[Freesurfer] FreeSurfer crashing

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon-all on schizophrenia patients and controls. For some reason freesurfer is crashing. I wanted to know the reason for frequent crashing. I'm using Ubuntu 16.04 LTS and freesurfer-Linux-centos6_x8

[Freesurfer] T1 hypointensities

External Email - Use Caution Hello, Are the WM-hypointensities segmented in the same way as the rest of the subcortical regions? i.e., using the probablistic atlas referenced in the 2002 Fischl et al paper? Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodis

Re: [Freesurfer] LME

External Email - Use Caution Dear Kersten, I have a question about how to interpret cortical thickness difference between groups. I have three groups(A, B, and C) and five time points(t=0,0.5, 1,2,3). To see the difference between group A and group B, I constructed the follow

Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution Thanks for the quick reply. Have sent the file to you now - James From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: 07 January 2019 17:42 To: freesurfer@nmr.mgh.harvard.edu S

Re: [Freesurfer] Pial surface error (failing dura removal)

Hi Douglas, Thanks for your swift reply. I just shared a link to a Partners Dropbox folder with you as our group (lazargp) does not have a folder in /cluster/outgoing. No T2 or FLAIR unfortunately. Other than MPRAGE T1 we only have fMRI and DTI scans. Thanks, Johann __

Re: [Freesurfer] Calculating volume using pial files

Hi Da-Yea mris_volume can be used to compute the volume of any closed surface. cheers Bruce On Mon, 7 Jan 2019, Song, Da-Yea wrote: External Email - Use Caution Hello,   I’m trying to calculate the volume using pial files. Is there a way to convert ?h.pial files into nii

Re: [Freesurfer] Calculating volume using pial files

Have you tried aparcstats2table? This command does not convert, but it extracts all the stats which allows you to play with the volume and any other stats. https://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table Johann From: freesurfer-boun...@nmr.mgh.harva

[Freesurfer] Calculating volume using pial files

External Email - Use Caution Hello, I'm trying to calculate the volume using pial files. Is there a way to convert ?h.pial files into nii formats? Or is there a command to calculate the volume? Thank you so much in advance for your help. Best regards, Da-Yea Song -

Re: [Freesurfer] (no subject)

External Email - Use Caution Hi Ruopeng, Thank you very much for your quick answer and advice. So I am going to update freeview! Thanks! Larissa Gesendet mit der WEB.DE Mail App Am 07.01.19 um 17:35 schrieb Ruopeng Wang > Hi Larissa, > > The latest development version of fr

Re: [Freesurfer] mris_apply_reg failing for area/volume

What is $SUBJECTS_DIR/${template}/surf/lh.sphere.reg ? If template is not fsaverage_sym, can you send this file to me too? On 1/7/19 5:21 AM, James Michael Roe wrote: External Email - Use Caution ​Dear freesurfer experts I am still unable to register RH area and volume files to the LH

Re: [Freesurfer] (no subject)

Hi Larissa, The latest development version of freeview supports drawing labels on surface. You can take a look here on how to update freeview: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview In the latest version, you can draw paths on surface and use custom fill to create/edit labels

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote: External Email - Use Caution I used the following command to obtain only rescaled voxel-wise PET image (with no PVC): mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mas

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution I used the following command to obtain only rescaled voxel-wise PET image (with no PVC): *mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc* If I omitted

[Freesurfer] (no subject)

External Email - Use Caution Hi everybody, after finishing my group analysis I am currently trying to run a ROI analysis. However I have some problems/general questions. I am trying to draw a ROI on fsaverage in order to use the mri_label2label command afterwards. I opened Freev

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

For MGX, the field of view is reduced to reduce computation and space usage; this requires a new registration matrix. For RBV, the voxel size is changed in addition. In both cases, a new registration is computed from the input registration On 12/21/18 2:29 PM, Matthieu Vanhoutte wrote:

Re: [Freesurfer] Pial surface error (failing dura removal)

Do you have a T2 or a FLAIR? Can you upload the subject so we can take a look? On 1/6/19 6:20 PM, Rusche, Johann wrote: Dear Freesurfers, I have been processing my T1 dataset through the longitudinal pipeline with the -3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large a

Re: [Freesurfer] Robust PET signal projection

No. You can use mri_concat with --mtx option, where the argument to --mtx is an asci matrix that is square and diagonal with the weighting factors on the diagonal. You could also use mri_glmfix with the --X option, where X is an ascii column matrix of weighting factors (make sure that the the su

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work? On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote: External Email - Use Caution Hi Douglas, Thanks for helping. To

Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

External Email - Use Caution Version 6.0 Thanks, Rachel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: Monday, January 7, 2019 2:50:57 AM To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list

Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution ​Dear freesurfer experts I am still unable to register RH area and volume files to the LH of a symmetrical template for a number of longitudinally processed subs. This is only the case when using the --jac flag (all run fine without). There appears