[Freesurfer] FsFastPreProc Registration of files from each session to their session's structural image

(Thanks for your feedback to my previous inquiry - I've resolved this problem) I'm running FsFastPreProc on a dataset with a number of subjects, where each subject has two sessions. There's a separate structural image taken in each session. I want to make sure each subject's functional data is

Re: [Freesurfer] Difficulties running tracula

Sorry to hear. Do the other registration files in the dmri/xmfs/ directory, including diff2anatorig.bbr.mat, look like this too? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of John Davis Sent:

[Freesurfer] Subjectwise extraction from ROIs

Hello experts, I identified two clusters (X for thickness and Y for volume) showing significant association between cortical measures (thickness and volume) and motor-performance. I followed steps from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and got several output

Re: [Freesurfer] Difficulties running tracula

Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank

Re: [Freesurfer] IndexError: list index out of range

Thanks Sarah, I haven’t been able to replicate this - do you mind sending the stats file that you’re using as input? Andrew On February 15, 2018 at 3:58:17 PM, Makaretz, Sara Johanna (smakar...@mgh.harvard.edu) wrote: Hi Andrew, python --version = Python

Re: [Freesurfer] IndexError: list index out of range

Hi Andrew, python --version = Python 2.7.3 -- EPD 7.3-1 (64-bit) Sara From: Hoopes, Andrew Sent: Thursday, February 15, 2018 3:56:22 PM To: Makaretz, Sara Johanna; Freesurfer support list Subject: Re: [Freesurfer] IndexError: list index out of range Hi Sara

Re: [Freesurfer] IndexError: list index out of range

Hi Sara and Arkadiy, What version of python2 are you using? python --version thanks Andrew On February 13, 2018 at 10:16:34 AM, Makaretz, Sara Johanna (smakar...@mgh.harvard.edu) wrote: *I also got this error when I ran w/ python 2: python2

Re: [Freesurfer] Problem with cortical parcellation of rh but not lh

Hi Amal this happens for multiple subjects? What version are you using? I have only ever seen this very rarely and usually for an atypical (e.g. multiple central sulci) folding pattern. Can you upload a subject so I can take a look? cheers Bruce On Tue, 13 Feb 2018, Amal Achaibou wrote: > >

Re: [Freesurfer] aparcstats2table subject space?

Yes, it is in native subject space On 02/07/2018 07:35 AM, Kasper Jessen wrote: > > Dear FreeSurfer, > > When you extract e.g. thickness from the command aparcstats2table – is > the data extracted from subject space? > > We need to know whether or not, we need to covariate for total brain >

Re: [Freesurfer] V1 functional ROI

You can use 1021/2021 for calcarine. Or you can use -label lh.V1_exvivo.thresh.label (instead of -seg) On 02/09/2018 02:18 PM, Sarah Cole wrote: > Dear Dr. Douge, > > I am a little bit confused about creating function ROI in V1. > > Basically, I have some localizers that for some ROIs I need to

Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

should be the same as when you use --regheader with tkregister On 02/09/2018 11:24 PM, Rita Elena Loiotile wrote: > Hi, > > I just noticed that when I open my volume file in tksurfer using > --overlay it gives a better volume to surface mapping than when I do > mri_vol2surf. Do you know what

Re: [Freesurfer] Removing labels after extending parcellation into white matter

No. I'd write a script to do it On 02/12/2018 12:17 PM, Michiko H. wrote: > Hi Doug, > > Thanks - this is extremely helpful! > > With regard to the first command: mri_binarize --replace 1001 3001 --i > aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz > Since I'd like to

Re: [Freesurfer] QDEC Set Up

Yes, that is the same On 02/12/2018 07:15 PM, Martin Juneja wrote: > Since I have 4 groups here: X1-M, X2-M, X1-F and X2-F, so can someone > please confirm if this is identical to this example: > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V > If so, then I can follow instructions on

Re: [Freesurfer] ROI extraction using functional masks

At what step is the failure happening? Do the masks look ok on the surface? On 02/12/2018 08:06 PM, Yann Quidé wrote: > Dear FS experts, > > I am trying to extract values for cortical thickness, surface area and > volumes, from different functional ROIs. These cortical ROIs have been > defined

Re: [Freesurfer] FIR analysis

You can  visualize it with tkmedit-sess or tksurfer-sess for the individual. It will automatically see that it is an FIR analysis and load the time courses (you may need to add the -tkmedit/-tksurfer flag because it only works in the old tkmedit/tksurfer programs). If you want to visualize

Re: [Freesurfer] inter-hemisphere registration on customised template

This is not an easy thing to do. The script to do it is make_folding_atlas with the --xhemi flag. Run  it with --help to get more info On 02/13/2018 11:49 AM, Ting Qi wrote: > Dear Freesurfer experts, > > I am writing to ask how to do the surface-based inter-hemispheric > registration based

Re: [Freesurfer] Percent Signal Change

That does not get computed. You can do it in matlab with something like f = MRIread('f.nii.gz'); fmn = mean(f.vol,4); fmnrep = repmat(fmn,[1 1 1 size(f.vol,3)]);; s = f; s.vol = f.vol./fmnrep; MRIwrite(s,'percentchange.nii.gz') On 02/15/2018 02:03 PM, Sarah Cole wrote: > Yes, that's

Re: [Freesurfer] Percent Signal Change

Yes, that's exactly what I am looking for. Raw waveform as a percent. On Thu, Feb 15, 2018 at 1:00 PM, Douglas N Greve wrote: > h-offset is the intensity offset (basically the mean signal). h.nii.gz > is a complicated combination of the betas (regression coefficients)

Re: [Freesurfer] Percent Signal Change

h-offset is the intensity offset (basically the mean signal). h.nii.gz is a complicated combination of the betas (regression coefficients) that is included for backwards compatibility. What do you mean by % signal change? Do you want the raw waveform as a percent? On 02/15/2018 01:52 PM,

Re: [Freesurfer] resting state motion censoring

Currently there is no way to do this. But it might not be hard to add. If I don't get back in a couple of weeks, send me a reminder. On 02/14/2018 12:13 PM, Adam Martersteck wrote: > Just a quick follow-up question, > For FD/DVARS or other "censoring" criteria -- using -tpexclusion > worked

Re: [Freesurfer] Percent Signal Change

Thank you, Doug. Sorry for not being clear. Could you please tell me what h.nii.gz and h-offset.nii.gz are? Also, do you have any recommendation on how to get % signal change on the signal intensity as oppose to % signal change on contrasts? Thank you On Thu, Feb 15, 2018 at 12:47 PM, Douglas

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

Can you send your glmfit command line and terminal output? On 02/15/2018 07:21 AM, amirhossein manzouri wrote: > Hi , > I did longitudinal analysis and now I made masks for Hippocampus and > amygdala masks from fsavergae/mri/aseg.mgz using mri_binarize .I use > the masks with mri_glmfit for

Re: [Freesurfer] Percent Signal Change

It divides the contast (ces) by voxel-wise mean. I'm not sure I understand your quesstion about h and h-offset On 02/15/2018 01:04 PM, Sarah Cole wrote: > Hi, > > Could someone please let me know how to get the percent signal change > for raw signal intensity? > > I think the cespct.nii.gz

[Freesurfer] Percent Signal Change

Hi, Could someone please let me know how to get the percent signal change for raw signal intensity? I think the cespct.nii.gz gives me the contrast as %. However, I am not sure about dividing h.nii and h-offset.nii. What are they? Thank you ___

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

Hi Donald - If you have recent dicoms from a standard manufacturer's sequence, then mri_convert should be able to read the b-values and gradient directions from the dicom header, in which case you don't have to provide them separately. About which b-values to use - there's no short answer

Re: [Freesurfer] Question regarding exporting subcortical segmentation to .nii ROIs for further analysis in SPM

Hi Joe you can use mri_convert to convert the .mgz volume to nifti if that is what you want: mri_convert aseg.mgz aseg.nii.gz should do the trick. Not sure if that counts as an ROI for SPM. If you want separate volumes for each structure I think you can use mri_binarize with the --match

[Freesurfer] Question regarding exporting subcortical segmentation to .nii ROIs for further analysis in SPM

Dear Experts I just recently started using Freesurfer (implemented as a virtual machine on a Windows machine). After having completed the recon-all procedure, I now want to export the subcortical segementation as .nii images for further use in SPM. My aim is to have a ROI for each segmented

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

Dear a.y. Thanks for getting back. I've set the wheels in motion to run tracula on the control scans that we have. I found your notes in the diffusion_tutorial download for grabbing the bval and bvecs from each DTI slice which looks like the biggest difficulty. On most of our controls, we have

[Freesurfer] Using masks from aseg.mgz with mri_glmfit

Hi , I did longitudinal analysis and now I made masks for Hippocampus and amygdala masks from fsavergae/mri/aseg.mgz using mri_binarize .I use the masks with mri_glmfit for volume_rate_stack but I get "dimensions mismatch 1 between y and mask" error . I wonder: 1) How can I run analysis in