Re: [Freesurfer] recon-all with FLAIR error no FSL installed

Dear all, How "fatal" is the FSL environment not being initialized for FreeSurfer 5.3 with FLAIR refinement? I do get results (which look good). Should I rerun them with FSL installed? Thank you very much in advance! Sincerely, Veronica -Original Message- From: Bruce Fischl [mailto:fi

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

On 5/27/13 10:42 PM, Salil Soman wrote: Thank you Doug, I think I initially misinderstood a number of things about this process. I have a 3D GRE volume (I guessed its contrast is closest to BOLD, bbregister set to T1 or T2 seemed to work more poorly). It is not a 2D. I would like to transfor

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

Thank you Doug, I think I initially misinderstood a number of things about this process. I have a 3D GRE volume (I guessed its contrast is closest to BOLD, bbregister set to T1 or T2 seemed to work more poorly). It is not a 2D. I would like to transform the 3D GRE volume into freesurfer space, so

Re: [Freesurfer] white matter volume per lobe...

you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then

Re: [Freesurfer] recon-all with FLAIR error no FSL installed

If FSL is not installed, then bbregister should have failed and recon-all should have stopped. Did that not happen? To answer your question, it might not make any difference. If the flair and T1 were acquired at the same time, then it probably just used the scanner coordinates to do the init

Re: [Freesurfer] mri_glmfit files

Look at mri_glmfit --help. The only one not explained there is cnr.mgh which is the contrasts (gamma) to residual noise stddev (rstd.mgh in the glmdir) doug On 5/27/13 4:48 AM, Joshua deSouza wrote: Hello all, I would just like to know what is the significance of the files that are produc

Re: [Freesurfer] FMRI surface transformation for vertex-wise connectivity analysis

It is based on the white. Notice that since you are using an average subject (fsaverage6) there is some scaling that happens because an average subject will have a surface area that is much less than the average of the subjects that went into. The average of the subjects is kept when the avera

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

yes On 5/26/13 4:56 PM, Salil Soman wrote: As I am working with a 3D volume and not an ADC map, should I still use --seg-erode 1 with mr segstats? Thank On Sun, May 26, 2013 at 1:11 PM, Salil Soman > wrote: Hi - I realize that the --inv tag was still in my

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

On 5/26/13 2:11 PM, Salil Soman wrote: Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainm

Re: [Freesurfer] BBR Register failing

Hi Sal, fsvol should be defined. Can you send me your fslregister? doug On 5/26/13 12:58 AM, Salil Soman wrote: Dear Freesurfer experts, WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investig

Re: [Freesurfer] Correction for multiple comparisons error

what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: > Hi! > > I have been running the mri_glmfit-sim command to do the correction for > multiple comparisons for my group analysis and for some voxel-based

[Freesurfer] white matter volume per lobe...

Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_an

Re: [Freesurfer] mri_anatomical_stats segmentation fault

Hi Rob, does the white surface look ok? How about the contents of the lh.PHC_1.label file? If both seem ok, then feel free to upload the subject and we'll figure it out Bruce On Mon, 27 May 2013, Rob Tennyson wrote: > Hi All, > > I'm running "mris_anatomical_stats" with a few manually defin

[Freesurfer] nuintensitycor and skullstrip problems

hi   i send you further information of the -nuintensitycor and skullstrip problem,about three control subjects. after running "recon_all -i", i decided to process my data step by step, i run "recon_all -autorecon1" for all of them and it ended with errors. i picked up three cases of the recon-al

[Freesurfer] mri_anatomical_stats segmentation fault

Hi All, I'm running "mris_anatomical_stats" with a few manually defined labels. For a few of my subjects, I am getting the error: "Segmentation fault" on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running "mri

Re: [Freesurfer] no hippocampal stats despite running FS 5.3 with -hippo-subfields

I can add that running the -hippo-subfields flag separately did work: recon-all -s SUBJECTIDENTIFIER -hippo-subfields Is there a reason the order of processing should matter? Is there a way I can change my recon-all call (below) so that hippo-subfields will get processed (so I do not have to make

Re: [Freesurfer] nuintensitycor and skullstrip problems

Hi Laouchedi if you upload the dataset we'll take a look Bruce On Mon, 27 May 2013, LAOUCHEDI MAKHLOUF wrote: hi all i run recon_all on some subjects having 512x512x154 , i noticed (using tkmedit) that there are no problems with orig.mgz, and rawavg.mgz but most of them were cropped

[Freesurfer] nuintensitycor and skullstrip problems

hi all i run recon_all on some subjects having 512x512x154 , i noticed (using tkmedit) that there are no problems with orig.mgz, and rawavg.mgz but most of them were cropped (more than half of the brain disappeared) after the "-nuintensity" step (nu.mgz); for one of these patients, the

Re: [Freesurfer] recon-all with FLAIR error no FSL installed

Hi Veronica thanks for the offer, but I don't need to see them. Glad it seems to be working. As for BBR, I'll leave that for Doug Bruce On Mon, 27 May 2013, Popescu, Veronica wrote: Dear Bruce, They look good to me. Should I upload a couple of them, so you can have a look? They're about 23

[Freesurfer] mri_glmfit files

Hello all, I would just like to know what is the significance of the files that are produced after a glmfit is done. I was trying to find a write up online but I was not able to. They include : - cnr.mgh - F.mgh - gamma.mgh - gammavar.mgh - sig.mgh Thank you

Re: [Freesurfer] FMRI surface transformation for vertex-wise connectivity analysis

Hi Doug and Bruce, Doug's comment about vertex spacing and its dependence on the surface of choice has gotten me thinking: When I smooth my fMRI data using 6mm kernel, I use the command "mri_surf2surf --hemi lh --s fsaverage6 --sval lh.fmri.nii.gz --cortex --fwhm-trg 6 --tval rh.fmri.nii.gz --res

Re: [Freesurfer] recon-all with FLAIR error no FSL installed

Dear Bruce, They look good to me. Should I upload a couple of them, so you can have a look? They're about 230MB each. My question is: how serious is the BBR not initializing? Should I run everything again with FSL installed? Best wishes, Veronica -Original Message- From: Bruce Fischl [