Re: [Freesurfer] FW: Topological defect

Ok, and is there anyway to know the vertex index of these voxels due to which topological defect happened? Thanks -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, February 27, 2014 11:00 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] FW: Topological defect

10:03 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Topological defect Hi Siddharth it means you have a huge defect that we are unable to automatically correct. If you look at the ?h.inflated.nofix it should be obvious what it is cheers Bruce On Tue, 25

[Freesurfer] FW: Topological defect

Hi all, I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject: Correction of the Topology Finding tru

Re: [Freesurfer] Topological defect

: Re: [Freesurfer] Topological defect Hi Siddharth, Bruce will have to answer this one. He's on vacation until next week. Can you repost on monday? doug On 02/20/2014 11:21 AM, Ray, Siddharth wrote: > > Hi all, > > I am having an topological defect error while running few of su

[Freesurfer] Topological defect

Hi all, I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject: Correction of the Topology Finding tru

[Freesurfer] tksurfer display

Hi, Is there any way in tksurfer GUI display, that I can set a NVtxs threshold to get rid of regions (that came up significant after monte carlo simulation) which have NVtxs less than my input threshold. For eg. In my table below, I don't want postcentral label to appear in my tksurfer view (a

[Freesurfer] MRISalloc: could not allocate vertices

Hi Freesurfers, Got this error while running some of my subjects: Correcting Topology of defect 1 with euler number -257 (129 loops) computing statistics for defect 1: 33364 vertices location: [ (156,125,84) - average intensity = 92.126 ]

[Freesurfer] Issue running Longitudnal Analysis

Hi all, I was trying to run freesurfer longitudinal analysis for my subjects at 2 time points and when I ran the pre_proc step it gave me an error that file 'lh/rh.thickness is missing'. Here is what I have done. 1) Run the Freesurfer till CA Normalize stage (till norm.mgz stage). 2)

[Freesurfer] Loosing data when using mri_convert

Hi all, So I am trying to reorient my sagittal scans (with messed up labels) to axial using mri_convert (to get right label), I am able to do so but I am loosing some data (some slices). When I checked voxel-to-ras transform for the original and reorient image, they were different. How can I

[Freesurfer] use mri_convert to flip A/P labels

Hi, I have niftii files of some subjects where A/P labels are flipped. Is there anyway I can flip those labels using mri_convert, like mri_convert -left-right-reverse for flipping L/R labels. Thanks, -Siddharth ___ Freesurfer mailing list Freesurfer@n

[Freesurfer] mri_convert and flips

Hi all, I have some of my subjects with their A/P and L/R labels flipped and using mri_convert convert command to make them right. I was little concerned that I am just providing command with -in_ourientation and -out_orientation info to get the right labeled images, is this anyway going to cha

[Freesurfer] ERROR! FOV=348.000 > 256

Hi all, I am coming across this error for couple of my subjects: WARNING ===== The physical sizes are (240.00 mm, 240.00 mm, 347.20 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 348 slices.

[Freesurfer] mri_convert

Hi free-surfer folks, I have some subjects with L-R header flipped in nifti's. Is it possible to flip the header using mri_convert so that I can have the right orientation information for subjects. Please let me know. Thanks, -Siddharth ___ Freesur

Re: [Freesurfer] mri_convert mgz to nifti

Thanks!! -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, June 04, 2013 9:51 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert mgz to nifti mri_convert file.mgz file.nii.gz should do the trick On Tue

[Freesurfer] mri_convert mgz to nifti

Hi all, I just want to convert .mgz files to .nifti using mri_convert, do I have to flip my image when I do that using RAS ? or I should simply use: Mri_convert input_file_name.mgz output_file_name.nii Thanks in advance, Siddharth ___ Freesurfer ma

[Freesurfer] image with Cerebellum

Hi, I am new to freesurfer and just want to know can I just have skull-stripped image (with cerebellum) anywhere between stages in Freesurfer 5.3?? Please let me know. Thanks, Siddharth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] F Problem running : mri_cc -aseg.auto_

...@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 2:26 PM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] F Problem running : mri_cc -aseg.auto_ Hi Siddharth can you cc the list so others can answer? Did you check the norm to make sure it's ok? Yo

[Freesurfer] F Problem running : mri_cc -aseg.auto_

Hi, I am new to freesurfer and was trying to run it on couple of my subjects but I am stuck (for last 40 hrs) at stage "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/sray2/Desktop/combirx/cr052_ip_output/mri/transforms/cc_up.lta cr052_ip_output" it seems. The last few lines o