiative database as input for recon-all -all.( version 5.3.1) I have 3 questions: (1) Does recon-all use the nu.mgz during

[Freesurfer] using different versions of Freesurfer?

Hi Freesurfer team, I have currently used version 5.3. for all my cortical parcellations of MRI data, but for PET images of those same subjects I used the gtmseg, mri_coregister, gtmpvc of the 6.0 beta version to get partial volume effect-corrected SUVR(standard uptake value ratios). I am

[Freesurfer] Freesurfer build stamps do not match

Hi FreeSurfer Team, After I have downloaded the FreeSurfer dev version, I get the following error whenever I use the recon-all comand: mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS':

Re: [Freesurfer] PVE correction tool on Freesurfer 6

mr.mgh.harvard.edu 제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6 the response is in the body f the mail On 7/18/16 9:27 PM, Lee Subin Kristine wrote: Hi Doug, It seems that the email reply you just sent to me was empty. Could you please check your email message again? Thank you as a

Re: [Freesurfer] PVE correction tool on Freesurfer 6

rfer-boun...@nmr.mgh.harvard.edu> 보낸 날짜: 2016년 7월 19일 화요일 오전 1:59:46 받는 사람: freesurfer@nmr.mgh.harvard.edu 제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6 On 07/12/2016 11:03 PM, Lee Subin Kristine wrote: > > Hi Doug, > > > Thanks a lot for the page! It was very

Re: [Freesurfer] PVE correction tool on Freesurfer 6

ubin, I just created this page this morning http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer do you want to take a look and see if it answers your questions. As for #2, yes you still need to run gtmseg. On 06/26/2016 07:45 AM, Lee Subin Kristine wrote: > > Hello, > > I am tryi

[Freesurfer] Tissue probability maps from aseg.mgz

Dear FreeSurfers, Is it possible to get tissue probability maps (for the purpose of using them in spm DARTEL, PVElab, etc) out of aseg.mgz? I did read in a previous post (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006384.html) that you can use mri_ca_label with the

[Freesurfer] Not able to find file in gtmseg

Dear FreeSurfer experts, Hello, I am trying to use Freesurfer's (developmental version) PVE correction tool and I haveone question. The data to be PVE-corrected are some preprocessed PET data downloaded from the Alzheimer's DIsease Neuroimaging Initiative (ADNI) database. Basiclly, the

[Freesurfer] PVE correction tool on Freesurfer 6

Hello, I am trying to use PVE correction on preprocessed PET data downloaded from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database. I have a couple of questions: 1) I am using the co-registered, averaged image of the dynamic images, and it seems from your answers here