Re: [Freesurfer] slice timing correction fmcstc files are lacking

Hi using Philips scanner (interleaved)Therefore, I'm running preproc-sess -sf sessid -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run -sliceorder odd However, as you can see below stc has been not produced.

Re: [Freesurfer] two functions' purpose and usage

Anyone knows this? > On Sep 2, 2015, at 11:12, Yun Wang wrote: > > Hi all experts, > > > I have questions about two functions purposes and usages. > > > mri_compute_layer_fractions and mris_compute_layer_intensities. > > > mri_compute_layer_fractions [options]

Re: [Freesurfer] Freesurfer ROI

Sorry, I haven't heard any replies so am re-posting this again for help please: Dear Experts, I have 3 groups: A, PC, HC I did a VBM analysis in SPM and found group differences in grey matter volume in 2 clusters: 1) Bilateral pre-/SMA, left middle/superior frontal gryi 2) left

[Freesurfer] recon-all

Hi freesurfers, I am interested in studying the difference between the outer and deep white matter volume in my study groups. I am thinking in the following procedures: 1. If there is any way in Freesurfer to do segmentation for the white matter (only in the depth of 3 cm) starting from the

Re: [Freesurfer] Freesurfer ROI

Hi Lena Sure, but you will need to run all your subjects through recon-all first. The if the ROI is in MNI space you can use mri_label2label to map it to our group space fsaverage. Cheers Bruce > On Sep 4, 2015, at 9:27 AM, Lim, Lena wrote: > > Sorry, I haven’t heard any

[Freesurfer] conjunction map

Hi list, is possible to obtained a conjunction map from vlrmerge command on FS-FAST (resting state) results? Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] Freesurfer ROI

Thanks, Bruce. I ran the recon-all for all subjects before and then did the group analysis using the mri-glmfit command and qdec. Sorry, I don’t quite understand. What exact command do I use? Mri_label2label --srcsubject fsaverage --srclabel fsaverage/label/(spm roi image file names?)

[Freesurfer] Elusive skull strip

Hello, I have one brain in a large dataset that is not skull stripping properly. I have tried the changing watershed parameters using the freesurfer tutorial, but brainmask.mgz does not seem to change and I am receiving this error: " The surface validation has detected a possible Error If

[Freesurfer] ERROR: loading aseg $SUBJ/mri/MRS_MASK.nii.gz.mgz

Hi list,I'm performing FS-FAST using as seed MRS voxel (MRS_MASK). MRS_MASK shows a god overlap with orig and both of these are located in $SUBJ/mri.Firstly, I have performed:fcseed-config -segid 1 -seg MRS_MASK.nii.gz -fsd rest -mean -cfg mean.MRS_MASK.configNext,fcseed-sess -s Sess101 -cfg

[Freesurfer] mri_glmfit-sim error

Hi, I got this error when run mri_glmfit-sim: missing name for redirect. I am running freesurfer 5.3. the command is: mri_glmfit --glmdir ces.nii --cache 2 --sim-sign . The ces.nii was generated from group level analysis (isxconcat-sess). Thanks for your help. Xiaomin

Re: [Freesurfer] Problem running Tracula

Hi Andrea - Make sure that the b-value table and gradient table are saved as plain text files. When you run the "more" command on them, you should see all the numbers and only numbers. This is what I get when I run more on your files (this may vary depending on the flavor of unix you have

[Freesurfer] Cortical editing issues

Hi, After doing cortical edits (removing part of the dura) and running RECON23, the *pial (red line) and white surface (yellow line) are crossing each other* (please see attached images) which are not present before the edits. We know that this is not correct and we wanted to ask your inputs or

[Freesurfer] generating new FREESURFER directory from linear transform

Hi all, I would like to take a single subject's freesurfer directory and apply a single linear transform (I already have the .dat file I would like to use) to all of the recon-all output (volumes, surfaces, label files, etc). Essentially I would like to apply the transform and make a new

Re: [Freesurfer] generating new FREESURFER directory from linear transform

Hi David I don't think there's an easy way to do it all at once unless you apply the transform to the orig.mgz then rerun recon-all (which will not be the same as applying it to the outputs) sorry Bruce On Fri, 4 Sep 2015, David Grayson wrote: Hi all,   I would like to take a single