[Freesurfer] recon-all error: ERROR! FOV=272.000 > 256

Hi experts, I'm trying to surface reconstruction using high-resolution T1 and T2 data using freesurfer version 6 So I typed like this: recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all and that excited with errors like this; \n*

[Freesurfer] extract values for significant cluster

Dear FreeSurfer experts, in the longitudinal 2 stage model I find a difference in rate between my two groups in right intra parietal sulcus for surface area (survives MC correction). I would like to look at the cortical thickness in that same cluster. Is it possible to use any of the output fil

Re: [Freesurfer] Pial surface missing GM

Hi Bruce, Thanks for the response. I just uploaded the subject using the ftp file exchange. The issue is visible in the region close to voxel coordinate [172, 123 ,134]. the missing gyrus is capped between coronal slice 141 to 118. I forgot to mention in my first message that we used a T2 to impro

Re: [Freesurfer] negative header after preproc-sess

Hi, Thanks for your reply. I tried mri_surf2surf --reshape or many other methods but none of them could help. Then based on your explanation, I tried *mri_convert *.nii.gz *.mgz*, and I could get data from mgz file, it really helps me, thank you! Besides, I am interested in the difference of dim

Re: [Freesurfer] error with fcseed-config & fcseed-sess

Hi Dr. Greeve, Oh I see, thank you for the fix for V1. To probe further, I'm curious why the visual areas weren't implemented? Is there an additional step I could take to access other regions in the visual hierarchy such as V2, V3, and V5? Thanks for your insight Dr. Greeve, Jess On Jul 26, 2017

Re: [Freesurfer] error with fcseed-config & fcseed-sess

Hi Dr. Greeve, Would the following commands be enough to map my regions of interest from the fsaverage map to my individual subjects?: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI Namely, the following bits of code: cd $SUBJECTS_DIR mri_label2label \ --srcsubject fsavera

Re: [Freesurfer] negative header after preproc-sess

Hi Doug, I wonder if there's a plan to move to NIfTI-2 as the default encoding for .nii(.gz) images that would can't be encoded in a standard-conforming NIfTI-1? I believe all of the major packages support NIfTI-2 in their latest releases (with the possible exception of ANTs, which I don't beli

[Freesurfer] mri_glmfit --cortex flag

From what I understand, the --cortex flag is simply supposed to zero out any signal in the medial wall with a mask, I checked mask.mgh, it is 0 on the medial wall and 1 everywhere else as expected... however when I analyze the data without this flag, the resulting sig.mgh file has completely cha

Re: [Freesurfer] mri_glmfit --cortex flag

right, that should not be happening On 07/27/2017 12:39 PM, Rockers, Elijah D. wrote: > From what I understand, the --cortex flag is simply supposed to zero > out any signal in the medial wall with a mask, I checked mask.mgh, it > is 0 on the medial wall and 1 everywhere else as expected... how

Re: [Freesurfer] Extract coordinates from .mgh file

yea, that works too On 07/26/2017 07:36 PM, Redwan Maatoug wrote: > Hi Doug, > > Thank you for your reply, > I have used the tool *surf_cluster* to have the MNI coordinates. > Is it a good alternative to *mri_cor2label *? > > Thank you very much, > Regards, > Redwan > > On Wed, Jul 26, 2017 at 2:

Re: [Freesurfer] Pial surface missing GM

you can also run defect-seg, then look at the help to get an idea of how to load the defect segmentation and see whether the defect is causing the problem On 07/26/2017 08:16 PM, Bruce Fischl wrote: > Hi Jake > > usually that means that there is a topology defect that is being > incorrectly fix

Re: [Freesurfer] Extract coordinates from .mgh file

Use mri_annotation2label to create a label, which will have tkregisterRAS coordinates On 07/26/2017 08:32 PM, Md. Mamun Al-Amin wrote: > Hi > I would like to extract cooridantes of "aparc.a2009s+aseg.mgz" file. > This file is stored in the mri folder. > Would you please help me in this regards?

Re: [Freesurfer] Pial surface missing GM

Hi Jake there are voxels like 173, 112, 122 that are incorrectly segmented as wm (that is, they have a value >=5 in the wm.mgz) that connect two adjenct gyri. You can either change the intensity thresholds in mri_segment, or manually erase some of them. The best way to see this is to look at t

Re: [Freesurfer] extract values for significant cluster

You can use mri_segstats specifying the ocn as the segmentation, the stack of thicknesses as the input, and --avgwf file.dat as the output. Make sure to add --excludeid 0 to exclude background voxels On 07/27/2017 06:18 AM, Clara Kühn wrote: > Dear FreeSurfer experts, > > in the longitudinal 2

Re: [Freesurfer] negative header after preproc-sess

where are you getting those dims? On 07/27/2017 09:24 AM, Bai Haohao wrote: > Hi, > > Thanks for your reply. I tried mri_surf2surf --reshape or many other > methods but none of them could help. > > Then based on your explanation, I tried *mri_convert *.nii.gz *.mgz*, > and I could get data from

Re: [Freesurfer] error with fcseed-config & fcseed-sess

Those labels should exist in your individual subject's label folder. There should be a V1 label in there too. You can use mri_label2vol to create a binary volume in the anatomical space (this will be a volume where voxels values are either 1 (in V1) or 0 (out of V1)). This volume will be 256^3,

Re: [Freesurfer] negative header after preproc-sess

Yes, it is on my to-do list :) On 07/27/2017 11:42 AM, Christopher Markiewicz wrote: > Hi Doug, > > I wonder if there's a plan to move to NIfTI-2 as the default encoding for > .nii(.gz) images that would can't be encoded in a standard-conforming > NIfTI-1? I believe all of the major packages su

Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256

Hi Juhyoung what FS version are you running with? If 6.0 you want to include the -highres flag cheers Bruce On Thu, 27 Jul 2017, juhyoung Ryu wrote: Hi experts, I'm trying to surface reconstruction using high-resolution T1 and T2 data using freesurfer version 6 So I typed like this: 

Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates

Hard to say whether the coords are right or not. You can run tksurfer and look at the coords in and around your region to see whether they are reasonable. The -1s need to go into the label that is used as input the mri_label2label. mri_label2label will assign vertex numbers based on the coordin

[Freesurfer] problem with bedpostx

Hi, Running trac-all -bedp and getting an error message I've never seen before. I'm running it on a desktop, not a cluster, which it warns agains - but it should still run, shouldn't it? larsrim:~/lbkabel/tbi/morfometri_test$ trac-all -bedp -c DWI/jobscripts/d1_1001_local.dmrirc INFO: SUBJECTS_

Re: [Freesurfer] problem with bedpostx

Hi – Is this on ubuntu by any chance? I remember it cropping up a while ago, and I think you had to change something in the first line of the script. It should be in the archives. From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Lars M. Rimol" mailto:lari...@gmail.com>> Repl

[Freesurfer] Is it possible to run a conjunction analysis on longitudinal sMRI data in Freesurfer?

Hi Freesurfer experts, I'm wondering if it's possible to do a conjunction analysis on sMRI data in Freesurfer. I would like to compare longitudinal results from 2 experimental training groups and 1 control, where I can examine: 1) which regions underwent structural changes in both of the experime

Re: [Freesurfer] Is it possible to run a conjunction analysis on longitudinal sMRI data in Freesurfer?

If you have two sig maps, then use mri_concat with the --conjunct option On 07/27/2017 02:37 PM, Jennifer Legault wrote: > Hi Freesurfer experts, > > I'm wondering if it's possible to do a conjunction analysis on sMRI > data in Freesurfer. I would like to compare longitudinal results from > 2

Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256

Hi Bruce, Yes I’m using v6.0. I found that there is -hires flag in version 6 (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon ) and i included that; recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all -cw256