Re: [Freesurfer] Are two T1 scans helpful for better recon-all?

Hi Hai, I agree with Bruce. In a recent paper (http://www.ncbi.nlm.nih.gov/pubmed/23668971), for a variety of 3T vendor and coil configurations, we confirmed previous findings that averaging two within-session uncorrupted MPRAGE scans did not significantly improve across session reproducibilit

[Freesurfer] Question about 7T MRI Datasets with isotropic voxels of 0, 7 mm

Hi,   we are currently using Freesurfer for a complete segmentation of 7T MRI Datasets with isotropic voxels of 0,7 mm. Now the question has come up whether Freesurfer calculates with this original submilimeter resolution or if it internally reslices our data (e.g. to 1mm), which could result in

Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6

Hi Muhammad have you looked at the help? It's pretty extensive. If you have trouble post again and Doug should be able to guide you cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: Thank you Bruce,   Please guide me how can I use mri_surf2vol command on lh/rh.thickness

Re: [Freesurfer] Are two T1 scans helpful for better recon-all?

thanks Jorge, nice to see that someone quantified this :) Bruce On Tue, 7 Jan 2014, Jorge Jovicich wrote: > Hi Hai, > > I agree with Bruce. In a recent paper > (http://www.ncbi.nlm.nih.gov/pubmed/23668971), for a variety of 3T vendor and > coil configurations, we confirmed previous findings th

Re: [Freesurfer] Question about 7T MRI Datasets with isotropic voxels of 0, 7 mm

Hi Valentin we do reslice it for the basic processing, but you can do post-hoc surface deformation and things like hippocampal subfield segmentation at the native resolution. Or you can use the -cm switch to prevent the reslicing, but it is something we don't have a ton of experience with. c

Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6

try adding "paint" after "surf/rh.thickness". The -surfval switch takes an optional format parameter after the file name I think cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: Hi Bruce, I have tried to convert by using the following commands but still some error occur

Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6

sorry, I wasn't clear. Try: mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon \ --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: Still the same error    UN:~> mri_surf2vol --surfval

Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6

does mri/orig.mgz exist? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: Now another error    UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 Using identity matrix

[Freesurfer] group analysis of functional data in custom volume space

Hi Freesurfer Experts, I would like to do a whole brain group analysis of functional data with mri_glmfit using a custom volume space instead of the MNI space Freesurfer provides. This is for primate data. I was wondering what the best way to do this would be. I have a T1 template in volume space

Re: [Freesurfer] Are two T1 scans helpful for better recon-all?

Hi Jorge, Thank you very much for your explanation. That's really helpful. Thank you, Hai On Tue, Jan 7, 2014 at 5:25 AM, Jorge Jovicich wrote: > Hi Hai, > > I agree with Bruce. In a recent paper (http://www.ncbi.nlm.nih.gov/ > pubmed/23668971), for a variety of 3T vendor and coil configurati

[Freesurfer] Transform sig.mgh file from fsaverage space into a subject's native space

Dear FS expert I tried to transform a sig.mgh file from fsaverage space into a subject's (called SCC1069) native space, but have some problems. I used: tkregister2 --mov fsaverage/mri/brain.mgz --targ SCC1069/mri/rawavg.mgz --regheader --reg register.dat mri_surf2surf --sval-xyz fsaverage/surf/p

Re: [Freesurfer] longitudinal hippocampal subfields analysis

Hi Salil, just run the hippo-subfields on the longitudinal results like this: recon-all -long -hippo-subfields to generate the subfield data. I am not familiar with the kvlQuantify... script and think it works on all subjects in the Subjects dir. Not sure what the best way is to solve this

Re: [Freesurfer] Problematic dilated ventricles

Hi Victor for each subject I think you want to run: set mdir=$SUBJECTS_DIR/$subject/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta $subject cp aseg.auto.mgz aseg.mgz then run recon-all from normalization2 forward (check the recon-all -help for thes

Re: [Freesurfer] Cannot run unpacksdcmdir on buckner_data/014-anon

Hi Doug, I ran the command you suggested and it appears to run without any errors or warnings. *OUTPUT: * anders@debian:~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon$ mri_convert 001.dcm delet

[Freesurfer] seeking a post-doc (fwd)

FYI Dear Colleagues, I hope this finds you well! I wanted to pass along an ad for a post-doc position on a motion correction project. We're having a tough time finding someone with both a strong interest in clinical autism research and technical sophistication with data analysis. Please pas

Re: [Freesurfer] reconall error.

Hi Rashmi how did you create this dataset? The non-black background is probably going to cause trouble. Is it an mp2rage or something similar? Could you try replacing the background value (386.997) with 0 and see if that helps. If there are really big defects the topology fixer will take forev

[Freesurfer] absolute value of effect size

Hi, I have two related questions. I have two conditions (e.g. C1 and C2) and I want to generate a map that shows all voxels that can differentiate C1 from C2 *irrespective* of whether C1>C2 or C1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

[Freesurfer] tksurfer display

Hi, Is there any way in tksurfer GUI display, that I can set a NVtxs threshold to get rid of regions (that came up significant after monte carlo simulation) which have NVtxs less than my input threshold. For eg. In my table below, I don't want postcentral label to appear in my tksurfer view (a

Re: [Freesurfer] tksurfer display

You can run mri_annotation2label on the annotation to break it up into labels, then run mris_label2annot using only the label(s) you want doug On 01/07/2014 04:05 PM, Ray, Siddharth wrote: > > Hi, > > Is there any way in tksurfer GUI display, that I can set a NVtxs > threshold to get rid of reg

[Freesurfer] Freesurfer templates for cross-ethnicity comparisons

Hi Bruce, I've been using Freesurfer to compare subcortical volumes and cortical thickness between Caucasian and Chinese controls. There are some significant findings, but the question of whether or not these may be biased due to the template has been raised (the assumption being that the majorit

Re: [Freesurfer] Freesurfer templates for cross-ethnicity comparisons

Hi Linda I actually don't know the ethnicity of the subjects in our atlas. I wouldn't expect it to be an issue for folding patterns, but it is possible. You could build your own atlas and redo the analyses if you want to see if that changes things. I'll cc Mike Chee who I think has looked at th

[Freesurfer] pial erosion/downsampling

Dear All, 1. I need to erode the ?h.pial surfaces be exactly 3 mm, then 2. I need to downsample each of the eroded surfaces to 7500 vertices each, then (3. Merge the downsampled surfaces (whether or not an intermediary voxelizing step is involved)) I would appreciate any help with command syntax