Re: [Freesurfer] T2 weighted images as input for recon-all command

arvard.edu<mailto:dgr...@mgh.harvard.edu>>: No, not currently On 05/03/2018 11:26 AM, M Janani wrote: > > Hi Team, > >I have one doubt. Can I input T2

[Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution Hi Team, I have one doubt. Can I input T2 weighted images for recon-all command? Regards, Janani ::DISCLAIMER::

[Freesurfer] Complete CSF value computation

External Email - Use Caution Hi Team, We would like to compute the CSF value from the MRI data. We have both T1 and T2 weighted images. Have processed the T1 images and obtained the CSF value(summation of ventricular system and CSF value). But

Re: [Freesurfer] Error in running make_average_subject

Thanks andrew... I will try this From: Hoopes, Andrew <ahoo...@mgh.harvard.edu> Sent: Tuesday, February 20, 2018 8:55:47 PM To: M Janani; Freesurfer support list Cc: Sasikala Sethu Subject: Re: [Freesurfer] Error in running make_average_subject Hi Janani, W

[Freesurfer] Error in running make_average_subject

Dear FreeSurfer Experts, I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

was not found? What is the terminal output? On 09/13/2017 07:07 AM, M Janani wrote: > No. > When we ran the unsetenv FS_LOAD_DWI, we got command not found error. > > Thanks, > Janani > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu &

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault Do you mean that the error is still there even after running the unsetenv command? And you ran them from the shell, one after the other? On 09/12/2017 02:27 AM, M Janani wrote: > Hi Douglas, > >

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault Try running unsetenv FS_LOAD_DWI then re-running recon-all On 09/11/2017 12:57 PM, M Janani wrote: > > Hi Team, > > Am getting segmentation

[Freesurfer] mri_convert: line 3: 38445 Segmentation fault

Hi Team, Am getting segmentation error during the reconstruction process. Please help in resolving the error. I have attached log for reference. Thanks, Janani ::DISCLAIMER::

[Freesurfer] PETSURFER - mri_gtmpvc option to use SGTM

Hi Team, Could you please tell me how to modify this command to perform SGTM mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output I have tried with

[Freesurfer] time.dat file in Kinetic Modelling MRTM1 step - Petsurfer processing

Hi team, Could anyone please tell how to create the time.dat file in the Kinetic Modelling MRTM1 step mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz Regards, Janani ::DISCLAIMER::

Re: [Freesurfer] Freesurfer PIB PET image processing

] On Behalf Of Douglas N Greve Sent: 15 August 2017 00:12 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer PIB PET image processing If you use mri_gtmpvc, then the gtm.stats file will have the intensity values. On 08/11/2017 02:37 AM, M Janani wrote: > Thanks for your supp

Re: [Freesurfer] Freesurfer PIB PET image processing

esurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Freesurfer PIB PET image processing > > We do not have any thing to specifically analyze PiB. You can look at > the PETsurfer page for more general instructions > > > On 08/09/2017 02:15 AM, M Janani wrote: >&

Re: [Freesurfer] Freesurfer PIB PET image processing

] Freesurfer PIB PET image processing We do not have any thing to specifically analyze PiB. You can look at the PETsurfer page for more general instructions On 08/09/2017 02:15 AM, M Janani wrote: > > Hi Team, > > I apologize, I am new to Freesurfer. > > Currently we are process

Re: [Freesurfer] Total White matter and CSF value Calculation

. I would not trust the 2nd formula since we don't compute actual ICV On 8/2/17 2:22 AM, M Janani wrote: Hi Douglas, Thanks for your support. From the below conclusion, can I say Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh + rh)Inf-Lat-Vent + (lh

[Freesurfer] Freesurfer PIB PET image processing

Hi Team, I apologize, I am new to Freesurfer . Currently we are processing PIB PET images. When we compare the SPM data along with FREESURFER outputs. We were able to see a large variation in the values. Could you please guide us in processing

Re: [Freesurfer] Total White matter and CSF value Calculation

Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+Greve%22> Mon, 31 Jul 2017 07:48:02 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20170731> On 7/31/17 3:12 AM, M Janani wrote:

[Freesurfer] Total White matter and CSF value Calculation

Hi Team, Could you please confirm whether the below mentioned formulas to compute Total WM and ventricular CSF are correct 1. Total White Matter = CerebralWhiteMatterVol + (lh+rh) Cerebellum White Matter 2. Total ventricular CSF = (lh + rh) Lateral-Ventricle + =

Re: [Freesurfer] How to create mask for Total Graymatter and White matter Volume

017 08:33 AM, M Janani wrote: > > Hi Team, > > I would like to create mask for Total Gray matter and > white matter volume. > > I was able to get the total white matter volume using the below > mentioned command > > mri_binarize -i aparc+

[Freesurfer] How to create mask for Total Graymatter and White matter Volume

Hi Team, I would like to create mask for Total Gray matter and white matter volume. I was able to get the total white matter volume using the below mentioned command mri_binarize -i aparc+aseg.mgz --wm --o wm.mgz But I couldn't find any option to create the mask for Total Gray

Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness

exactly the same error? On 07/14/2017 02:05 AM, M Janani wrote: > > Hi Douglas Greve > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+Greve%22>, > > Thanks for your support. > > I tried with the --reshape-factor 6

Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness

Janani --- How did you create the segmentation? You can change the shape of the seg with mri_surf2surf --reshape 6 --s fsaverage --hemi lh --sval seg.mgh --tval seg.reshape.mgh On 7/7/17 10:15 AM, M Janani wrote: Hi Team, I'm attempting to extract co

[Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness

Hi Team, I'm attempting to extract cortical thickness values for a region-of-interest (ROI) defined in volume spacesubject for PiB MRI. I got the below mentioned error while computing the stats value cwd cmdline mri_segstats --seg freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh

[Freesurfer] ROI analyses using SPM AAL ROIs

Hi Team, Currently I'm working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(TT_avg152T1.nii) they are referring to? I took AAL ROIs from

[Freesurfer] ROI analyses using SPM AAL ROIs

Hi Team, Currently I'm working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(TT_avg152T1.nii) they are referring to? I took AAL ROIs from

[Freesurfer] Left Cerebellum Exterior and Right Cerebellum Exterior mean value generation

Hi freesurfer team, I apologize, I am new to freesurfer. I'm doing analysis on PiB. I have successfully got my .stats files by running the recon-all command. When I checked for Left Cerebellum Exterior and Right Cerebellum Exterior value in the