[Freesurfer] PET processing seg fault with mri_glmfit --mrtm1

Hi Freesurfer developers, I’m trying to perform BP analysis with mri_glmfit —mrtm1. I ran mri_gtmpvc without PVC, which finished without error. However, the km.hb.tac.nii.gz appears empty when I open it with fslview or tkmedit, although this may be due to the nature of the file (I’m not sure w

Re: [Freesurfer] FW: problem with hard coded directory (/scratch)

Do you have the problem if you do not include the hippo subfields? On 01/07/2016 08:15 AM, Fengji Geng wrote: > Hi Douglas, > You asked us to give you an example of the problem program. I will try > to do it here, but if it is not what you want, please let me know. > > we ran recon-all -all -s

Re: [Freesurfer] searchable Destrieux atlas by recon all labels?

freeview partial solution If this is important to you, you could write a quick script to do this for you: 1. mri_annotation2label to output all labels 2. write a script to launch freeview and load all of the labels (reading the color and applying it from the FS ctab file) e.g. freeview -f surf/

Re: [Freesurfer] Mask out medial wall?

Hi Stephanie in tksurfer I think you can type: mask_label lh.cortex (or rh.cortex) at the tcl (%) command line cheers Bruce On Thu, 7 Jan 2016, DeCross, Stephanie N. wrote: Hi, Is there a way to mask out the medial wall in the tksurfer command? I’m looking for a way to have the map visua

[Freesurfer] Mask out medial wall?

Hi, Is there a way to mask out the medial wall in the tksurfer command? I’m looking for a way to have the map visually look as if there’s simply no activation within the medial wall (showing a plain gray striped/curvature shown brain in that area instead), as opposed to having the medial wall be

Re: [Freesurfer] searchable Destrieux atlas by recon all labels?

Hi Andrea I'm not sure what you mean but I'm pretty certain the answer is "no". sorry Bruce On Thu, 7 Jan 2016, Andrea Bozoki wrote: Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)? It would be very helpful to be able

[Freesurfer] searchable Destrieux atlas by recon all labels?

Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)? It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitati

Re: [Freesurfer] MPRAGE Data

I see. Is there a reason it has to be raw data? If it is Siemens we have code for processing it, but I'm pretty sure we aren't allowed to distribute it (is that correct Andre?). If it was a one-time thing you could send it to us, we could convert it and then send it back, but of course that won

Re: [Freesurfer] Recon-all get stucked without error during processing

try specifying -no-wsgcaatlas or -no-wsatlas and rerunning just the skull stripping and see if it fixes things cheers Bruce On Thu, 7 Jan 2016, Matthieu Vanhoutte wrote: Hi Bruce, This problem isn't resolved yet. I uploaded the subject raw 3D T1 on FileDrop. Changing the watershed param

Re: [Freesurfer] MPRAGE Data

Hi Bruce, Thanks for your response. I'm writing software that involves processing the data; currently I have one sample set but expect to be working with more in future. Scott > On Jan 7, 2016, at 6:45 AM, Bruce Fischl wrote: > > Hi Scott > > we are almost certainly not allowed to do so ei

[Freesurfer] R: Re: FDR correction

Thanks. - on question 2: I have run rh = MRIread('sig.mgh'); but this error occur Undefined function 'MRIread' for input arguments of type 'char'. no help is permitted on MRIread -on question 3: I'm using this command line to visualize the map describing the functional connectivity form seed to

Re: [Freesurfer] Recon-all get stucked without error during processing

Hi Bruce, This problem isn't resolved yet. I uploaded the subject raw 3D T1 on FileDrop. Changing the watershed parameters could be done in the recon-all command ? Thanks in advance ! Best regards, Matthieu 2016-01-07 14:58 GMT+01:00 Bruce Fischl : > Hi Matthieu > > was this ever resolved? If

Re: [Freesurfer] FW: problem with hard coded directory (/scratch)

can you be more specific? Which program failed? Also, please send us the recon-all.log file so we have the information we need to help you. cheers Bruce On Thu, 7 Jan 2016, Fengji Geng wrote: Hi Douglas,  You asked us to give you an example of the problem program. I will try to do it here, b

Re: [Freesurfer] MPRAGE Data

Hi Scott we are almost certainly not allowed to do so either. Is this Siemens data? Why do you have raw data? Is it just this one dataset or do you need to process raw data more often? cheers Bruce On Wed, 6 Jan 2016, Scott E wrote: > Hi folks, > Hopefully I'm not asking this question in the

Re: [Freesurfer] FW: problem with hard coded directory (/scratch)

Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s -hippocampal-subfields-T1T2 . We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and

[Freesurfer] claustrum segmentation

Hi freesurfer experts, I have a few questions on claustra segmentations. I tried to look into archives but did not find an answer to all my points so far.. I have a group of subjects in which I would like to segment claustrum. Looking at lookup table a color is assignied for both left and right c