Re: [Freesurfer] Caret to Freesurfer

Kara, the gifti format is used to convert between caret and freesurfer surfaces. use mris_convert (see --help). Nick > Matt, > > Yes, I think the plan is to discuss this and other potential options. I > had a feeling you may know the most, but I thought I would send out the > question in case

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

Hi, Bruce Sorry for the late reply as I was trying to figure it out by myself. I mean the average of the subjects in the volume space that were used for generating the surface template. Actually I kind of found a volume average in the mri folder named as T1.mgz that seems to correspond to the

Re: [Freesurfer] running mris_preproc for each glm?

yep, once per measure. doug On 3/15/13 10:56 PM, Laura M. Tully wrote: Thanks Doug. just to be clear - I'd need to run it once per surface measure correct? i.e. once for thickness analyses on each hemi, and once for area analyses on each hemi? On Fri, Mar 15, 2013 at 11:05 AM, Douglas Greve

Re: [Freesurfer] running mris_preproc for each glm?

Thanks Doug. just to be clear - I'd need to run it once per surface measure correct? i.e. once for thickness analyses on each hemi, and once for area analyses on each hemi? On Fri, Mar 15, 2013 at 11:05 AM, Douglas Greve wrote: > Hi Laura, you would only need to run preproc multiple times if th

Re: [Freesurfer] Help with vertices

Hi Neha the vertices are indices into the surface file. You can load it in with read_surf, and find the corresponding vertex in the surface (e.g. ?h.white). These are in "surface RAS" or "tkreg RAS" coords, which you will then need to convert to volume coords. I believe Doug has documented thi

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

Hi Longchuan what kind of volume template do you mean? Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: > Hi, FreeSurfer experts > > I have a question regarding making a volume template based on the surface > template for non-human primates. I have made a surface template using a > group of monke

[Freesurfer] make a volume template from the surface-based template for non-human primates

Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I

[Freesurfer] Definition of temporal lobe

Hello all, Which labels reside in temporal lobe? Do I look at aseg or aseg+aparc.? I am very new to freesurfer therefore forgive me for my naive questions. Best, Akshay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.ha

Re: [Freesurfer] running mris_preproc for each glm?

Hi Laura, you would only need to run preproc multiple times if the subjects changed between analyses. If it is the same subjects in the same order, then you only need to run it once. doug On 3/15/13 4:42 PM, Laura M. Tully wrote: Hi freesurfer experts, I'm planning to run a few different glm

Re: [Freesurfer] Caret to Freesurfer

Matt, Yes, I think the plan is to discuss this and other potential options. I had a feeling you may know the most, but I thought I would send out the question in case anyone else has tried. As it stands, it sounds like no method currently exists for a Caret surface-to-Freesurfer transition? I

Re: [Freesurfer] mri_convert problem

Thanks a lot! Date: Fri, 15 Mar 2013 13:09:41 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem just: mri_convert volume.mgz cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: > Sorr

Re: [Freesurfer] mri_convert problem

just: mri_convert volume.mgz cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: Sorry, I am also a beginner in   Linux environment. Now it works.  I try : - esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA total 13892 -rwxr--r-- 1 esther esther 14224696 12 mar 23:33 t1_icbm_nor

Re: [Freesurfer] Error messages and empty surf files

it seems like the watershed failed and nothing got created after that. You need to track down why. Usually it's either the talaraich that failed or the volume is oriented incorrectly. Can you bring the T1.mgz up in tkmedit and confirm that the directions it shows are anatomically correct? Then

[Freesurfer] running mris_preproc for each glm?

Hi freesurfer experts, I'm planning to run a few different glms on surface data using glm_fit e.g. diagnosis * age; diagnosis * age * symptoms; diagnosis * age * somebehavioral variable etc.. Do I have to run mris_preproc using the specific fsgd file for each glm? My data are already qcached, and

Re: [Freesurfer] mri_convert problem

Sorry, I am also a beginner in Linux environment. Now it works. I try :-esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AAtotal 13892-rwxr--r-- 1 esther esther 14224696 12 mar 23:33 t1_icbm_normal_1mm_pn3_rf20.mnc[esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc-

Re: [Freesurfer] mri_convert problem

can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote: I get this error- esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.m

Re: [Freesurfer] mri_convert problem

I get this error-esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mncmincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.mnc---I check in the directory enad the file is right there, > Date: Fri, 15 Mar 201

Re: [Freesurfer] mri_convert problem

Hi Valtina you can convert directly without going through nii. What happens when you run ls -l on that file? Or mri_info? cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: Hi,  I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first conver

[Freesurfer] Correcting CPs and Pial

Hi everyone, I'm a very new fresurfer user and I have to understand the very simple basis of its use yet. So I have some maybe stupid questions about that. I heve to work on cortical thickness, so I suppose I have to complete the segmentation and then correcting CPs and Pial surface. The first ques

Re: [Freesurfer] question about autorecon2-cp, autorecon-pial and autorecon-wm flags

That's correct. On Thu, 14 Mar 2013, Mehul Sampat wrote: Hi Folks,I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm flags in recon-all help and also here http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags My interpretation is when I use autorecon-pial, I only need the

[Freesurfer] "rm:No match." when executing recon-all -qcache

Hi all, When I run "recon-all –qcache", there are a lot of Error messages saying "rm: No match." (although just this error message, no others). I'm wondering if this is something of concern, or something I can simply ignore. Thanks! Daniel ___ Free

Re: [Freesurfer] mri_convert problem

Do you have read permission to the file? Also, you can convert straight to mgz, not need to use nii as an intermediate. doug On 3/15/13 5:13 AM, Valtina Pouegue wrote: Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii

[Freesurfer] subcortseg flag

Hi, After upgrading to FreeSurfer 5.2.0, the command with "-subcortseg" flag exited with the following error. MRISread(/usr/local/freesurfer/5.2.0/dist/subjects/test/surf/lh.white): could not open file The "-autorecon1" stage finished without error, so I'm wondering if there is any change in mr