[Freesurfer] Ask question about QAtools

Dear Freesurfer experts, I installed the QAtools and tried a subject with this commond: $QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt but I encountered the following Error message, can someone help me figure it out? Any help is appriciated, thanks! Error message 1:

[Freesurfer] save custom made path on surface as label

Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label

Re: [Freesurfer] Output volume along with its calculated pia

Hi Octavian try using mris_fill with the pial surface to generate a binary volume that is 1 in the interior of the pial and 0 outside of it. cheers Bruce On Sun, 4 Mar 2012, octavian lie wrote: Dear All,   I am increasingly fascinated by freesurfer. Here is a rookie issue: I use a source

Re: [Freesurfer] Help! What does the error mean

can you run mri_info /home/wb/test_data/ZWK/34810194 and send us the results? It will probably tell you that that volume has multiple frames, so the next question is why? What acquisition are you using? cheers Bruce On Mon, 5 Mar 2012, bowan...@mail.ustc.edu.cn wrote: Dear All I was

Re: [Freesurfer] Coordinates of output files

The nifti qform should be that of the scanner. doug octavian lie wrote: Dear All, I am using a pipeline for electrode coregistration including freesurfer for pial surface generation, run by default recon-all -all and mris_volmask with --save_distance option. The FS files

Re: [Freesurfer] aseg segmentation problem

wow, that's pretty bad. We haven't seen that in a while. What version are you running? If you upload the subject I'll take a look Bruce On Mon, 5 Mar 2012, Margaret Sheridan wrote: Hi all, I know on principle the aseg is not supposed to be edited but we have a case (attached) where the

[Freesurfer] -mprage flags

Hi all, What does -washu_mprage and -mprage flags do in autorecon step. How does it help in segmentation? -SK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] -mprage flags

it changes some of the assumptions about CNR and SNR. Bascially, the mprage has higher CNR and lower SNR than FLASH/SGPR, so for example when we are doing region growing to find control points the -mprage switch will ue a higher threshold to allow the control points to grow more liberally than

Re: [Freesurfer] Create summary images

Hi Charlotte, With these scripts you can take snapshots of the aseg for several subjects in tkmedit. I'd suggest including the -snaps-detailed flag to get a large sample of slices from the aseg. https://surfer.nmr.mgh.harvard.edu/fswiki/QATools -Louis On Fri, 2 Mar 2012, Bruce Fischl

[Freesurfer] Qdec Error in analyze: command failed

Hi, I'm getting an error in analyze: command failed: mri_concat notification when trying to run qdec on a within subjects analysis (N=29, looking at thickness and social functioning whilst controlling for ICV). I'm not sure what this means. See the output below. Thanks! Laura. Data table

[Freesurfer] pwd: permission denied

Hi, I am new to FS and have encountered a weird problem that I do not know how to solve and did not find any earlier postings on. When I run recon-all on a file in my own home directory everything works normally: recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test -i BIG1026_1.nii.gz

[Freesurfer] controls points in 5.1

Bruce, You had posted that there is a 'backwards compatibility flag' regarding control points manually specified to the aseg normalization in Freesurfer version 5.1 (see your thread from 1/27/12 below). You said that Nick might know about this flag. I too had noticed very different behavior

[Freesurfer] mri_vol2surf error writing to nifti volume

Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type

[Freesurfer] (no subject)

Hello all, I'm encountering a problem when I try to compare two timepoints for a particular subject. I run the command recon-all -all -s 7107-46-tp1 -i 7107-46-1/001.mgz and the end of the output stream where I receive errors shows the following below. Any help is greatly appreciated! painting

Re: [Freesurfer] (no subject)

Hi Ryan what is your SUBJECTS_DIR? You probably want it to be somewhere other than $FREESURFER_HOME/subjects as it is trying to create a symlink. cheers Bruce On Mon, 5 Mar 2012, Ryan wrote: Hello all,    I'm encountering a problem when I try to compare two timepoints for a particular

[Freesurfer] Ask question about QAtools

Dear Freesurfer experts, I installed the QAtools and tried a subject with this commond: $QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt but I encountered the following Error message, can someone help me figure it out? Any help is appriciated, thanks! Error message 1: